Publikationen von Michael Krawczak
Wolf A, Caliebe A, Thomas NS, Ball EV, Mort M, Stenson PD, Krawczak M, Cooper DN.
Single base-pair substitutions at the translation initiation sites of human genes as a cause of inherited disease.Hum Mutat,
(2011).
[abstract]
Abstract:
A total of 405 unique single base-pair substitutions, located within the ATG translation initiation codons (TICs) of 255 different genes, and reported to cause human genetic disease, were retrieved from the Human Gene Mutation Database (HGMD). Although these lesions comprised only 0.7% of coding sequence mutations in HGMD, they nevertheless were 3.4-fold over-represented as compared to other missense mutations. The distance between a TIC and the next downstream in-frame ATG codon was significantly greater for genes harbouring TIC mutations than for the remainder of genes in HGMD ('control genes'). This suggests that the absence of an alternative ATG codon in the vicinity of a TIC increases the likelihood that a given TIC mutation will come to clinical attention. An additional 42 single base-pair substitutions in 37 different genes were identified in the vicinity of TICs (positions -6 to +4, comprising the so-called 'Kozak consensus sequence'). These substitutions were not evenly distributed, being significantly more abundant at position +4. Finally, contrary to our initial expectation, the match between the original TIC and the Kozak consensus sequence was significantly better (rather than worse) for genes harbouring TIC mutations than for the HGMD control genes. © 2011 Wiley-Liss, Inc.
Nebel A, Kleindorp R, Caliebe A, Nothnagel M, Blanché H, Junge O, Wittig M, Ellinghaus D, Flachsbart F, Wichmann HE, Meitinger T, Nikolaus S, Franke A, Krawczak M, Lathrop M, Schreiber S.
A genome-wide association study confirms APOE as the major gene influencing survival in long-lived individuals.Mech Ageing Dev,
(2011).
[abstract]
Abstract:
We conducted a case-control genome-wide association study (GWAS) of human longevity, comparing 664,472 autosomal SNPs in 763 long-lived individuals (LLI; mean age: 99.7 years) and 1085 controls (mean age: 60.2 years) from Germany. Only one association, namely that of SNP rs4420638 near the APOC1 gene, achieved genome-wide significance (allele-based P=1.8×10(-10)). However, logistic regression analysis revealed that this association, which was replicated in an independent German sample, is fully explicable by linkage disequilibrium with the APOE allele ɛ4, the only variant hitherto established as a major genetic determinant of survival into old age. Our GWAS failed to identify any additional autosomal susceptibility genes. One explanation for this lack of success in our study would be that GWAS provide only limited statistical power for a polygenic phenotype with loci of small effect such as human longevity. A recent GWAS in Dutch LLI independently confirmed the APOE-longevity association, thus strengthening the conclusion that this locus is a very, if not the most, important genetic factor influencing longevity.
Nothnagel M, Herrmann A, Wolf A, Schreiber S, Platzer M, Siebert R, Krawczak M, Hampe J.
Technology-specific error signatures in the 1000 Genomes Project data.Hum Genet,
(2011).
[abstract]
Abstract:
Next-generation sequencing (NGS) will likely facilitate a better understanding of the causes and consequences of human genetic variability. In this context, the validity of NGS-inferred single-nucleotide variants (SNVs) is of paramount importance. We therefore developed a statistical framework to assess the fidelity of three common NGS platforms. Using aligned DNA sequence data from two completely sequenced HapMap samples as included in the 1000 Genomes Project, we unraveled remarkably different error profiles for the three platforms. Compared to confirmed HapMap variants, newly identified SNVs included a substantial proportion of false positives (3-17%). Consensus calling by more than one platform yielded significantly lower error rates (1-4%). This implies that the use of multiple NGS platforms may be more cost-efficient than relying upon a single technology alone, particularly in physically localized sequencing experiments that rely upon small error rates. Our study thus highlights that different NGS platforms suit different practical applications differently well, and that NGS-based studies require stringent data quality control for their results to be valid.
Jochens A, Caliebe A, Rösler U, Krawczak M.
Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-chromosomal Microsatellites.Genetics,
189 (2011), 1403-1411.
[abstract]
Abstract:
The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analysed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analysed (DYS19, DYS389I, DYS390, DYS391, DYS392 and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's Information Criterion. This implies that the mutation probability at the loci increases (non-linearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion.
Mangold E, Ludwig KU, Birnbaum S, Baluardo C, Ferrian M, Herms S, Reutter H, de Assis NA, Chawa TA, Mattheisen M, Steffens M, Barth S, Kluck N, Paul A, Becker J, Lauster C, Schmidt G, Braumann B, Scheer M, Reich RH, Hemprich A, Pötzsch S, Blaumeiser B, Moebus S, Krawczak M, Schreiber S, Meitinger T, Wichmann HE, Steegers-Theunissen RP, Kramer FJ, Cichon S, Propping P, Wienker TF, Knapp M, Rubini M, Mossey PA, Hoffmann P, Nöthen MM.
Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate.Nat Genet,
42 (2010), 24-6.
[abstract]
Abstract:
We conducted a genome-wide association study for nonsyndromic cleft lip with or without cleft palate (NSCL/P) in 401 affected individuals and 1,323 controls, with replication in an independent sample of 793 NSCL/P triads. We report two new loci associated with NSCL/P at 17q22 (rs227731, combined P = 1.07 x 10(-8), relative risk in homozygotes = 1.84, 95% CI 1.34-2.53) and 10q25.3 (rs7078160, combined P = 1.92 x 10(-8), relative risk in homozygotes = 2.17, 95% CI 1.32-3.56).
Nothnagel M, Schmidtke J, Krawczak M.
Potentials and limits of pairwise kinship analysis using autosomal short tandem repeat loci.Int J Legal Med,
(2010).
[abstract]
Abstract:
At least in principle, most instances of complex kinship testing can be reduced to pairwise kinship cases involving two critical family members that either link or separate presumed sub-branches of a family. In the European population, the 34 short tandem repeats (STRs) currently used in forensic genetics are sufficiently powerful to allow assessment of disputed first and second but not lower degrees of pairwise blood relatedness. We provide estimates of the means and variances of marker-specific log-likelihood ratios, using large-sample approximation and assuming different scenarios of pairwise kinship analysis. These estimates allow power calculations to be performed for any combination of the available STRs. Since some of the markers considered are physically linked, chromosome-wide likelihood calculations in kinship cases other than parent-child duos (and trios) have to take the reduced rates of meiotic inter-marker recombination into account. We show by simulation that this requirement may be ignored when discriminating distant hypotheses about kinship, but that linkage may play an important role in the biostatistical analysis of more intricate cases.
Nothnagel M, Wolf A, Herrmann A, Szafranski K, Vater I, Brosch M, Huse K, Siebert R, Platzer M, Hampe J, Krawczak M.
Statistical inference of allelic imbalance from transcriptome data.Hum Mutat,
(2010).
[abstract]
Abstract:
Next-generation sequencing and the availability of high-density genotyping arrays have facilitated an analysis of somatic and meiotic mutations at unprecedented level, but drawing sensible conclusions about the functional relevance of the detected variants still remains a formidable challenge. In this context, the study of allelic imbalance in intermediate RNA phenotypes may prove a useful means to elucidate the likely effects of DNA variants of unknown significance. We developed a statistical framework for the assessment of allelic imbalance in next-generation transcriptome sequencing (RNA-seq) data that requires neither an expression reference nor the underlying nuclear genotype(s), and that allows for allele miscalls. Using extensive simulation as well as publicly available whole-transcriptome data from European-descent individuals in HapMap, we explored the power of our approach in terms of both genotype inference and allelic imbalance assessment under a wide range of practically relevant scenarios. In so doing, we verified a superior performance of our methodology, particularly at low sequencing coverage, compared to the more simplistic approach of completely ignoring allele miscalls. Since the proposed framework can be used to assess somatic mutations and allelic imbalance in one and the same set of RNA-seq data, it will be particularly useful for the analysis of somatic genetic variation in cancer studies. © 2010 Wiley-Liss, Inc.
Fiebig A, Krusche P, Wolf A, Krawczak M, Timm B, Nikolaus S, Frings N, Schreiber S.
Heritability of chronic venous disease.Hum Genet,
(2010).
[abstract]
Abstract:
Varicose veins without skin changes have a prevalence of approximately 20% in Northern and Western Europe whereas advanced chronic venous insufficiency affects about 3% of the population. Genetic risk factors are thought to play an important role in the aetiology of both these chronic venous diseases (CVD). We evaluated the relative genetic and environmental impact upon CVD risk by estimating the heritability of the disease in 4,033 nuclear families, comprising 16,434 individuals from all over Germany. Upon clinical examination, patients were classified according to the CEAP guidelines as either C2 (simple varicose veins), C3 (oedema), C4 (skin changes without ulceration), C5 (healed ulceration), or C6 (active ulcers). The narrow-sense heritability (h (2)) of CVD equals 17.3% (standard error 2.5%, likelihood ratio test P = 1.4 x 10(-13)). The proportion of disease risk attributable to age (at ascertainment) and sex, the two main risk factors for CVD, was estimated as 10.7% (Kullback-Leibler deviance R (2)). The heritability of CVD is high, thereby suggesting a notable genetic component in the aetiology of the disease. Systematic population-based searches for CVD susceptibility genes are therefore warranted.
Caliebe A, Jochens A, Krawczak M, Rösler U.
A Markov chain description of the stepwise mutation model: local and global behaviour of the allele process.J Theor Biol,
266 (2010), 336-42.
[abstract]
Abstract:
The stepwise mutation model (SMM) is a simple, widely used model to describe the evolutionary behaviour of microsatellites. We apply a Markov chain description of the SMM and derive the marginal and joint properties of this process. In addition to the standard SMM, we also consider the normalised allele process. In contrast to the standard process, the normalised process converges to a stationary distribution. We show that the marginal stationary distribution is unimodal. The standard and normalised processes capture the global and the local behaviour of the SMM, respectively.
Nothnagel M, Lu TT, Kayser M, Krawczak M.
Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans.Hum Mol Genet,
19 (2010), 2927-35.
[abstract]
Abstract:
The availability of high-density panels of genetic polymorphisms has led to the discovery of extended regions of apparent autozygosity in the human genome. At the genotype level, these regions present as sizeable stretches, or 'runs', of homozygosity (ROH). Here, we investigated both the genomic and the geographic distribution of ROHs in a large European sample of individuals originating from 23 subpopulations. The genomic ROH distribution was found to be characterized by a pattern of highly significant non-uniformity that was virtually identical in all subpopulations studied. Some 77 chromosomal regions contained ROHs at considerable frequency, thereby forming 'ROH islands' that were not explicable by high linkage disequilibrium alone. At the geographic level, the number and cumulative length of ROHs followed a prominent South to North gradient in agreement with expectations from European population history. The individual ROH length, in contrast, showed only minor and unsystematic geographic variation. While our findings are thus consistent with a larger effective population size in Southern than in Northern Europe, combined with a higher historic population density and mobility, they also indicate that the patterns of meiotic recombination in humans must have been very similar throughout the continent. Extending previous reports of a strong correlation between geography and identity-by-state, our data show that the genomic identity-by-descent patterns of Europeans are also clinal. As a consequence, the planning, design and interpretation of ROH-based genetic studies must take sample origin into account in order for such studies to be sensible and valid.
Schmidtke J, Krawczak M.
Psychomotor developmental delay and epilepsy in an offspring of father-daughter incest: quantification of the causality probability.Int J Legal Med,
(2009).
[abstract]
Abstract:
A 20-year-old offspring of father-daughter incest, who has been suffering from serious psychomotoric health problems since early childhood, is seeking financial compensation under the German federal act of victim indemnification. For her appeal to be valid, the probability X that the incest was causal for her disorder must exceed 50%. Based upon the available medical records, we show that this is indeed the case and that X is even likely to exceed 65%, thereby rendering the victim's claim scientifically and legally justified.
Estrada K, Krawczak M, Schreiber S, van Duijn K, Stolk L, van Meurs JB, Liu F, Penninx BW, Smit JH, Vogelzangs N, Hottenga JJ, Willemsen G, de Geus EJ, Lorentzon M, von Eller-Eberstein H, Lips P, Schoor N, Pop V, de Keijzer J, Hofman A, Aulchenko YS, Oostra BA, Ohlsson C, Boomsma DI, Uitterlinden AG, van Duijn CM, Rivadeneira F, Kayser M.
A genome-wide association study of northwestern Europeans involves the CNP signaling pathway in the etiology of human height variation.Hum Mol Genet,
(2009).
[abstract]
Abstract:
Northwestern Europeans are among the tallest of human populations. The increase in body height in these people appears to have reached a plateau, suggesting the ubiquitous presence of an optimal environment in which genetic factors may have exerted a particularly strong influence on human growth. Therefore, we performed a genome-wide association study (GWAS) of body height using 2.2 million markers in 10,074 individuals from three Dutch and one German population-based cohorts. Upon genotyping the 12 most significantly height-associated single nucleotide polymorphisms (SNPs) from this GWAS in 6912 additional individuals of Dutch and Swedish origin, a genetic variant (rs6717918) on chromosome 2q37.1 was found to be associated with height at a genome-wide significance level (P(combined) = 3.4 x 10(-9)). Notably, a second SNP (rs6718438) located approximately 450 bp away and in strong LD (r(2) = 0.77) with rs6717918 was previously found to be suggestive of a height association in 29,820 individuals of mainly northwestern European ancestry, and the over-expression of a nearby natriuretic peptide precursor type C (NPPC) gene, has been associated with overgrowth and skeletal anomalies. We also found a SNP (rs10472828) located on 5p14 near the natriuretic peptide receptor 3 (NPR3) gene, encoding a receptor of the NPPC ligand, to be associated with body height (P(combined) = 2.1 x 10(-7)). Taken together, these results suggest that variation in the C-type natriuretic peptide (CNP) signaling pathway, involving the NPPC and NPR3 genes, plays an important role in determining human body height.
Nelis M, Esko T, Mägi R, Zimprich F, Zimprich A, Toncheva D, Karachanak S, Piskácková T, Balascák I, Peltonen L, Jakkula E, Rehnström K, Lathrop M, Heath S, Galan P, Schreiber S, Meitinger T, Pfeufer A, Wichmann HE, Melegh B, Polgár N, Toniolo D, Gasparini P, Klovins J, Nikitina-Zake L, Kucinskas V, Kasnauskiene J, Lubinski J, Debniak T, Limborska S, Khrunin A, Estivill X, Rabionet R, Marsal S, Julià A, Antonarakis SE, Deutsch S, Borel C, Attar H, Gagnebin M, Macek M, Krawczak M, Remm M, Metspalu A.
Genetic structure of Europeans: a view from the North-East.PLoS One,
4 (2009), e5472.
[abstract]
Abstract:
Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (lambda) (ranging from 1.00 to 4.21), fixation index (F(st)) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).
Lu TT, Lao O, Nothnagel M, Junge O, Freitag-Wolf S, Caliebe A, Balascakova M, Bertranpetit J, Bindoff LA, Comas D, Holmlund G, Kouvatsi A, Macek M, Mollet I, Nielsen F, Parson W, Palo J, Ploski R, Sajantila A, Tagliabracci A, Gether U, Werge T, Rivadeneira F, Hofman A, Uitterlinden AG, Gieger C, Wichmann HE, Ruether A, Schreiber S, Becker C, Nürnberg P, Nelson MR, Kayser M, Krawczak M.
An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.Eur J Hum Genet,
17 (2009), 967-75.
[abstract]
Abstract:
Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309 790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.European Journal of Human Genetics advance online publication, 21 January 2009; doi:10.1038/ejhg.2008.266.
Goebel JW, Pickardt T, Bedau M, Fuchs M, Lenk C, Paster I, Spranger TM, Stockter U, Bauer U, Cooper DN, Krawczak M.
Legal and ethical consequences of international biobanking from a national perspective: the German BMB-EUCoop project.Eur J Hum Genet,
(2009).
[abstract]
Abstract:
The international transfer of human biomaterial and data has become a prerequisite for collaborative biomedical research to be successful. However, although a national legal framework for 'biobanking' has already been formulated in many countries, little is known about how an international exchange of data and samples might affect the legal position of national biobanks and their donors. The German Telematics Platform and the Competence Network 'Congenital Heart Defects' jointly instigated a project (BMB-EUCoop) to (i) identify and assess the legal risks ensuing for biobanks and their donors in the context of Europe-wide research collaborations, (ii) devise practical recommendations to minimize or avoid these risks, and (iii) provide generic informational text, contracts and agreements to facilitate their practical implementation. Four different countries were included in the study; namely, the UK, Netherlands, Austria and Switzerland. The results of the study indicate that the degree of similarity between legal systems in different countries varies according to the respective field of jurisdiction. Although personality and property rights have long been enshrined in virtually identical pieces of law, the applicable medical professional regulations were found to be somewhat heterogeneous. Furthermore, clear-cut differences were often found to be lacking between regulations that reflect either 'soft law' or the nationally binding 'hard law' that has emerged from it. In view of the potential ambiguities, the experts uniformly concluded that the rights and interests of national (in this case, German) biobanks and their donors would be best protected by explicitly addressing any uncertainties in formal contractual agreements.European Journal of Human Genetics advance online publication, 2 December 2009; doi:10.1038/ejhg.2009.214.
Nothnagel M, Ellinghaus D, Schreiber S, Krawczak M, Franke A.
A comprehensive evaluation of SNP genotype imputation.Hum Genet,
125 (2009), 163-71.
[abstract]
Abstract:
Genome-wide association studies have contributed significantly to the genetic dissection of complex diseases. In order to increase the power of existing marker sets even further, methods have been proposed to predict individual genotypes at un-typed loci from other marker sets by imputation, usually employing HapMap data as a reference. Although various imputation algorithms have been used in practice already, a comprehensive evaluation and comparison of these approaches, using genome-wide SNP data from one and the same population is still lacking. We therefore investigated four publicly available programs for genotype imputation (BEAGLE, IMPUTE, MACH, and PLINK) using data from 449 German individuals genotyped in our laboratory for three genome-wide SNP sets [Affymetrix 5.0 (500 k), Affymetrix 6.0 (1,000 k), and Illumina 550 k]. We observed that HapMap-based imputation in a northern European population is powerful and reliable, even in highly variable genomic regions such as the extended MHC on chromosome 6p21. However, while genotype predictions were found to be highly accurate with all four programs, the number of SNPs for which imputation was actually carried out ('imputation efficacy') varied substantially. BEAGLE, IMPUTE, and MACH yielded nearly identical trade-offs between imputation accuracy and efficacy whereas PLINK performed consistently poorer. We nevertheless recommend either MACH or BEAGLE for practical use because these two programs are more user-friendly and generally require less memory than IMPUTE.
Wolf A, Millar DS, Caliebe A, Horan M, Newsway V, Kumpf D, Steinmann K, Chee IS, Lee YH, Mutirangura A, Pepe G, Rickards O, Schmidtke J, Schempp W, Chuzhanova N, Kehrer-Sawatzki H, Krawczak M, Cooper DN.
A gene conversion hotspot in the human growth hormone (GH1) gene promoter.Hum Mutat,
30 (2009), 239-247.
[abstract]
Abstract:
To assess the evolutionary importance of nonallelic (or interlocus) gene conversion for the highly polymorphic human growth hormone (GH1) gene promoter, sequence variation in this region was studied in four different ethnic groups. For 14 SNPs in the proximal GH1 promoter (535 bp), 60 different haplotypes were observed in 577 individuals (156 Britons, 116 Spaniards, 163 West-Africans, 142 Asians). Using a novel coalescence-based statistical test, significant evidence was found in the British, Spanish, and African groups for GH1 having acted as an acceptor of gene conversion, with at least one of the four paralogous GH gene promoters serving as the donor (and specifically GH2 in the Britons and Spaniards). The average gene conversion tract length was estimated to be 84 bp. A gene conversion hotspot was identified, spanning the GH1 transcriptional initiation site (positions -6 to +25). Although these findings serve to highlight the importance of gene conversion for the recent evolution of the human GH1 promoter, its relative frequency does not appear to be related simply to the presence of specific DNA sequence motifs or secondary structures, the degree of homology between GH paralogs, the distance between them, or their transcriptional orientation. The GH1 promoter was also found to be highly polymorphic in chimpanzee but not in macaque. This may reflect the lower degree of pair-wise similarity between the GH1 promoter and its paralogs in macaque (mean, 92.0%) as compared to chimpanzee (93.5%) and human (94.0%), and hence provides further support for the idea of a threshold (perhaps around 92%) below which gene conversion is reduced or abolished. Hum Mutat 0,1-9, 2008. (c) 2008 Wiley-Liss, Inc.
Fritsche LG, Freitag-Wolf S, Bettecken T, Meitinger T, Keilhauer CN, Krawczak M, Weber BH.
Age-related macular degeneration and functional promoter and coding variants of the apolipoprotein E gene.Hum Mutat,
30 (2009), 1048-53.
[abstract]
Abstract:
Age-related macular degeneration (AMD) is a frequent, multifactorial disease of the central retina and a major cause of irreversible vision loss in industrialized countries. Apolipoprotein E (APOE) has been consistently associated with AMD, particularly its two functional isoforms E2 (predisposing) and E4 (protective). The biological correlate of this association, however, is still unclear. In this study, we have defined an extended haplotype block encompassing the entire APOE gene locus, including known coding as well as cis-regulatory promoter variants. Of the five extended APOE haplotypes common in the general population, two were found to be significantly associated with AMD, namely G-G-G-G-epsilon2 (odds ratio [OR], 1.59; 95% confidence interval [CI], 1.19-2.12) and T-G-A-G-epsilon4 (OR, 0.76; 95% CI, 0.58-0.99). When analyzing common extended haplotype combinations, T-C-G-G-epsilon3/T-G-A-G-epsilon4 exhibited the most prominent effect (OR, 0.32; 95% CI, 0.20-0.51). Intriguingly, we also found one extended epsilon3-haplotype, G-G-G-A-epsilon3, to be protective in the homozygous state (OR, 0.65; 95% CI, 0.49-0.87). Since single nucleotide polymorphism (SNP) rs405509:G>T is a constituent of the extended epsilon-haplotype block and is known to significantly influence APOE promoter activity, we hypothesize that both the relative rate of APOE isoform expression in conjunction with established functional differences of the respective isoforms may be crucial in mediating AMD pathology. This would also imply that genotyping of the core epsilon-haplotypes alone is not sufficient to estimate AMD risk, but that determination of extended haplotype combinations, including the functional promoter SNP rs405509, is required instead.
ElSharawy A, Hundrieser B, Brosch M, Wittig M, Huse K, Platzer M, Becker A, Simon M, Rosenstiel P, Schreiber S, Krawczak M, Hampe J.
Systematic evaluation of the effect of common SNPs on pre-mRNA splicing.Hum Mutat,
30 (2009), 625-32.
[abstract]
Abstract:
The evolutionary and biomedical importance of differential mRNA splicing is well established. Numerous studies have assessed patterns of differential splicing in different genes and correlated these patterns to the genotypes for adjacent single-nucleotide polymorphisms (SNPs). Here, we have chosen a reverse approach and screened dbSNP for common SNPs at either canonical splice sites or exonic splice enhancers (ESEs) that would be classified as putatively splicing-relevant by bioinformatic tools. The 223 candidate SNPs retrieved from dbSNP were experimentally tested using a previously established panel of 92 matching DNAs and cDNAs. For each SNP, 16 cDNAs providing a balanced representation of the genotypes at the respective SNP were investigated by nested RT-PCR and subsequent sequencing. Putative allele-dependent splicing was verified by the cloning of PCR products. The positive predictive value of the bioinformatics tools turned out to be low, ranging from 0% for ESEfinder to 9% (in the case of acceptor-site SNPs) for a recently reported neural network. The results highlight the need for a better understanding of the sequence characteristics of functional splice-sites to improve our ability to predict in silico the splicing relevance of empirically observed DNA sequence variants.
Feulner TM, Laws SM, Friedrich P, Wagenpfeil S, Wurst SH, Riehle C, Kuhn KA, Krawczak M, Schreiber S, Nikolaus S, Förstl H, Kurz A, Riemenschneider M.
Examination of the current top candidate genes for AD in a genome-wide association study.Mol Psychiatry,
(2009).
[abstract]
Abstract:
With the advent of technologies that allow simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) across the genome, the genetic contributions to complex diseases can be explored at an unprecedented detail. This study is among the first to apply the genome-wide association study (GWAS) approach to Alzheimer disease (AD). We present our GWAS results from the German population for genes included in the 'Top Results' list on the AlzGene database website. In addition to the apolipoprotein E locus, we identified nominally significant association signals in six of the ten genes investigated, albeit predominantly for SNPs other than those already published as being disease associated. Further, all of the four AD genes previously identified through GWAS also showed nominally significant association signals in our data. The results of our comparative study reinforce the necessity for replication and validation, not only of GWAS but also of candidate gene case-control studies, in different populations. Furthermore, cross-platform comparison of genotyping results can also identify new association signals. Finally, our data confirm that GWAS, regardless of the platform, are valuable for the identification of genetic variants associated with AD.Molecular Psychiatry advance online publication, 6 January 2009; doi:10.1038/mp.2008.141.
Singh KK, Krawczak M, Dawson WW, Schmidtke J.
Association of HTRA1 and ARMS2 gene variation with drusen formation in rhesus macaques.Exp Eye Res,
88 (2009), 479-82.
[abstract]
Abstract:
Age-related macular degeneration (AMD) is a clinically heterogeneous disease and constitutes the major cause of visual impairment in the elderly population worldwide. Rhesus macaques also possess a macula and, like humans, develop drusen-associated, age-related macular pathologies. Susceptibility to AMD in humans and drusen formation in rhesus macaques both have been shown to be associated with variation in the HTRA1 and ARMS2 genes. To corroborate these results we genotyped a cohort of 116 rhesus macaques with and without macular drusen. Like in humans, markers in the two genes showed a significant association with drusen formation at the genotype level. Joint haplotype analysis revealed, however, that the disease association observed in rhesus macaques was entirely attributable to a promoter polymorphism (-558G>T) of the HTRA1 gene.
Schafmayer C, Buch S, Völzke H, von Schönfels W, Egberts JH, Schniewind B, Brosch M, Ruether A, Franke A, Mathiak M, Sipos B, Henopp T, Catalcali J, Hellmig S, ElSharawy A, Katalinic A, Lerch MM, John U, Fölsch UR, Fändrich F, Kalthoff H, Schreiber S, Krawczak M, Tepel J, Hampe J.
Investigation of the colorectal cancer susceptibility region on chromosome 8q24.21 in a large German case-control sample.Int J Cancer,
124 (2009), 75-80.
[abstract]
Abstract:
Human chromosome 8q24.21 has been implicated as a susceptibility region for colorectal cancer (CRC) as a result of genome-wide association and candidate gene studies. To assess the impact of molecular variants at 8q24.21 upon the CRC risk of German individuals and to refine the disease-associated region, a total of 2,713 patients with operated CRC (median age at diagnosis: 63 years) were compared with 2,718 sex-matched control individuals (median age at inclusion: 65 years). Information on microsatellite instability in tumors was available for 901 patients. Association analysis of SNPs rs10505477 and rs6983267 yielded allelic p-values of 1.42 x 10(-7) and 2.57 x 10(-7), respectively. For both polymorphisms, the odds ratio was estimated to be 1.50 (95% CI: 1.29-1.75) under a recessive disease model. The strongest candidate interval, outside of which significance dropped by more than 4 orders of magnitude, was delineated by SNPs rs10505477 and rs7014346 and comprised 17 kb. In a subgroup analysis, the disease association was found to be more pronounced in MSI-stable tumors (odds ratio: 1.71). Our study confirms the role of genetic variation at 8q24.21 as a risk factor for CRC and localizes the corresponding susceptibility gene to a 17 kb candidate region.
Wolf A, Millar DS, Caliebe A, Horan M, Newsway V, Kumpf D, Steinmann K, Chee IS, Lee YH, Mutirangura A, Pepe G, Rickards O, Schmidtke J, Schempp W, Chuzhanova N, Kehrer-Sawatzki H, Krawczak M, Cooper DN.
A gene conversion hotspot in the human growth hormone (GH1) gene promoter.Hum Mutat,
30 (2009), 239-47.
[abstract]
Abstract:
To assess the evolutionary importance of nonallelic (or interlocus) gene conversion for the highly polymorphic human growth hormone (GH1) gene promoter, sequence variation in this region was studied in four different ethnic groups. For 14 SNPs in the proximal GH1 promoter (535 bp), 60 different haplotypes were observed in 577 individuals (156 Britons, 116 Spaniards, 163 West-Africans, 142 Asians). Using a novel coalescence-based statistical test, significant evidence was found in the British, Spanish, and African groups for GH1 having acted as an acceptor of gene conversion, with at least one of the four paralogous GH gene promoters serving as the donor (and specifically GH2 in the Britons and Spaniards). The average gene conversion tract length was estimated to be 84 bp. A gene conversion hotspot was identified, spanning the GH1 transcriptional initiation site (positions -6 to +25). Although these findings serve to highlight the importance of gene conversion for the recent evolution of the human GH1 promoter, its relative frequency does not appear to be related simply to the presence of specific DNA sequence motifs or secondary structures, the degree of homology between GH paralogs, the distance between them, or their transcriptional orientation. The GH1 promoter was also found to be highly polymorphic in chimpanzee but not in macaque. This may reflect the lower degree of pair-wise similarity between the GH1 promoter and its paralogs in macaque (mean, 92.0%) as compared to chimpanzee (93.5%) and human (94.0%), and hence provides further support for the idea of a threshold (perhaps around 92%) below which gene conversion is reduced or abolished.
Siddiqui RA, Sauermann U, Altmüller J, Fritzer E, Nothnagel M, Dalibor N, Fellay J, Kaup FJ, Stahl-Hennig C, Nürnberg P, Krawczak M, Platzer M.
X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women.Am J Hum Genet,
85 (2009), 228-39.
[abstract]
Abstract:
AIDS has changed from a mostly male-specific health problem to one that predominantly affects females. Although sex differences in HIV-1 susceptibility are beyond doubt, the extent to which sex affects the onset and progression of AIDS has remained elusive. Here, we provide evidence for an influence of X chromosomal variation on the course of retroviral infection, both in HIV-1-infected patients and in the rhesus macaque model of AIDS. A two-stage, microsatellite-based GWAS of SIV-infected monkeys revealed MHC class I markers and a hitherto-unknown X chromosomal locus as being associated with a nominal score measuring progression to AIDS (Fisher's exact p < 10(-6)). The X chromosomal association was subsequently confirmed in HIV-1-infected patients with published SNP genotype data. SNP rs5968255, located at human Xq21.1 in a conserved sequence element near the RPS6KA6 and CYLC1 genes, was identified as a significant genetic determinant of disease progression in females (ANOVA p = 8.8 x 10(-5)), but not in males (p = 0.19). Heterozygous female carriers of the C allele showed significantly slower CD4 cell decline and a lower viral load at set point than TT homozygous females and than males. Inspection of HapMap revealed that the CT genotype is significantly more frequent among Asians than among Europeans or Africans. Our results suggest that, in addition to the individual innate and adaptive immunity status, sex-linked genetic variation impacts upon the rate of progression to AIDS. Elucidating the mechanisms underlying this sex-specific effect will promote the development of antiretroviral therapies with high efficacy in both sexes.
Möckelmann N, von Schönfels W, Buch S, von Kampen O, Sipos B, Egberts JH, Rosenstiel P, Franke A, Brosch M, Hinz S, Röder C, Kalthoff H, Fölsch UR, Krawczak M, Schreiber S, Bröring CD, Tepel J, Schafmayer C, Hampe J.
Investigation of innate immunity genes CARD4, CARD8 and CARD15 as germline susceptibility factors for colorectal cancer.BMC Gastroenterol,
9 (2009), 79.
[abstract]
Abstract:
BACKGROUND: Variation in genes involved in the innate immune response may play a role in the predisposition to colorectal cancer (CRC). Several polymorphisms of the CARD15 gene (caspase activating recruitment domain, member 15) have been reported to be associated with an increased susceptibility to Crohn disease. Since the CARD15 gene product and other CARD proteins function in innate immunity, we investigated the impact of germline variation at the CARD4, CARD8 and CARD15 loci on the risk for sporadic CRC, using a large patient sample from Northern Germany. METHODS: A total of 1044 patients who had been operated with sporadic colorectal carcinoma (median age at diagnosis: 59 years) were recruited and compared to 724 sex-matched, population-based control individuals (median age: 68 years). Genetic investigation was carried out following both a coding SNP and haplotype tagging approach. Subgroup analyses for N = 143 patients with early manifestation of CRC (<or=50 age at diagnosis) were performed for all CARD loci and subgroup analyses for diverse age strata were carried out for CARD15 mutations R702W, G908R and L1007fs. In addition, all SNPs were tested for association with disease presentation and family history of CRC. RESULTS: No significant differences were observed between the patient and control allelic or haplotypic spectra of the three genes under study for the total cohort (N = 1044 patients). None of the analysed SNPs was significantly associated with either tumour location or yielded significant association in the familial or non-familial CRC patient subgroups. However, in a patient subgroup (<or=45 age at diagnosis) with early disease manifestation the mutant allele of CARD15 R702W was found to be significantly associated with disease susceptibility (9.7% in cases vs 4.6% in controls; P(allelic) = 0.008, P(genotypic) = 0.0008, OR(allelic) = 2.22 (1.21-4.05) OR(ressessive) = 21.9 (1.96-245.4). CONCLUSION: Variation in the innate immunity genes CARD4, CARD8 and CARD15 is unlikely to play a major role in the susceptibility to CRC in the German population. But, we report a significant disease contribution of CARD15 for CRC patients with very early disease manifestation, mainly driven by variant R702W.
Nebel A, Flachsbart F, Till A, Caliebe A, Blanché H, Arlt A, Häsler R, Jacobs G, Kleindorp R, Franke A, Shen B, Nikolaus S, Krawczak M, Rosenstiel P, Schreiber S.
A functional EXO1 promoter variant is associated with prolonged life expectancy in centenarians.Mech Ageing Dev,
130 (2009), 691-99.
[abstract]
Abstract:
Human longevity is heritable with a genetic component of 25-32%. Variation in genes regulating the levels of somatic maintenance and DNA repair functions is thought to modulate the aging process and to contribute to survival at advanced age. We tested 92 non-synonymous SNPs in 49 DNA repair genes for a possible association with longevity in a sample of 395 German centenarians and 411 controls. The obtained association signal in exonuclease 1 (EXO1) was further investigated by fine mapping and mutation detection, leading to the identification of the functionally relevant SNP rs1776180. Our detailed analyses revealed that the common allele (C) of this promoter SNP is significantly enriched in female centenarians. This finding replicated in 455 female French centenarians and 109 controls. The C allele leads to the loss of a binding site for the basic helix-loop-helix transcription factor E47, resulting in higher EXO1 expression. Thus, we have detected a hitherto undescribed role for E47 as a negative regulator of EXO1 transcription and a genetic variant in the EXO1 promoter that counteracts the E47-mediated repression of the gene. Given the survival advantage that is associated with the C allele of rs1776180, EXO1 can be considered a candidate for a novel longevity-enabling gene.
Franke A, Balschun T, Karlsen TH, Hedderich J, May S, Lu T, Schuldt D, Nikolaus S, Rosenstiel P, Krawczak M, Schreiber S.
Replication of signals from recent studies of Crohn's disease identifies previously unknown disease loci for ulcerative colitis.Nat Genet,
40 (2008), 713-5.
[abstract]
Abstract:
Following up on recent genome-wide association studies (GWAS) of Crohn's disease, we investigated 50 previously reported susceptibility loci in a German sample of individuals with Crohn's disease (n = 1,850) or ulcerative colitis (n = 1,103) and healthy controls (n = 1,817). Among these loci, we identified variants in 3p21.31, NKX2-3 and CCNY as susceptibility factors for both diseases, whereas variants in PTPN2, HERC2 and STAT3 were associated only with ulcerative colitis in our sample collection.
Schafmayer C, Freitag-Wolf S, Wolken H, Buch S, Brosch M, Egberts JH, Shekarriz H, Fölsch UR, Fändrich F, Krawczak M, Schreiber S, Tepel J, Hampe J.
Increased heritability of gallstone disease in early onset cases.Liver Int,
28 (2008), 895-7.
Bosy-Westphal A, Wolf A, Bührens F, Hitze B, Czech N, Mönig H, Selberg O, Settler U, Pfeuffer M, Schrezenmeir J, Krawczak M, Müller MJ.
Familial influences and obesity-associated metabolic risk factors contribute to the variation in resting energy expenditure: the Kiel Obesity Prevention Study.Am J Clin Nutr,
87 (2008), 1695-701.
[abstract]
Abstract:
BACKGROUND: A low metabolic rate may be inherited and predispose to obesity, whereas a higher metabolic rate in obesity may be acquired by obesity-associated cardiometabolic risk. OBJECTIVE: We aimed to explain the interindividual variation in resting energy expenditure (REE) by assessing 1) the association between REE and body composition, thyroid hormones, and obesity-related cardiometabolic risk factors, and 2) the familial (genetic and environmental) contribution to REE. DESIGN: REE and metabolic risk factors (ie, blood pressure and plasma insulin, glucose, and C-reactive protein concentrations) were assessed in 149 two- or three-generation families, including at least one overweight or obese member. Heritability of REE, respiratory quotient (RQ), thyroid hormones [thyrotropin (TSH), free triiodothyronine (FT3) and free thyroxine (FT4)], and body composition (fat-free mass and fat mass) were estimated by using variance components-based quantitative genetic models. RESULTS: REE adjusted for body composition, sex, and age (REEadj) significantly correlated with systolic and diastolic blood pressure, plasma insulin and glucose concentrations, and the homeostasis model assessment (HOMA) (r = 0.14-0.31, P < 0.05). Thyroid hormones had a modest influence on REE variance only. Heritability was 0.30 +/- 0.07 for REEadj and 0.29 +/- 0.08 for REE after additional adjustment for thyroid hormones and metabolic risk. Furthermore, heritability was estimated to be 0.22 +/- 0.08 for RQ, 0.37 +/- 0.08 for TSH, 0.68 +/- 0.06 for FT4, and 0.69 +/- 0.05 for FT3 (all significantly larger than zero). CONCLUSIONS: Obesity-related cardiometabolic risk factors contribute to interindividual variation in REE, with hypertension and insulin resistance being associated with a higher REE. REE was moderately heritable, independent of body composition, sex, age, thyroid function, and cardiometabolic risk.
Kirsch S, Pasantes J, Wolf A, Bogdanova N, Muench C, Pennekamp P, Krawczak M, Dworniczak B, Schempp W.
Chromosomal evolution of the PKD1 gene family in primates.BMC Evol Biol,
8 (2008), 263.
[abstract]
Abstract:
ABSTRACT: BACKGROUND: The autosomal dominant polycystic kidney disease (ADPKD) is mostly caused by mutations in the PKD1 (polycystic kidney disease 1) gene located in 16p13.3. Moreover, there are six pseudogenes of PKD1 that are located proximal to the master gene in 16p13.1. In contrast, no pseudogene could be detected in the mouse genome, only a single copy gene on chromosome 17. The question arises how the human situation originated phylogenetically. To address this question we applied comparative FISH-mapping of a human PKD1-containing genomic BAC clone and a PKD1-cDNA clone to chromosomes of a variety of primate species and the dog as a non-primate outgroup species. RESULTS: Comparative FISH with the PKD1-cDNA clone clearly shows that in all primate species studied distinct single signals map in subtelomeric chromosomal positions orthologous to the short arm of human chromosome 16 harbouring the master PKD1 gene. Only in human and African great apes, but not in orangutan, FISH with both BAC and cDNA clones reveals additional signal clusters located proximal of and clearly separated from the PKD1 master genes indicating the chromosomal position of PKD1 pseudogenes in 16p of these species, respectively. Indeed, this is in accordance with sequencing data in human, chimpanzee and orangutan. Apart from the master PKD1 gene, six pseudogenes are identified in both, human and chimpanzee, while only a single-copy gene is present in the whole-genome sequence of orangutan. The phylogenetic reconstruction of the PKD1-tree reveals that all human pseudogenes are closely related to the human PKD1 gene, and all chimpanzee pseudogenes are closely related to the chimpanzee PKD1 gene. However, our statistical analyses provide strong indication that gene conversion events may have occurred within the PKD1 family members of human and chimpanzee, respectively. CONCLUSION: PKD1 must have undergone amplification very recently in hominid evolution. Duplicative transposition of the PKD1 gene and further amplification and evolution of the PKD1 pseudogenes may have arisen in a common ancestor of Homo, Pan and Gorilla ~ 8 MYA. Reticulate evolutionary processes such as gene conversion and non-allelic homologous recombination (NAHR) may have resulted in concerted evolution of PKD1 family members in human and chimpanzee and, thus, simulate an independent evolution of the PKD1 pseudogenes from their master PKD1 genes in human and chimpanzee.
Oprea GE, Kröber S, McWhorter ML, Rossoll W, Müller S, Krawczak M, Bassell GJ, Beattie CE, Wirth B.
Plastin 3 is a protective modifier of autosomal recessive spinal muscular atrophy.Science,
320 (2008), 524-7.
[abstract]
Abstract:
Homozygous deletion of the survival motor neuron 1 gene (SMN1) causes spinal muscular atrophy (SMA), the most frequent genetic cause of early childhood lethality. In rare instances, however, individuals are asymptomatic despite carrying the same SMN1 mutations as their affected siblings, thereby suggesting the influence of modifier genes. We discovered that unaffected SMN1-deleted females exhibit significantly higher expression of plastin 3 (PLS3) than their SMA-affected counterparts. We demonstrated that PLS3 is important for axonogenesis through increasing the F-actin level. Overexpression of PLS3 rescued the axon length and outgrowth defects associated with SMN down-regulation in motor neurons of SMA mouse embryos and in zebrafish. Our study suggests that defects in axonogenesis are the major cause of SMA, thereby opening new therapeutic options for SMA and similar neuromuscular diseases.
Milde-Kellers A, Krawczak M, Augustin C, Boomgaarden-Brandes K, Simeoni E, Kaatsch HJ, Mühlbauer B, Schuchardt S.
An illicit love affair during the Third Reich: who is my grandfather?.J Forensic Sci,
53 (2008), 377-9.
[abstract]
Abstract:
More than 60 years after an illicit love affair had occurred between Erika H, wife of a Wehrmacht soldier, and a Polish slave worker during World War II, we could clarify the blood relationships of her daughter Uta. When Erika H had become pregnant both of the men could have fathered the child. Erika H was found guilty of fraternization and imprisoned at Ravensbrück concentration camp. She gave birth to Uta and died there in 1944. Uta survived the war as did Erika's husband Gustav, who accepted Uta as his child. Blood samples from family members were taken and DNA extracted. A panel of 16 short tandem repeat (STR) loci were amplified and separated by capillary electrophoresis and the likelihoods calculated using the MLINK software. The combined genotypes yielded a cumulative likelihood ratio of over 200,000 against paternity of Gustav H. This case serves to illustrate the utility of STR profiles for complex deficiency kinship analysis.
Luca D, Ringquist S, Klei L, Lee AB, Gieger C, Wichmann HE, Schreiber S, Krawczak M, Lu Y, Styche A, Devlin B, Roeder K, Trucco M.
On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.Am J Hum Genet,
82 (2008), 453-63.
[abstract]
Abstract:
Resources being amassed for genome-wide association (GWA) studies include "control databases" genotyped with a large-scale SNP array. How to use these databases effectively is an open question. We develop a method to match, by genetic ancestry, controls to affected individuals (cases). The impact of this method, especially for heterogeneous human populations, is to reduce the false-positive rate, inflate other spuriously small p values, and have little impact on the p values associated with true positive loci. Thus, it highlights true positives by downplaying false positives. We perform a GWA by matching Americans with type 1 diabetes (T1D) to controls from Germany. Despite the complex study design, these analyses identify numerous loci known to confer risk for T1D.
Sauermann U, Siddiqui R, Suh YS, Platzer M, Leuchte N, Meyer H, Mätz-Rensing K, Stoiber H, Nürnberg P, Hunsmann G, Stahl-Hennig C, Krawczak M.
Mhc class I haplotypes associated with survival time in simian immunodeficiency virus (SIV)-infected rhesus macaques.Genes Immun,
9 (2008), 69-80.
[abstract]
Abstract:
In both human immunodeficiency virus-infected humans and simian immunodeficiency virus (SIV)-infected macaques, genes encoded in the major histocompatibility complex (MHC) class I region are important determinants of disease progression. However, compared to the human human lymphocyte antigen complex, the macaque MHC region encodes many more class I genes. Macaques with the same immunodominant class I genes express additional Mhc genes with the potential to influence the disease course. We therefore assessed the association between of the Mhc class I haplotypes, rather than single gene variants, and survival time in SIV-infected rhesus macaques (Macaca mulatta). DNA sequence analysis and Mhc genotyping of 245 pedigreed monkeys identified 17 Mhc class I haplotypes that constitute 10 major genotypes. Among 81 vaccination-naive, SIV-infected macaques, 71 monkeys carried at least one Mhc class I haplotype encoding only MHC antigens that were incapable of inducing an effective anti-SIV cytotoxic T lymphocytes response. Study of these macaques enabled us to relate individual Mhc class I haplotypes to slow, medium and rapid disease progression. In a post hoc analysis, classification according to disease progression was found to explain at least 48% of the observed variation of survival time.
Lao O, Lu TT, Nothnagel M, Junge O, Freitag-Wolf S, Caliebe A, Balascakova M, Bertranpetit J, Bindoff LA, Comas D, Holmlund G, Kouvatsi A, Macek M, Mollet I, Parson W, Palo J, Ploski R, Sajantila A, Tagliabracci A, Gether U, Werge T, Rivadeneira F, Hofman A, Uitterlinden AG, Gieger C, Wichmann HE, Rüther A, Schreiber S, Becker C, Nürnberg P, Nelson MR, Krawczak M, Kayser M.
Correlation between genetic and geographic structure in Europe.Curr Biol,
18 (2008), 1241-8.
[abstract]
Abstract:
Understanding the genetic structure of the European population is important, not only from a historical perspective, but also for the appropriate design and interpretation of genetic epidemiological studies. Previous population genetic analyses with autosomal markers in Europe either had a wide geographic but narrow genomic coverage [1, 2], or vice versa [3-6]. We therefore investigated Affymetrix GeneChip 500K genotype data from 2,514 individuals belonging to 23 different subpopulations, widely spread over Europe. Although we found only a low level of genetic differentiation between subpopulations, the existing differences were characterized by a strong continent-wide correlation between geographic and genetic distance. Furthermore, mean heterozygosity was larger, and mean linkage disequilibrium smaller, in southern as compared to northern Europe. Both parameters clearly showed a clinal distribution that provided evidence for a spatial continuity of genetic diversity in Europe. Our comprehensive genetic data are thus compatible with expectations based upon European population history, including the hypotheses of a south-north expansion and/or a larger effective population size in southern than in northern Europe. By including the widely used CEPH from Utah (CEU) samples into our analysis, we could show that these individuals represent northern and western Europeans reasonably well, thereby confirming their assumed regional ancestry.
Franke A, Balschun T, Karlsen TH, Sventoraityte J, Nikolaus S, Mayr G, Domingues FS, Albrecht M, Nothnagel M, Ellinghaus D, Sina C, Onnie CM, Weersma RK, Stokkers PC, Wijmenga C, Gazouli M, Strachan D, McArdle WL, Vermeire S, Rutgeerts P, Rosenstiel P, Krawczak M, Vatn MH, , Mathew CG, Schreiber S.
Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility.Nat Genet,
40 (2008), 1319-23.
[abstract]
Abstract:
Inflammatory bowel disease (IBD) typically manifests as either ulcerative colitis (UC) or Crohn's disease (CD). Systematic identification of susceptibility genes for IBD has thus far focused mainly on CD, and little is known about the genetic architecture of UC. Here we report a genome-wide association study with 440,794 SNPs genotyped in 1,167 individuals with UC and 777 healthy controls. Twenty of the most significantly associated SNPs were tested for replication in three independent European case-control panels comprising a total of 1,855 individuals with UC and 3,091 controls. Among the four consistently replicated markers, SNP rs3024505 immediately flanking the IL10 (interleukin 10) gene on chromosome 1q32.1 showed the most significant association in the combined verification samples (P = 1.35 x 10(-12); OR = 1.46 (1.31-1.62)). The other markers were located in ARPC2 and in the HLA-BTNL2 region. Association between rs3024505 and CD (1,848 cases, 1,804 controls) was weak (P = 0.013; OR = 1.17 (1.01-1.34)). IL10 is an immunosuppressive cytokine that has long been proposed to influence IBD pathophysiology. Our findings strongly suggest that defective IL10 function is central to the pathogenesis of the UC subtype of IBD.
Franke A, Fischer A, Nothnagel M, Becker C, Grabe N, Till A, Lu T, Müller-Quernheim J, Wittig M, Hermann A, Balschun T, Hofmann S, Niemiec R, Schulz S, Hampe J, Nikolaus S, Nürnberg P, Krawczak M, Schürmann M, Rosenstiel P, Nebel A, Schreiber S.
Genome-wide association analysis in sarcoidosis and Crohn's disease unravels a common susceptibility locus on 10p12.2.Gastroenterology,
135 (2008), 1207-15.
[abstract]
Abstract:
BACKGROUND & AIMS: Crohn's disease (CD) and sarcoidosis (SA) are chronic inflammatory barrier diseases that share several clinical and immunological features, including the occurrence of granulomas. METHODS: A 100k genome-wide association study with 83,360 single-nucleotide polymorphisms (SNPs) was performed on 382 CD patients, 398 SA patients, and 394 control individuals. The 24 SNPs that were most strongly associated in the combined CD/SA phenotype were selected for verification in an independent sample of 1,317 patients (660 CD and 657 SA) and 1,091 controls. RESULTS: The most significant association (Bonferroni corrected P = .036) was obtained at SNP rs1398024 on chromosome 10p12.2, with an odds ratio (OR) for both diseases of 0.81 (95% confidence interval [CI], 0.69-0.96) for carriership of the rarer allele A. The P value in the overall combined sample was 4.24 x 10(-6). During further follow-up, a moderate association (OR, 0.83; 95% CI, 0.72-0.96; P = .015) was observed between rs1398024 and ulcerative colitis (1,080 patients vs 1,091 controls), the second main subphenotype of inflammatory bowel disease in addition to CD. Extensive fine mapping of the 10p12.2 locus points to yet unidentified variants in the C10ORF67 gene region as the most likely underlying risk factors. CONCLUSION: Our study demonstrates that the combined analysis of different, albeit clinically related, phenotypes can lead to the identification of common susceptibility loci.
Hofmann S, Franke A, Fischer A, Jacobs G, Nothnagel M, Gaede KI, Schürmann M, Müller-Quernheim J, Krawczak M, Rosenstiel P, Schreiber S.
Genome-wide association study identifies ANXA11 as a new susceptibility locus for sarcoidosis.Nat Genet,
(2008).
[abstract]
Abstract:
Sarcoidosis is a complex chronic inflammatory disorder with predominant manifestation in the lung. In the first genome-wide association study (>440,000 SNPs) of this disease, comprising 499 German individuals with sarcoidosis and 490 controls, we detected a series of genetic associations. The strongest association signal maps to the ANXA11 (annexin A11) gene on chromosome 10q22.3. Validation in an independent sample (1,649 cases, 1,832 controls) confirmed the association (SNP rs2789679: P = 3.0 x 10(-13), rs7091565: P = 1.0 x 10(-5), allele-based test). Extensive fine mapping located the association signal to a region between exon 5 and exon 14 of ANXA11. A common nonsynonymous SNP (rs1049550, T > C, R230C) was found to be strongly associated with sarcoidosis. The GWAS lead SNP and additional risk variants in the region (rs1953600, rs2573346, rs2784773) were in strong linkage disequilibrium with rs1049550. Annexin A11 has complex and essential functions in several biological pathways, including apoptosis and proliferation.
Nothnagel M, Lu TT, Krawczak M.
Hypotheses in genome-wide association scans.Eur J Hum Genet,
16 (2008), 1174-5; author reply 1175.
Singh KK, Dawson WW, Krawczak M, Schmidtke J.
IMPG1 gene variation in rhesus macular drusen.Vet Ophthalmol,
10 (2007 Sep-Oct), 274-7.
[abstract]
Abstract:
Drusen is a hallmark of human age-related maculopathy. Rhesus macaques (Macaca mulatta) represent a natural model of age-related maculopathy with drusen. We have already mapped the macular drusen susceptibility locus in rhesus macaques to the homolog of human chromosome 6q14-15 and shown that a particular IMPG1 gene SNP haplotype was apparently associated with drusen formation in the rhesus macaques maintained by the Caribbean Primate Research Center (CPRC), Puerto Rico, USA. The aim of the present study was to verify this finding in the macaques kept at the German Primate Research Center (DPZ), Germany. The study group comprised 64 animals (34 affected, 30 unaffected). These monkeys were genotyped for all known variations in the IMPG1 gene and haplotype analysis was performed. A total absence of the previously identified risk haplotype of the IMPG1 gene, and a much lower drusen prevalence in comparison to the CPRC group, was observed in the DPZ samples. This prompted a re-analysis of the original disease association in the CPRC, which revealed that the implied risk haplotype was in fact a sequencing artifact. Taken together, the data highlight that additional factors, other than IMPG1 variation, must play a role in drusen pathogenesis in rhesus macaques.
Caliebe A, Neininger R, Krawczak M, Rösler U.
On the length distribution of external branches in coalescence trees: genetic diversity within species.Theor Popul Biol,
72 (2007), 245-52.
[abstract]
Abstract:
Let Z(n) denote the length of an external branch, chosen at random from a Kingman n-coalescent. Based on a recursion for the distribution of Z(n), we show that nZ(n) converges in distribution, as n tends to infinity, to a non-negative random variable Z with density x--> 8/(2+x)(3), x>or=0. This result facilitates the study of the time to the most recent common ancestor of a randomly chosen individual and its closest relative in a given population. This time span also reflects the maximum relatedness between a single individual and the rest of the population. Therefore, it measures the uniqueness of a random individual, a central characteristic of the genetic diversity of a population.
Buch S, Schafmayer C, Völzke H, Becker C, Franke A, von Eller-Eberstein H, Kluck C, Bässmann I, Brosch M, Lammert F, Miquel JF, Nervi F, Wittig M, Rosskopf D, Timm B, Höll C, Seeger M, ElSharawy A, Lu T, Egberts J, Fändrich F, Fölsch UR, Krawczak M, Schreiber S, Nürnberg P, Tepel J, Hampe J.
A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease.Nat Genet,
39 (2007), 995-9.
[abstract]
Abstract:
With an overall prevalence of 10-20%, gallstone disease (cholelithiasis) represents one of the most frequent and economically relevant health problems of industrialized countries. We performed an association scan of >500,000 SNPs in 280 individuals with gallstones and 360 controls. A follow-up study of the 235 most significant SNPs in 1,105 affected individuals and 873 controls replicated the disease association of SNP A-1791411 in ABCG8 (allelic P value P(CCA) = 4.1 x 10(-9)), which was subsequently attributed to coding variant rs11887534 (D19H). Additional replication was achieved in 728 German (P = 2.8 x 10(-7)) and 167 Chilean subjects (P = 0.02). The overall odds ratio for D19H carriership was 2.2 (95% confidence interval: 1.8-2.6, P = 1.4 x 10(-14)) in the full German sample. Association was stronger in subjects with cholesterol gallstones (odds ratio = 3.3), suggesting that His19 might be associated with a more efficient transport of cholesterol into the bile.
Krawczak M, Thomas NS, Hundrieser B, Mort M, Wittig M, Hampe J, Cooper DN.
Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing.Hum Mutat,
28 (2007), 150-8.
[abstract]
Abstract:
Although single base-pair substitutions in splice junctions constitute at least 10% of all mutations causing human inherited disease, the factors that determine their phenotypic consequences at the RNA level remain to be fully elucidated. Employing a neural network for splice-site recognition, we performed a meta-analysis of 478 disease-associated splicing mutations, in 38 different genes, for which detailed laboratory-based mRNA phenotype assessment had been performed. Inspection of the +/-50-bp DNA sequence context of the mutations revealed that exon skipping was the preferred phenotype when the immediate vicinity of the affected exon-intron junctions was devoid of alternative splice-sites. By contrast, in the presence of at least one such motif, cryptic splice-site utilization, became more prevalent. This association was, however, confined to donor splice-sites. Outside the obligate dinucleotide, the spatial distribution of pathological mutations was found to differ significantly from that of SNPs. Whereas disease-associated lesions clustered at positions -1 and +3 to +6 for donor sites and -3 for acceptor sites, SNPs were found to be almost evenly distributed over all sequence positions considered. When all putative missense mutations in the vicinity of splice-sites were extracted from the Human Gene Mutation Database for the 38 studied genes, a significantly higher proportion of changes at donor sites (37/152; 24.3%) than at acceptor splice-sites (1/142; 0.7%) was found to reduce the neural network signal emitted by the respective splice-site. Based upon these findings, we estimate that some 1.6% of disease-causing missense substitutions in human genes are likely to affect the mRNA splicing phenotype. Taken together, our results are consistent with correct donor splice-site recognition being a key step in exon recognition.
Witsch-Baumgartner M, Schwentner I, Gruber M, Benlian P, Bertranpetit J, Bieth E, Chevy F, Clusellas N, Estivill X, Gasparini P, Giros M, Kelley RI, Krajewska-Walasek M, Menzel J, Miettinen TA, Ogorelkova M, Rossi M, Scala I, Schinzel A, Schmidt K, Schönitzer D, Seemanova E, Sperling K, Syrrou M, Talmud P, Wollnik B, Krawczak M, Labuda D, Utermann G.
Age and origin of major Smith-Lemli-Opitz Syndrome (SLOS) mutations in European populations.J Med Genet,
(2007).
[abstract]
Abstract:
BACKGROUND: Smith-Lemli-Opitz Syndrome (SLOS [MIM 270 400] is an autosomal recessive multiple congenital anomalies/mental retardation syndrome caused by mutations in the 7-sterol reductase (DHCR7, E.C.1.3.1.21) gene. The prevalence of SLOS has been estimated to range between 1:15000 and 1:60000 in populations of European origin. We have analyzed the frequency, origin, and age of DHCR7 mutations in European populations. METHODS AND RESULTS: In 263 SLOS patients ten common alleles (c.964-1G>C, p.Trp151X, p.Thr93Met, p.Val326Leu, p.Arg352Trp, p.Arg404Cys, p.Phe302Leu, p.Leu157Pro, p.Gly410Ser, p.Arg445Gln) were found to constitute approximately 80% of disease-causing mutations. As reported before, the mutational spectra differed significantly between populations and frequency peaks of common mutations were observed in North-West (c.964-1G>C), North-East (p.Trp151X, p.Val326Leu) and Southern Europe (p.Thr93Met). SLOS was virtually absent from Finland. The analysis of nearly 8000 alleles from ten different European populations confirmed a geographical distribution of DHCR7 mutations as reported in previous studies. The common Null mutations in Northern Europe (combined ca. 1:70) occurred at a much higher frequency than expected from the reported prevalence of SLOS. In contrast the most common mutation in Mediterranean SLOS patients (p.Thr93Met) had a low population frequency. Haplotypes were constructed for SLOS chromosomes, and for wild-type chromosomes of African and European origins using eight cSNPs in the DHCR7 gene. The DHCR7 orthologue was sequenced in eight chimpanzees (Pan Troglodytes) and three microsatellites were analyzed in 50 of the SLOS families in order to estimate the age of the three major SLOS causing mutations. CONCLUSION: The results indicate a time of first appearance of c.964-1G>C and p.Trp151X some 3000 years ago in North-West and North-East Europe respectively. The p.Thr93Met mutations on the J haplotype has probably first arisen approximately 6000 years ago in the Eastern Mediterranean. Together, it appears that a combination of founder effects, recurrent mutations, and drift have shaped the present frequency distribution of DHCR7 mutations in Europe.
Wollstein A, Herrmann A, Wittig M, Nothnagel M, Franke A, Nürnberg P, Schreiber S, Krawczak M, Hampe J.
Efficacy assessment of SNP sets for genome-wide disease association studies.Nucleic Acids Res,
35 (2007), e113.
[abstract]
Abstract:
The power of a genome-wide disease association study depends critically upon the properties of the marker set used, particularly the number and physical spacing of markers, and the level of inter-marker association due to linkage disequilibrium. Extending our previously devised theoretical framework for the entropy-based selection of genetic markers, we have developed a local measure of the efficacy of a marker set, relative to including a maximally polymorphic single nucleotide polymorphism (SNP) at the map position of interest. Using this quantitative criterion, we evaluated five currently available SNP sets, namely Affymetrix 100K and 500K, and Illumina 100K, 300K and 550K in the CEU, YRI and JPT + CHB HapMap populations. At 50% relative efficacy, the commercial marker sets cover between 19 and 68% of the human genome, depending upon the population under study. An optimal technology-independent 500K marker set constructed from HapMap for Caucasians, in contrast, would achieve 73% coverage at the same relative efficacy.
Schafmayer C, Völzke H, Buch S, Egberts J, Spille A, von Eberstein H, Franke A, Seeger M, Hinz S, Elsharawy A, Rosskopf D, Brosch M, Krawczak M, Foelsch UR, Schafmayer A, Lammert F, Schreiber S, Faendrich F, Hampe J, Tepel J.
Investigation of the Lith6 candidate genes APOBEC1 and PPARG in human gallstone disease.Liver Int,
27 (2007), 910-9.
[abstract]
Abstract:
BACKGROUND: Genetic susceptibility contributes to the aetiology of gallbladder diseases as shown by multiple epidemiological studies. A major gallstone susceptibility locus (Lith6) was identified in 2003 by quantitative trait locus mapping in mice. Two attractive positional and functional candidate genes in apolipoprotein B mRNA-editing protein (APOBEC1) and peroxisome proliferator-activated receptor gamma (PPARG) are located in this interval. AIMS: To investigate APOBEC1 and PPARG as candidate genes for common symptomatic gallstone disease in humans. PATIENTS AND METHODS: Eight hundred and ten patients who underwent cholecystectomy for symptomatic gallstone disease (median age of onset 50) were compared with 718 sex-matched control individuals. An independent additional sample included 368 gallstone patients and 368 controls. Control individuals were sonographically free of gallstones. Haplotype tagging and all known coding single nucleotide polymorphisms were genotyped for PPARG (N=32) and APOBEC1 (N=11). RESULTS: The investigated high-risk patient sample provides a power of greater than 80% for the detection of odds ratios down to 1.45. No evidence of association of the two genes in the single-point tagging markers, coding variants and in the sliding window haplotype analysis was detected (all nominal single point P-values >0.04). A logistic regression analysis including age, sex and BMI as covariates was also negative (nominal P-values > or =0.08). CONCLUSIONS: In the investigated German samples, no evidence of association of APOBEC1 and PPARG with gallstone susceptibility was detected. Systematic fine mapping of the complete Lith6 region is required to identify the causative genetic variants for gallstone in mice and humans.
Franke A, Hampe J, Rosenstiel P, Becker C, Wagner F, Häsler R, Little RD, Huse K, Ruether A, Balschun T, Wittig M, Elsharawy A, Mayr G, Albrecht M, Prescott NJ, Onnie CM, Fournier H, Keith T, Radelof U, Platzer M, Mathew CG, Stoll M, Krawczak M, Nürnberg P, Schreiber S.
Systematic association mapping identifies NELL1 as a novel IBD disease gene.PLoS ONE,
2 (2007), e691.
[abstract]
Abstract:
Crohn disease (CD), a sub-entity of inflammatory bowel disease (IBD), is a complex polygenic disorder. Although recent studies have successfully identified CD-associated genetic variants, these susceptibility loci explain only a fraction of the heritability of the disease. Here, we report on a multi-stage genome-wide scan of 393 German CD cases and 399 controls. Among the 116,161 single-nucleotide polymorphisms tested, an association with the known CD susceptibility gene NOD2, the 5q31 haplotype, and the recently reported CD locus at 5p13.1 was confirmed. In addition, SNP rs1793004 in the gene encoding nel-like 1 precursor (NELL1, chromosome 11p15.1) showed a consistent disease-association in independent German population- and family-based samples (942 cases, 1082 controls, 375 trios). Subsequent fine mapping and replication in an independent sample of 454 French/Canadian CD trios supported the authenticity of the NELL1 association. Further confirmation in a large German ulcerative colitis (UC) sample indicated that NELL1 is a ubiquitous IBD susceptibility locus (combined p<10(-6); OR = 1.66, 95% CI: 1.30-2.11). The novel 5p13.1 locus was also replicated in the French/Canadian sample and in an independent UK CD patient panel (453 cases, 521 controls, combined p<10(-6) for SNP rs1992660). Several associations were replicated in at least one independent sample, point to an involvement of ITGB6 (upstream), GRM8 (downstream), OR5V1 (downstream), PPP3R2 (downstream), NM_152575 (upstream) and HNF4G (intron).
Nothnagel M, Wollstein A, Krawczak M.
Comparative assessment of the association information captured by SNP tagging.Hum Hered,
64 (2007), 27-34.
[abstract]
Abstract:
Exploiting the association between single nucleotide polymorphisms (SNP) can potentially reduce the costs of association mapping of common disease genes. Different methods have been proposed for defining subsets of SNPs as proxies (or tagSNPs) for other SNPs, some of which rely upon a model of haplotype blocks. Other approaches only consider the pair-wise correlation between markers as a basis for selecting tagSNPs. Yet another, recently proposed model-based method takes marker heterozygosity and genetic distance into account in order to maximize the expected utility of a marker set to map frequent, but unobserved genetic variants. We compared these tagging approaches with regard to their ability to correlate tagSNPs and bi-allelic, potentially disease-causing genetic variants. We used the CEU sample of chromosome 19 from the HapMap project for an initial comparison, and demonstrated a comparable performance of both approaches but a difference in terms of tagSNPs selected and variants captured. In any case, we conclude that a considerable loss of information appears to be inherent to any type of SNP tagging, even when dense marker sets are available for SNP selection.
Schafmayer C, Buch S, Egberts JH, Franke A, Brosch M, El Sharawy A, Conring M, Koschnick M, Schwiedernoch S, Katalinic A, Kremer B, Fölsch UR, Krawczak M, Fändrich F, Schreiber S, Tepel J, Hampe J.
Genetic investigation of DNA-repair pathway genes PMS2, MLH1, MSH2, MSH6, MUTYH, OGG1 and MTH1 in sporadic colon cancer.Int J Cancer,
121 (2007), 555-8.
[abstract]
Abstract:
Mutations in DNA repair genes have previously been identified as causative factors for hereditary nonpolyposis colon cancer (HNPCC). Recent evidence also supports an association between DNA sequence variation in these genes and sporadic colorectal carcinoma (CRC). Genetic investigation of DNA repair genes PMS2, MLH1, MSH2, MSH6, MUTYH, OGG1 and MTH1, as possible susceptibility factors for sporadic CRC, was done using both a haplotype tagging and a candidate (i.e. coding) single nucleotide polymorphism (SNP) approach. Some 1,068 patients with operated CRC (median age at diagnosis: 59 years) were compared to 738 sex-matched control individuals (median age: 67 years). Haplotype tagging SNPs, previously reported risk variants and all known coding SNPs with a minor allele frequency >0.005 were genotyped in PMS2 (N = 10), MLH1 (N = 11), MSH2 (N = 18), MSH6 (N = 15), MUTYH (N = 7), OGG1 (N = 11) and MTH1 (N = 3). No evidence for an association between CRC and any of the 7 genes was detected, neither with the tagging or coding SNPs nor in a sliding window haplotype analysis (all nominal p-values >0.05). The previously reported risk variants D132H in MLH1 and R154H in OGG1 were not even observed in the German population. Genetic CRC risk factors so far identified in DNA repair genes seem to be rare and population-specific. Their association with the disease could not be replicated in German CRC samples. It remains to be elucidated by more systematic, large-scale experiments whether common variants in the same genes, but present across populations, represent risk factors for sporadic CRC.
Simon J, Paslack R, Robienski J, Cooper DN, Goebel JW, Krawczak M.
A legal framework for biobanking: the German experience.Eur J Hum Genet,
15 (2007), 528-32.
[abstract]
Abstract:
Although biobanks are vital for modern medical research, serious concerns have been raised about the legal basis and framework of such endeavours. This led the German 'Telematics Platform for Medical Research Networks' ('Telematikplattform für Medizinische Forschungsnetze', TMF) to initiate a project in 2004 that was designed to place German biobanks on a sound legal footing. This project involved the planning, writing and evaluation of an expert report that addresses in great detail the legal issues concerning property rights, medical professional regulations, general liability insurance, resource continuity and research secrecy. Here, we provide a brief summary of the major results of this project.
Bogdanova N, Horst J, Chlystun M, Croucher PJ, Nebel A, Bohring A, Todorova A, Schreiber S, Gerke V, Krawczak M, Markoff A.
A common haplotype of the annexin A5 (ANXA5) gene promoter is associated with recurrent pregnancy loss.Hum Mol Genet,
16 (2007), 573-8.
[abstract]
Abstract:
We sought to verify whether variation in the promoter of the gene encoding placental anticoagulant protein annexin A5 (ANXA5) represents a risk factor for recurrent pregnancy loss (RPL). Sequence analysis of 70 German RPL patients, all known to carry neither factor V Leiden nor a prothrombin mutation, revealed four consecutive nucleotide substitutions in the ANXA5 promoter, which were transmitted as a joint haplotype (M2). Reporter gene assays revealed that M2 reduces the in vitro activity of the ANXA5 promoter to 37-42% of the normal level. The possible relationship between M2 and RPL was evaluated by comparing RPL patients with two independent control groups recruited from the registry of the Institut für Humangenetik in Münster and the PopGen biobank in Kiel, respectively. Carriers of M2 were found to exhibit a > 2-fold higher RPL risk than non-carriers (odds ratio, 2.42; 95% confidence interval, 1.27-4.58) when using unselected controls (PopGen) and an almost 4-fold higher risk when using the Münster 'super-controls', i.e. women with successful pregnancies and no previous history of pregnancy losses (odds ratio, 3.88; 95% confidence interval, 1.98-7.54). This statistically significant association should facilitate the development of improved prognostic algorithms for RPL, involving a more precise assessment of individual disease risks, and provide a guide to offering adequate therapies where relevant.
Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Günther S, Prescott NJ, Onnie CM, Häsler R, Sipos B, Fölsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S.
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1.Nat Genet,
39 (2007), 207-11.
[abstract]
Abstract:
We performed a genome-wide association study of 19,779 nonsynonymous SNPs in 735 individuals with Crohn disease and 368 controls. A total of 7,159 of these SNPs were informative. We followed up on all 72 SNPs with P <or= 0.01 with an allele-based disease association test in 380 independent Crohn disease trios, 498 Crohn disease singleton cases and 1,032 controls. Disease association of rs2241880 in the autophagy-related 16-like 1 gene (ATG16L1) was replicated in these samples (P = 4.0 x 10(-8)) and confirmed in a UK case-control sample (P = 0.0004). By haplotype and regression analysis, we found that marker rs2241880, a coding SNP (T300A), carries virtually all the disease risk exerted by the ATG16L1 locus. The ATG16L1 gene encodes a protein in the autophagosome pathway that processes intracellular bacteria. We found a statistically significant interaction with respect to Crohn disease risk between rs2241880 and the established CARD15 susceptibility variants (P = 0.039). Together with the lack of association between rs2241880 and ulcerative colitis (P > 0.4), these data suggest that the underlying biological process may be specific to Crohn disease.
Vyletal P, Sokolová J, Cooper DN, Kraus JP, Krawczak M, Pepe G, Rickards O, Koch HG, Linnebank M, Kluijtmans LA, Blom HJ, Boers GH, Gaustadnes M, Skovby F, Wilcken B, Wilcken DE, Andria G, Sebastio G, Naughten ER, Yap S, Ohura T, Pronicka E, Laszlo A, Kozich V.
Diversity of cystathionine beta-synthase haplotypes bearing the most common homocystinuria mutation c.833T>C: a possible role for gene conversion.Hum Mutat,
28 (2007), 255-64.
[abstract]
Abstract:
Homozygosity or compound heterozygosity for the c.833T>C transition (p.I278 T) in the cystathionine beta-synthase (CBS) gene represents the most common cause of pyridoxine-responsive homocystinuria in Western Eurasians. However, the frequency of the pathogenic c.833C allele, as observed in healthy newborns from several European countries (q(c.833C) approximately equals 3.3 x 10(-3)), is approximately 20-fold higher than expected on the basis of the observed number of symptomatic homocystinuria patients carrying this mutation (q(c.833C) approximately equals 0.18 x 10(-3)), implying clinical underascertainment. Intriguingly, the c.833C mutation is also present in combination with a 68-bp insertion, c.[833C; 844_845ins68], in a substantial proportion of chromosomes from nonhomocystinuric individuals worldwide. We have sought to study the relationship between the pathogenic and nonpathogenic c.833C-bearing chromosomes and to determine whether the pathogenic c.[833C; -] chromosomes are identical-by-descent or instead arose by recurrent mutation. Initial haplotype analysis of 780 randomly selected Czech and sub-Saharan African wild-type chromosomes, employing 12 intragenic markers, revealed 29 distinct CBS haplotypes, of which 10 carried the c.[833C; 844_845ins68] combination; none carried an isolated c.833C or c.844_845ins68 mutation. Subsequent examination of 69 pathogenic c.[833C; -] chromosomes, derived from homocystinuria patients of predominantly European origin, disclosed three unrelated haplotypes that differed from their wild-type counterparts by virtue of the presence of c.833C, thereby indicating that c.833T>C transition has occurred repeatedly and independently in the past. Since c.833T does not reside within an obvious mutational hotspot, we surmise that the three pathogenic and comparatively prevalent c.[833C; -] chromosomes may have originated by recurrent gene conversion employing the common nonpathogenic c.[833C; 844_845ins68] chromosomes as templates.
Bosy-Westphal A, Onur S, Geisler C, Wolf A, Korth O, Pfeuffer M, Schrezenmeir J, Krawczak M, Müller MJ.
Common familial influences on clustering of metabolic syndrome traits with central obesity and insulin resistance: the Kiel obesity prevention study.Int J Obes (Lond),
31 (2007), 784-90.
[abstract]
Abstract:
OBJECTIVE: The phenotypic heterogeneity of metabolic syndrome (MSX) suggests heterogeneity of the underlying genotype. The aim of the present study was to examine the common genetic background that contributes to the clustering between the two main features (insulin resistance, central obesity) and different MSX component traits. METHODS: In all, 492 individuals from 90 families were investigated in a three-generation family path study as part of the Kiel Obesity Prevention Study (KOPS, 162 grandparents, 66.1+/-6.7 years, 173 parents, 41.3+/-5.4 years and 157 children, 10.8+/-3.4 years). Overall heritability was estimated and common familial (genetic and environmental) influences on insulin resistance (HOMA-IR) or central obesity (elevated waist circumference, WC), respectively, and different MSX traits were compared in a bivariate cross-trait correlation model. RESULTS: Prevalence of MSX (according to NCEP criteria) was 27.2% (f) and 27.8% (m) in adults and 3.5% (f) and 8.5% (m) in children and adolescents, respectively. MSX phenotype was found to be highly variable, comprising 16 subtypes of component trait combinations. Within-trait heritability was 38.5% for HOMA-IR and 53.5% for WC, cross-trait heritability was 53.4%. As much as 6-18% and 3-10% of the shared variance between different MSX component traits (lipid profile, blood pressure) and WC or HOMA-IR, respectively, may be genetic. With the exception of HDL-C, the shared genetic variance between MSX component traits and WC was higher than the genetic variance shared with HOMA-IR. CONCLUSION: A common genetic background contributes to the clustering of different MSX component traits and central obesity or insulin resistance. Common genetic influences favour central obesity as a major characteristic linking these traits.
El-Harith el-HA, Kühnau W, Schmidtke J, Gadzicki D, Ahmed M, Krawczak M, Stuhrmann M.
Hereditary hemorrhagic telangiectasia is caused by the Q490X mutation of the ACVRL1 gene in a large Arab family: support of homozygous lethality.Eur J Med Genet,
49 (2006 Jul-Aug), 323-30.
[abstract]
Abstract:
In a large Saudi Arabian family with hereditary hemorrhagic telangiectasia (HHT), we identified ACVRL1 (ALK1) nonsense mutation Q490X in 40 HHT patients and three healthy children, but neither in 11 individuals with epistaxis, 41 other healthy family members, nor in 50 healthy unrelated Saudi Arabian controls. Sequence analysis of the entire coding region of the ACVRL1 and ENG genes in five of the 11 epistaxic individuals did not reveal any other disease-causing mutation. Epistaxis seems to be a relatively common phenocopy of HHT in the family under study. One couple, both affected by HHT and carriers of Q490X, had 12 pregnancies. Three of them ended in spontaneous abortion, four in early neonatal death, and only five yielded living offspring, all of which had HHT and were Q490X heterozygous. This observation corroborates previous claims that homozygosity for HHT-causing mutations is lethal.
Franke A, Wollstein A, Teuber M, Wittig M, Lu T, Hoffmann K, Nürnberg P, Krawczak M, Schreiber S, Hampe J.
GENOMIZER: an integrated analysis system for genome-wide association data.Hum Mutat,
27 (2006), 583-8.
[abstract]
Abstract:
Genome-wide association analysis appears to be a promising way to identify heritable susceptibility factors for complex human disorders. However, the feasibility of large-scale genotyping experiments is currently limited by an incomplete marker coverage of the genome, a restricted understanding of the functional role of given genomic regions, and the small sample sizes used. Thus, genome-wide association analysis will be a screening tool to facilitate subsequent gene discovery rather than a means to completely resolve individual genetic risk profiles. The validation of association findings will continue to rely upon the replication of "leads" in independent samples from either the same or different populations. Even under such pragmatic conditions, the timely analysis of the large data sets in question poses serious technical challenges. We have therefore developed public-domain software, GENOMIZER, that implements the workflow of an association experiment, including data management, single-point and haplotype analysis, "lead" definition, and data visualization. GENOMIZER (www.ikmb.uni-kiel.de/genomizer) comes with a complete user manual, and is open-source software licensed under the GNU Lesser General Public License. We suggest that the use of this software will facilitate the handling and interpretation of the currently emerging genome-wide association data.
Steffens M, Lamina C, Illig T, Bettecken T, Vogler R, Entz P, Suk EK, Toliat MR, Klopp N, Caliebe A, König IR, Köhler K, Ludemann J, Diaz Lacava A, Fimmers R, Lichtner P, Ziegler A, Wolf A, Krawczak M, Nūrnberg P, Hampe J, Schreiber S, Meitinger T, Wichmann HE, Roeder K, Wienker TF, Baur MP.
SNP-based analysis of genetic substructure in the German population.Hum Hered,
62 (2006), 20-9.
[abstract]
Abstract:
OBJECTIVE: To evaluate the relevance and necessity to account for the effects of population substructure on association studies under a case-control design in central Europe, we analysed three samples drawn from different geographic areas of Germany. Two of the three samples, POPGEN (n = 720) and SHIP (n = 709), are from north and north-east Germany, respectively, and one sample, KORA (n = 730), is from southern Germany. METHODS: Population genetic differentiation was measured by classical F-statistics for different marker sets, either consisting of genome-wide selected coding SNPs located in functional genes, or consisting of selectively neutral SNPs from 'genomic deserts'. Quantitative estimates of the degree of stratification were performed comparing the genomic control approach [Devlin B, Roeder K: Biometrics 1999;55:997-1004], structured association [Pritchard JK, Stephens M, Donnelly P: Genetics 2000;155:945-959] and sophisticated methods like random forests [Breiman L: Machine Learning 2001;45:5-32]. RESULTS: F-statistics showed that there exists a low genetic differentiation between the samples along a north-south gradient within Germany (F(ST)(KORA/POPGEN): 1.7 . 10(-4); F(ST)(KORA/SHIP): 5.4 . 10(-4); F(ST)(POPGEN/SHIP): -1.3 . 10(-5)). CONCLUSION: Although the F(ST )-values are very small, indicating a minor degree of population structure, and are too low to be detectable from methods without using prior information of subpopulation membership, such as STRUCTURE [Pritchard JK, Stephens M, Donnelly P: Genetics 2000;155:945-959], they may be a possible source for confounding due to population stratification.
Schafmayer C, Hartleb J, Tepel J, Albers S, Freitag S, Völzke H, Buch S, Seeger M, Timm B, Kremer B, Fölsch UR, Fändrich F, Krawczak M, Schreiber S, Hampe J.
Predictors of gallstone composition in 1025 symptomatic gallstones from Northern Germany.BMC Gastroenterol,
6 (2006), 36.
[abstract]
Abstract:
BACKGROUND: Gallstones represent a prevalent and costly health problem. The changing epidemiology and the emerging non-surgical interventions for gallstone disease necessitate the definition of target populations for future therapies. This study aimed to define patterns of gallstone composition and identify demographic predictors of gallstone composition in a large sample of symptomatic gallstones from Northern Germany. METHODS: One thousand and seventy-four post-cholecystectomy gallstone specimens were obtained. Demographic and clinical information was provided by questionnaire (N = 1025 independent individuals with complete information). Two samples from each gallstone were analyzed using Fourier transformed infrared spectrometry. RESULTS: The most prevalent substance was cholesterol, which was detected in 95.0% of gallstone specimens. Bilirubin and bilirubinate were present in 30.0% and calcium was detected in 10.0% of the spectra. Ninety-two percent of measurements from the same stone yielded the same "main" substances, indicating a homogenous stone composition in most cases. Female sex and higher body mass index (BMI) were associated with the presence of cholesterol as a main substance in the gallstones (p < 0.001). CONCLUSION: The changing epidemiology of gallstone disease is reflected by a marked shift in stone composition: Only two percent of stones in this study were pigment stones as compared to 91% percent of stones containing cholesterol as a main substance. Obese individuals from Germany with a BMI > 30 kg/m2 have in 95% cholesterol-dominant gallstones and represent a potential target population for non-surgical interventions for the prevention or treatment of cholesterol stones.
Widdig A, Nürnberg P, Bercovitch FB, Trefilov A, Berard JB, Kessler MJ, Schmidtke J, Streich WJ, Krawczak M.
Consequences of group fission for the patterns of relatedness among rhesus macaques.Mol Ecol,
15 (2006), 3825-32.
[abstract]
Abstract:
When mammalian social groups exceed their optimal size, they often tend to split. In view of the potential evolutionary benefits, it should be more advantageous for animals to stay with kin, rather than nonkin, during such fission events. In the present study, the spontaneous fission of two social groups, R and S, of rhesus macaques living on Cayo Santiago, Puerto Rico, provided the opportunity to compare the kinship structure of the corresponding parent and daughter groups, using information on both maternal and paternal relatedness. In both instances, maternal half-siblings and pairs of animals from the same family were significantly more prevalent in the fission products than in the parent group. During the split of group R, significantly more paternal half-siblings stayed in the remnants of the parent group than joined the seceding group. Our findings are compatible with previous behavioural studies demonstrating that female primates bias their social behaviour more to maternal than to paternal kin, but that both types of half-siblings prefer each other more than unrelated animals. It remains to be clarified by future research, however, whether the observed co-segregation of paternal half-sibs in our study reflects active choice or is a by-product of the group-specific kin structures, prior to fission.
Zschocke J, Nebel A, Wicks K, Peters V, El Mokhtari NE, Krawczak M, van der Woude F, Janssen B, Schreiber S.
Allelic variation in the CNDP1 gene and its lack of association with longevity and coronary heart disease.Mech Ageing Dev,
127 (2006), 817-20.
[abstract]
Abstract:
Carnosine, a cytoprotective dipeptide found at very high concentrations in skeletal muscle, heart and brain, is cleaved in blood by serum carnosinase which is encoded by the CNDP1 gene. We recently found that homozygosity of a 5-leucine variant in the leader peptide of this enzyme protects diabetes mellitus patients against nephropathy. Hypothesising that the same allele could also be associated with longevity or a reduced incidence of cardiovascular problems, we examined the frequency of CNDP1 alleles in German centenarians, patients with premature coronary heart disease, and matched controls. A total of 1382 individuals was investigated. The 5-leucine allele was the most common allele in all groups investigated. There was no difference in allele or genotype frequency between centenarians and their control group, or between cardiovascular patients and their control group. The recently identified functional carnosinase variant therefore does neither contribute to longevity nor protect against coronary heart disease in our probands. In addition to the known trinucleotide repeat alleles in the CNDP1 gene, we detected a rare 8-leucine allele, a rare duplication, p.L13_V15dup, and a more common frameshift deletion, L17fsX20. Homozygosity for L17fsX20, estimated to have a prevalence of approximately 1:20,000, would be expected to cause carnosinaemia, an autosomal recessive trait with uncertain clinical relevance.
Gill P, Brenner CH, Buckleton JS, Carracedo A, Krawczak M, Mayr WR, Morling N, Prinz M, Schneider PM, Weir BS, .
DNA commission of the International Society of Forensic Genetics: Recommendations on the interpretation of mixtures.Forensic Sci Int,
160 (2006), 90-101.
[abstract]
Abstract:
The DNA commission of the International Society of Forensic Genetics (ISFG) was convened at the 21st congress of the International Society for Forensic Genetics held between 13 and 17 September in the Azores, Portugal. The purpose of the group was to agree on guidelines to encourage best practice that can be universally applied to assist with mixture interpretation. In addition the commission was tasked to provide guidance on low copy number (LCN) reporting. Our discussions have highlighted a significant need for continuing education and research into this area. We have attempted to present a consensus from experts but to be practical we do not claim to have conveyed a clear vision in every respect in this difficult subject. For this reason, we propose to allow a period of time for feedback and reflection by the scientific community. Then the DNA commission will meet again to consider further recommendations.
Horan M, Newsway V, Yasmin , Lewis MD, Easter TE, Rees DA, Mahto A, Millar DS, Procter AM, Scanlon MF, Wilkinson IB, Hall IP, Wheatley A, Blakey J, Bath PM, Cockcroft JR, Krawczak M, Cooper DN.
Genetic variation at the growth hormone (GH1) and growth hormone receptor (GHR) loci as a risk factor for hypertension and stroke.Hum Genet,
119 (2006), 527-40.
[abstract]
Abstract:
An increased prevalence of both hypertension and cerebrovascular stroke is apparent in growth hormone (GH) deficiency whilst hypertension is a frequent complication in acromegaly. This has suggested a possible link between GH, stature and arterial function. Since the risk of both hypertension and stroke also appears to be inversely correlated with adult height, we have instigated an exploratory study to assess whether inter-individual variation in the genes encoding human growth hormone (GH1) and the GH receptor (GHR) might be associated with an increased risk of hypertension and stroke. GH1 promoter haplotypes were found to differ significantly not only between hypertensive patients (n = 111) and controls (n = 121) but also between stroke patients (n = 155) and controls (n = 158). Intriguingly, the association between GH1 promoter haplotype and risk of hypertension was much greater in females than in males. An inverse correlation between height and central systolic blood pressure was apparent in both hypertensive patients and normal controls but was much stronger in individuals carrying at least one GH1 promoter risk haplotype. The GH1 genotype therefore constitutes a risk factor for hypertension that interacts with stature. A strong association was found between the presence of at least one GH1 risk haplotype and a family history of stroke at an early age (odds ratio: 9.07, 95% confidence interval: 1.14-72.22). Three novel GH variants (Arg16His, Phe176Cys, Cys189Arg) were identified during the course of this study. Although two exhibited markedly reduced biological activity in vitro, their clinical significance remains unclear. No association was found between GHR genotype and either hypertension or stroke, nor was any interaction noted between GHR and GH1 genotypes in terms of a disease association. However, an association between GHRd3 genotype and hypertension was observed among stroke patients, particularly females. Elevated HDL was found to be a risk factor for hypertension in individuals lacking a copy of the GHRd3 allele. Weak associations with GHR genotype were also noted for peripheral systolic and diastolic blood pressure in hypertensive patients. Although the underlying mechanisms are still unclear, our findings are consistent with a complex relationship between height, hypertension, GH1 promoter haplotype, GHR polymorphism and the risk of stroke.
Krawczak M, Nikolaus S, von Eberstein H, Croucher PJ, El Mokhtari NE, Schreiber S.
PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships.Community Genet,
9 (2006), 55-61.
[abstract]
Abstract:
OBJECTIVE: Patient samples used for mapping complex human disease genes are unlikely to be representative of the phenotype spectrum of the respective population as a whole. On the other hand, most ongoing prospective studies are probably too small for evaluating polygenic disease markers. DESIGN: Precise estimates of population-specific genotypic risks can be obtained efficiently through the complete ascertainment of patients in a geographically confined area. The PopGen project uses the most northern part of Germany as a target region for such a pursuit. RESULTS: PopGen currently pursues recruitment, sampling and processing activities in close collaboration with a multitude of clinical partners, covering cardiovascular, neuropsychiatric and environmental diseases. CONCLUSION: PopGen has successfully established itself as a large-scale genetic epidemiological project of international recognition.
Immel UD, Krawczak M, Udolph J, Richter A, Rodig H, Kleiber M, Klintschar M.
Y-chromosomal STR haplotype analysis reveals surname-associated strata in the East-German population.Eur J Hum Genet,
14 (2006), 577-82.
[abstract]
Abstract:
In human populations, the correct historical interpretation of a genetic structure is often hampered by an almost inherent inability to differentiate between ancient and more recent influences upon extant gene pools. One method to trace recent population movements is the analysis of surnames, which, at least in Central Europe, can be thought of as traits 'linked' to the Y chromosome. Illegitimacy, extramarital birth and changes of surnames may have substantially obscured this linkage. In order to assess the actual extent of correlation between surnames and Y-chromosomal haplotypes in Central Europe, we typed Y-chromosomal short tandem repeat markers in 419 German males from Halle. These individuals were subdivided into three groups according to the origin of their respective surname, namely German (G), Slavic (S) or 'Mixed' (M). The distribution of the haplotypes was compared by Analysis of Molecular Variance. While the M group was indistinguishable from group G (PhiST=-0.0008, P>0.5), a highly significant difference (PhiST=0.0277, P<0.001) was observed between the S group and the combined G+M group. This surprisingly strong differentiation is comparable to that of European populations of much larger geographic and linguistic difference. In view of the major migration from Slavic countries into Germany in the 19th century, it appears likely that the observed concurrence of Slavic surnames and Y chromosomes is of a recent rather than an early origin. Our results suggest that surnames may provide a simple means to stratify, and thereby to render more efficient, Y-chromosomal analyses of Central Europeans that target more ancient events.
McCune CA, Ravine D, Carter K, Jackson HA, Hutton D, Hedderich J, Krawczak M, Worwood M.
Iron loading and morbidity among relatives of HFE C282Y homozygotes identified either by population genetic testing or presenting as patients.Gut,
(2005).
[abstract]
Abstract:
BACKGROUND AND AIMS: Although most cases of hereditary haemochromatosis are associated with homozygosity for the C282Y mutation of the HFE gene, the clinical penetrance varies and other genes may modify disease expression. If so, relatives from clinically affected families, by inheriting such genes, may accumulate more iron. To seek evidence for this, we compared iron status and morbidity in unselected first- degree relatives of two groups of index cases from South Wales, namely asymptomatic C282Y homozygotes identified by genetic screening of blood donors (n=56) and C282Y homozygous haemochromatosis patients presenting clinically (n=60). METHODS: All participating relatives had a structured interview, clinical assessment and laboratory investigations. Health-related quality of life was measured (SF-36 v2). RESULTS: 92% of 180 eligible first-degree relatives were interviewed in the "screened" family group and 85% of 143 eligible relatives in the "patient" group. Of 59 relatives homozygous for C282Y, 76% of the men and 32% of the women had the "iron phenotype" (raised transferrin saturation and serum ferritin). Logistic regression modelling of the iron phenotype risk showed that 42% of the initial model deviance could be explained by homozygosity for C282Y, another 6% by life style factors and 6 % by being male. Family group membership was not a significant risk factor. Morbidity and SF-36 scores did not differ significantly either between C282Y homozygotes and relatives lacking C282Y, or between C282Y homozygotes from the "screened" and "patient" groups. Serious morbidity (including cirrhosis) was low in both groups of relatives. CONCLUSIONS: HFE C282Y homozygosity has a high penetrance for iron accumulation but a low clinical penetrance. The lack of excess morbidity among C282Y homozygous relatives of index cases who presented clinically suggests that residual unknown genetic or environmental factors do not greatly influence clinical outcome among C282Y homozygotes.
Roewer L, Croucher PJ, Willuweit S, Lu TT, Kayser M, Lessig R, de Knijff P, Jobling MA, Tyler-Smith C, Krawczak M.
Signature of recent historical events in the European Y-chromosomal STR haplotype distribution.Hum Genet,
116 (2005), 279-91.
[abstract]
Abstract:
Previous studies of human Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) established a link between the extant Y-SNP haplogroup distribution and the prehistoric demography of Europe. By contrast, our analysis of seven rapidly evolving Y-chromosomal short tandem repeat loci (Y-STRs) in over 12,700 samples from 91 different locations in Europe reveals a signature of more recent historic events, not previously detected by other genetic markers. Cluster analysis based upon molecular variance yields two clearly identifiable sub-clusters of Western and Eastern European Y-STR haplotypes, and a diverse transition zone in central Europe, where haplotype spectra change more rapidly with longitude than with latitude. This and other observed patterns of Y-STR similarity may plausibly be related to particular historical incidents, including, for example, the expansion of the Franconian and Ottoman Empires. We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history.
Trefilov A, Croucher PJ, Krawczak M, Schmidtke J.
Genetic influence on reproductive behavior in female rhesus macaques.Twin Res Hum Genet,
8 (2005), 551-2.
Singh KK, Ristau S, Dawson WW, Krawczak M, Schmidtke J.
Mapping of a macular drusen susceptibility locus in rhesus macaques to the homologue of human chromosome 6q14-15.Exp Eye Res,
81 (2005), 401-6.
[abstract]
Abstract:
Rhesus macaques (Macaca mulatta) are a natural model for retinal drusen formation. The present study aimed at clarifying whether chromosomal regions homologous to candidate genes for drusen formation and progression in humans are also associated with a drusen phenotype in rhesus macaques. Some 42 genetic markers from seven chromosomal regions implicated in macular degeneration syndromes in humans were tested for whether they identified homologous, polymorphic sequences in rhesus DNA. This was found to be the case for seven markers, all of which were subsequently screened for the presence of potentially disease-predisposing alleles in 52 randomly chosen adult animals from the Cayo Santiago population of rhesus macaques (Caribbean Primate Research Center, PR, USA). The high drusen prevalence expected in the Cayo Santiago colony was confirmed in our sample in that 38 animals were found to have drusen (73%). Logistic regression analysis revealed that some alleles of the rhesus homologue of anonymous human marker D6S1036 were consistently over-represented among affected animals. Of two candidate genes located in the respective region, allelic variation in one (IMPG1) showed strong association with drusen formation. We conclude that one or more genes located at the rhesus homologue of human 6q14-15 are likely to play a role in retinal drusen formation, a finding that represents a first step towards the identification of genetic factors implicated in macular drusen formation in rhesus macaques. This is an important tool for the separation of genetic and environmental factors which must occur before satisfactory management methods can be developed.
Szibor R, Hering S, Kuhlisch E, Plate I, Demberger S, Krawczak M, Edelmann J.
Haplotyping of STR cluster DXS6801-DXS6809-DXS6789 on Xq21 provides a powerful tool for kinship testing.Int J Legal Med,
119 (2005), 363-9.
[abstract]
Abstract:
Short tandem repeat (STR) markers DXS6801 (GATA41B11), DXS6809 (GATA69B129) and DXS6789 (GATA31F01) are located in a 3-Mb region on human chromosome Xq21, spanning approximately 3-6 cM. Theoretically, this cluster could give rise to 1,144 different haplotypes in the German population. In fact, genotyping of 806 males revealed the presence of 207 different haplotypes. Since the three STRs have been shown to be in strong linkage disequilibrium (LD), haplotype frequencies cannot be computed on the basis of single locus allele frequencies alone, but have to be estimated directly instead. In this work, we present data on linkage, haplotype frequencies and LD in the German population. To highlight the potential of the STR cluster for forensic analysis, we also report two examples of its successful application in pedigree-based kinship testing.
Ball EV, Stenson PD, Abeysinghe SS, Krawczak M, Cooper DN, Chuzhanova NA.
Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity.Hum Mutat,
26 (2005), 205-13.
[abstract]
Abstract:
In the Human Gene Mutation Database (www.hgmd.org), microdeletions and microinsertions causing inherited disease (both defined as involving < or = 20 bp of DNA) account for 8,399 (17%) and 3,345 (7%) logged mutations, in 940 and 668 genes, respectively. A positive correlation was noted between the microdeletion and microinsertion frequencies for 564 genes for which both microdeletions and microinsertions are reported in HGMD, consistent with the view that the propensity of a given gene/sequence to undergo microdeletion is related to its propensity to undergo microinsertion. While microdeletions and microinsertions of 1 bp constitute respectively 48% and 66% of the corresponding totals, the relative frequency of the remaining lesions correlates negatively with the length of the DNA sequence deleted or inserted. Many of the microdeletions and microinsertions of more than 1 bp are potentially explicable in terms of slippage mutagenesis, involving the addition or removal of one copy of a mono-, di-, or trinucleotide tandem repeat. The frequency of in-frame 3-bp and 6-bp microinsertions and microdeletions was, however, found to be significantly lower than that of mutations of other lengths, suggesting that some of these in-frame lesions may not have come to clinical attention. Various sequence motifs were found to be over-represented in the vicinity of both microinsertions and microdeletions, including the heptanucleotide CCCCCTG that shares homology with the complement of the 8-bp human minisatellite conserved sequence/chi-like element (GCWGGWGG). The previously reported indel hotspot GTAAGT and its complement ACTTAC were also found to be overrepresented in the vicinity of both microinsertions and microdeletions, thereby providing a first example of a mutational hotspot that is common to different types of gene lesion. Other motifs overrepresented in the vicinity of microdeletions and microinsertions included DNA polymerase pause sites and topoisomerase cleavage sites. Several novel microdeletion/microinsertion hotspots were noted and some of these exhibited sufficient similarity to one another to justify terming them "super-hotspot" motifs. Analysis of sequence complexity also demonstrated that a combination of slipped mispairing mediated by direct repeats, and secondary structure formation promoted by symmetric elements, can account for the majority of microdeletions and microinsertions. Thus, microinsertions and microdeletions exhibit strong similarities in terms of the characteristics of their flanking DNA sequences, implying that they are generated by very similar underlying mechanisms.
Nebel A, Croucher PJ, Stiegeler R, Nikolaus S, Krawczak M, Schreiber S.
No association between microsomal triglyceride transfer protein (MTP) haplotype and longevity in humans.Proc Natl Acad Sci U S A,
102 (2005), 7906-9.
[abstract]
Abstract:
Human longevity is a multifactorial condition with a significant genetic contribution. A recent association study in two independent samples of long-lived U.S. Caucasians [long-lived individuals (LLI)] identified a SNP haplotype of the microsomal triglyceride transfer protein (MTP, 4q25) that was underrepresented among LLI when compared with younger controls. This suggested that variation in the MTP gene might modify human longevity. Because of its function in lipid metabolism, the MTP gene product could plausibly play a pivotal role in the physiology of aging. However, the association observed in the U.S. samples could not be replicated by the same authors in a larger French LLI sample. We have therefore investigated the MTP "risk" haplotype in our own collection of 1,589 German nonagenarians, centenarians, and appropriately matched controls. No statistically significant differences were observed between LLI and controls at the allele, genotype, or haplotype level. This indicates that a noteworthy influence of the respective MTP haplotype on human longevity in the German population is unlikely. Furthermore, in comparison with all other U.S. and European samples analyzed, the MTP "risk" haplotype was found to be overrepresented only in the U.S. controls. This implies that the putative association is more likely to reflect recent changes in the genetic structure of the U.S. Caucasian population as a whole, rather than genetic effects upon survival to old age. In our view, the original study therefore highlights potential problems that arise when the case-control design is used as a means to map longevity genes in humans.
Schreiber S, Rosenstiel P, Albrecht M, Hampe J, Krawczak M.
Genetics of Crohn disease, an archetypal inflammatory barrier disease.Nat Rev Genet,
6 (2005), 376-88.
[abstract]
Abstract:
Chronic inflammatory disorders such as Crohn disease, atopic eczema, asthma and psoriasis are triggered by hitherto unknown environmental factors that function on the background of some polygenic susceptibility. Recent technological advances have allowed us to unravel the genetic aetiology of these and other complex diseases. Using Crohn disease as an example, we show how the discovery of susceptibility genes furthers our understanding of the underlying disease mechanisms and how it will, ultimately, give rise to new therapeutic developments. The long-term goal of such endeavours is to develop targeted prophylactic strategies. These will probably target the molecular interaction on the mucosal surface between the products of the genome and the microbial metagenome of a patient.
Kwak KD, Jin HJ, Shin DJ, Kim JM, Roewer L, Krawczak M, Tyler-Smith C, Kim W.
Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia.Int J Legal Med,
119 (2005), 195-201.
[abstract]
Abstract:
We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the "minimal haplotype" (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160-163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103-111). All of the individual east Asian populations examined here had high haplotype diversity (> or =0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on Phi(ST) or rho genetic distance measures revealed clustering according to the traditional northeast-southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.
Valentonyte R, Hampe J, Huse K, Rosenstiel P, Albrecht M, Stenzel A, Nagy M, Gaede KI, Franke A, Haesler R, Koch A, Lengauer T, Seegert D, Reiling N, Ehlers S, Schwinger E, Platzer M, Krawczak M, Müller-Quernheim J, Schürmann M, Schreiber S.
Sarcoidosis is associated with a truncating splice site mutation in BTNL2.Nat Genet,
37 (2005), 357-64.
[abstract]
Abstract:
Sarcoidosis is a polygenic immune disorder with predominant manifestation in the lung. Genome-wide linkage analysis previously indicated that the extended major histocompatibility locus on chromosome 6p was linked to susceptibility to sarcoidosis. Here, we carried out a systematic three-stage SNP scan of 16.4 Mb on chromosome 6p21 in as many as 947 independent cases of familial and sporadic sarcoidosis and found that a 15-kb segment of the gene butyrophilin-like 2 (BTNL2) was associated with the disease. The primary disease-associated variant (rs2076530; P(TDT) = 3 x 10(-6), P(case-control) = 1.1 x 10(-8); replication P(TDT) = 0.0018, P(case-control) = 1.8 x 10(-6)) represents a risk factor that is independent of variation in HLA-DRB1. BTNL2 is a member of the immunoglobulin superfamily and has been implicated as a costimulatory molecule involved in T-cell activation on the basis of its homology to B7-1. The G --> A transition constituting rs2076530 leads to the use of a cryptic splice site located 4 bp upstream of the affected wild-type donor site. Transcripts of the risk-associated allele have a premature stop in the spliced mRNA. The resulting protein lacks the C-terminal IgC domain and transmembrane helix, thereby disrupting the membrane localization of the protein, as shown in experiments using green fluorescent protein and V5 fusion proteins.
Krawczak M, Trefilov A, Berard J, Bercovitch F, Kessler M, Sauermann U, Croucher P, Nürnberg P, Widdig A, Schmidtke J.
Male reproductive timing in Rhesus macaques is influenced by the 5HTTLPR promoter polymorphism of the serotonin transporter gene.Biol Reprod,
72 (2005), 1109-13.
[abstract]
Abstract:
The 5HTTLPR polymorphism in the promoter region of the human serotonin transporter (SLC6A4) gene is known to be associated with various stress-related psychological and psychiatric phenomena. We observed that a similar diallelic polymorphism in the orthologous gene of rhesus macaques (Macaca mulatta) was related to the reproductive life history of 580 males residing in the free-ranging colony of Cayo Santiago, Puerto Rico, between 1985 and 1998. At first glance, the polymorphism appeared to be selectively neutral because no difference in total reproductive output was noted between males of different 5HTTLPR genotypes. However, whereas heterozygotes were significantly more reproductive than homozygotes at intermediate age (10-13 yr), the opposite held true before and after this period (n = 682 offspring; randomization P = 0.014). This association, which explains approximately 7% of the observed variation in sire age, most likely reflects different natal dispersal patterns and represents the first reported instance of a genetic influence on reproductive timing in mammals.
Wolf A, Caliebe A, Junge O, Krawczak M.
Forensic interpretation of Y-chromosomal DNA mixtures.Forensic Sci Int,
152 (2005), 209-13.
[abstract]
Abstract:
The mathematical concept previously introduced for the forensic interpretation of DNA mixtures using non-associated genetic markers has been adapted to the assessment of haplotypes. Such calculus is required, for example, when Y-chromosomal markers are used in forensics. In addition to outlining the general mathematical framework, we devise two approaches to its practical computational implementation, involving either the inclusion-exclusion principle of probability theory or a recursion in the number of unknown contributors invoked. The two approaches scale differently, depending upon the complexity of the case and the diversity of the markers used. The performance of Y-chromosomal microsatellites (Y-STRs) as a means of trace donor discrimination has been assessed by simulation, using the derived formulas. Based upon data from the Y-chromosomal Haplotype Reference Database (YHRD), the exclusion chance of a non-contributor is shown to vary between 95% in the case of two contributors, and 70% for five contributors. With only one additional contributor, half of all contributing suspects would yield a log-likelihood ratio in favour of donorship of 1.61 or higher, although the median drops to 0.66 with four additional contributors. It must be emphasised that these estimates of the discriminatory power of Y-STRs are likely to be conservative since the simulations involved only haplotypes known to occur in YHRD.
Caliebe A, Freitag S, Krawczak M.
Stochastische Modelle für Interaktion und Effektmodifikation.Medizinische genetik,
17 (2005), 14-9.
Stenzel A, Lu T, Koch WA, Hampe J, Guenther SM, De La Vega FM, Krawczak M, Schreiber S.
Patterns of linkage disequilibrium in the MHC region on human chromosome 6p.Hum Genet,
114 (2004), 377-85.
[abstract]
Abstract:
Single nucleotide polymorphisms (SNPs) in the human genome are thought to be organised into blocks of high internal linkage disequilibrium (LD), separated by intermittent recombination hotspots. Since understanding haplotype structure is critical for an accurate assessment of inter-individual genetic differences, we investigated up to 968 SNPs from a 10-Mb region on chromosome 6p21, including the human major histocompatibility complex (MHC), in five different population samples (45-550 individuals). Regions of well-defined block structure were found to coexist alongside large areas lacking any clear structure; occasional long-range LD was observed in all five samples. The four white populations analysed were remarkably similar in terms of the extend and spatial distribution of local LD. In US African Americans, the distribution of LD was similar to that in the white populations but the observed haplotype diversity was higher. The existence of large regions without any clear block structure renders the systematic and thorough construction of SNP haplotype maps a crucial prerequisite for disease-association studies.
Schmidtke J, Kühnau W, Wand D, Edelmann J, Szibor R, Krawczak M.
Prenatal exclusion without involving the putative fathers of an incestuous father-daughter parenthood.Prenat Diagn,
24 (2004), 662-4.
Widdig A, Bercovitch FB, Streich WJ, Sauermann U, Nürnberg P, Krawczak M.
A longitudinal analysis of reproductive skew in male rhesus macaques.Proc Biol Sci,
271 (2004), 819-26.
[abstract]
Abstract:
One of the basic tenets of sexual selection is that male reproductive success should be large in polygynous species. Here, we analysed 6 years of molecular genetic data from a semi-free-ranging population of rhesus macaques (Macaca mulatta), using Nonac's B index, to assess the level of male reproductive skew in the study troop. On average, the top sire in each year produced 24% of the infants, while 71% of troop males sired no offspring at all. Consequently, 74% of infants had at least one paternal half-sibling in their own birth cohort. Reproductive success was greatest for high-ranking males, males who spent the whole mating season in the troop and males of 9-11 years of age. Heterozygosity for major histocompatibility complex (MHC) class II gene DQB1 was the strongest single predictor of male reproductive success. A negative relationship suggestive of female mate choice was noted between the B index and the proportion of extragroup paternities. Reproductive skew was not associated with relatedness among potential sires or with female cycle synchrony. We conclude that reproductive skew in male rhesus macaques is best accounted for by the 'limited-control' model, with multiple factors interacting to regulate individual reproductive output.
Abeysinghe SS, Stenson PD, Krawczak M, Cooper DN.
Gross Rearrangement Breakpoint Database (GRaBD).Hum Mutat,
23 (2004), 219-21.
[abstract]
Abstract:
Translocations and gross gene deletions are an important cause of both cancer and inherited disease. Such DNA rearrangements are nonrandomly distributed in the human genome as a consequence of selection for growth advantage and/or the inherent potential of some DNA sequences to be particularly susceptible to breakage and recombination. The Gross Rearrangement Breakpoint Database (GRaBD; http://www.uwcm.ac.uk/uwcm/mg/grabd/) was established primarily for the analysis of the sequence context of translocation and deletion breakpoints in a search for characteristics that might have rendered these sequences prone to rearrangement. GRaBD, which contains 397 germline and somatic DNA breakpoint junction sequences derived from 219 different rearrangements underlying human inherited disease and cancer, is the only comprehensive collection of gross gene rearrangement breakpoint junctions currently available.
Horan M, Millar DS, Hedderich J, Lewis G, Newsway V, Mo N, Fryklund L, Procter AM, Krawczak M, Cooper DN.
Human growth hormone 1 (GH1) gene expression: complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region.Hum Mutat,
21 (2003), 408-23.
[abstract]
Abstract:
The proximal promoter region of the human pituitary expressed growth hormone (GH1) gene is highly polymorphic, containing at least 15 single nucleotide polymorphisms (SNPs). This variation is manifest in 40 different haplotypes, the high diversity being explicable in terms of gene conversion, recurrent mutation, and selection. Functional analysis showed that 12 haplotypes were associated with a significantly reduced level of reporter gene expression whereas 10 haplotypes were associated with a significantly increased level. The former tend to be more prevalent in the general population than the latter (p<0.01), possibly as a consequence of selection. Although individual SNPs contributed to promoter strength in a highly interactive and non-additive fashion, haplotype partitioning was successful in identifying six SNPs as major determinants of GH1 gene expression. The prediction and functional testing of hitherto unobserved super-maximal and sub-minimal promoter haplotypes was then used to test the efficacy of the haplotype partitioning approach. Electrophoretic mobility shift assays demonstrated that five SNP sites exhibit allele-specific protein binding. An association was noted between adult height and the mean in vitro expression value corresponding to an individual's GH1 promoter haplotype combination (p=0.028) although only 3.3% of the variance of adult height was found to be explicable by reference to this parameter. Three additional SNPs, identified within sites I and II of the upstream locus control region (LCR), were ascribed to three distinct LCR haplotypes. A series of LCR-GH1 proximal promoter constructs were used to demonstrate that 1) the LCR enhanced proximal promoter activity by up to 2.8-fold depending upon proximal promoter haplotype, and that 2) the activity of a given proximal promoter haplotype was also differentially enhanced by different LCR haplotypes. The genetic basis of inter-individual differences in GH1 gene expression thus appears to be extremely complex.
Croucher PJ, Mascheretti S, Hampe J, Huse K, Frenzel H, Stoll M, Lu T, Nikolaus S, Yang SK, Krawczak M, Kim WH, Schreiber S.
Haplotype structure and association to Crohn's disease of CARD15 mutations in two ethnically divergent populations.Eur J Hum Genet,
11 (2003), 6-16.
[abstract]
Abstract:
Current debate focuses on the relevance of linkage disequilibrium (LD), ethnicity and underlying haplotype structure to the search for genes involved in complex disorders. The recently described association between single nucleotide polymorphisms (SNPs) of the CARD15 (NOD2) gene and Crohn's disease (CD) in populations of north-European descent provides a test case that we have subjected to detailed SNP haplotype based analyses. We examined 23 SNPs spanning 290 kb, including CARD15, in large North-European and Korean samples of patients with Crohn's disease and normal controls. In Europeans we confirmed that the three disease-associated SNPs occur independently but share a common background haplotype. This suggests a common origin and the possibility of an undiscovered more strongly predisposing mutation. Korean CD patients present a phenotype identical to the European patients and have not previously been screened for CARD15. The three disease-associated SNPs were absent and there was no evidence of association between CARD15 and CD. Consequently, the disease-associated mutations in the Europeans, which are rare, have arisen recently (after the Asian-European split). Our results highlight important issues relevant to mapping the genes that predispose to complex disorders. First, although ethnically divergent populations may present identical phenotypes they do not necessarily share the same set of predisposing genes. Second, although single-locus tests of association showed consistent association with markers throughout the gene, pair-wise LD between markers (r(2) and D') yielded very little information about actual disease-association. Third, a population comparative approach allowed refining of the marker set through the examination of shared polymorphisms and common LD-groups. This approach, in conjunction with the examination of the mutational steps in a haplotype network, allows unambiguous identification of the potentially causative mutations.
Hampe J, Schreiber S, Krawczak M.
Entropy-based SNP selection for genetic association studies.Hum Genet,
114 (2003), 36-43.
[abstract]
Abstract:
Because of their abundance, density, and ease of practical use, single-nucleotide polymorphisms (SNPs) have become the major source of information for association gene mapping in humans. Sensible strategies for selecting practically useful SNPs are therefore required. Among the factors influencing the mapping utility of a given set of SNPs are (1). their individual diversity, (2). their haplotype structure in the population of interest, and (3). their physical distribution. We propose a strategy integrating these aspects into a single mapping utility measure, which is based upon Shannon entropy, and which maximizes the amount of information extracted from a genomic region under a Malecot model of linkage disequilibrium (LD) decay. The same utility measure has also been used to define a criterion guiding SNP discovery and rational decision-making about the continuation or termination of a mapping study. The proposed strategy performs consistently well in a data set comprising 549 German control individuals, genotyped for 136 SNPs from four genomic regions of different LD structure. Adoption of the method in practice is estimated to save up to 30% of genotyping load when compared with equidistant SNP localization or pair-wise LD minimization alone.
Chuzhanova N, Abeysinghe SS, Krawczak M, Cooper DN.
Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.Hum Mutat,
22 (2003), 245-51.
[abstract]
Abstract:
Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions.
Abeysinghe SS, Chuzhanova N, Krawczak M, Ball EV, Cooper DN.
Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs.Hum Mutat,
22 (2003), 229-44.
[abstract]
Abstract:
Translocations and gross deletions are important causes of both cancer and inherited disease. Such gene rearrangements are nonrandomly distributed in the human genome as a consequence of selection for growth advantage and/or the inherent potential of some DNA sequences to be frequently involved in breakage and recombination. Using the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] (containing 397 germ-line and somatic DNA breakpoint junction sequences derived from 219 different rearrangements underlying human inherited disease and cancer), we have analyzed the sequence context of translocation and deletion breakpoints in a search for general characteristics that might have rendered these sequences prone to rearrangement. The oligonucleotide composition of breakpoint junctions and a set of reference sequences, matched for length and genomic location, were compared with respect to their nucleotide composition. Deletion breakpoints were found to be AT-rich whereas by comparison, translocation breakpoints were GC-rich. Alternating purine-pyrimidine sequences were found to be significantly over-represented in the vicinity of deletion breakpoints while polypyrimidine tracts were over-represented at translocation breakpoints. A number of recombination-associated motifs were found to be over-represented at translocation breakpoints (including DNA polymerase pause sites/frameshift hotspots, immunoglobulin heavy chain class switch sites, heptamer/nonamer V(D)J recombination signal sequences, translin binding sites, and the chi element) but, with the exception of the translin-binding site and immunoglobulin heavy chain class switch sites, none of these motifs were over-represented at deletion breakpoints. Alu sequences were found to span both breakpoints in seven cases of gross deletion that may thus be inferred to have arisen by homologous recombination. Our results are therefore consistent with a role for homologous unequal recombination in deletion mutagenesis and a role for nonhomologous recombination in the generation of translocations.
Lessig R, Willuweit S, Krawczak M, Wu FC, Pu CE, Kim W, Henke L, Henke J, Miranda J, Hidding M, Benecke M, Schmitt C, Magno M, Calacal G, Delfin FC, de Ungria MC, Elias S, Augustin C, Tun Z, Honda K, Kayser M, Gusmao L, Amorim A, Alves C, Hou Y, Keyser C, Ludes B, Klintschar M, Immel UD, Reichenpfader B, Zaharova B, Roewer L.
Asian online Y-STR Haplotype Reference Database.Leg Med (Tokyo),
5 Suppl 1 (2003), S160-3.
[abstract]
Abstract:
For several years Y-chromosomal microsatellites (short tandem repeats, STRs) have been well established in forensic practice. In this context, the genetic characteristics of the Y chromosome (i.e. its paternal inheritance and lack of recombination) render STRs particularly powerful. However, genetic differences between male populations appear to be larger for Y-STRs than for autosomal STRs, a fact that is most likely due to the higher sensitivity of Y-chromosomal lineages to genetic drift (Forensic Sci Int 118 (2001) 153). The assessment of probabilities for matches between haplotyped male persons or traces/persons requires the typing of a large number of haplotypes in the appropriate reference populations. The haplotype data of a large number of European as well as South and North American populations have been collected and are continuously published online (Y-STR Haplotype Reference Database--YHRD; http://www.ystr.org). The most recent multicentric effort has led to the establishment of an Asian YHRD (http://www.ystr.org/asia) which has been available since January 2002. All databases are maintained and curated at the Institute of Legal Medicine, Humboldt-University, Berlin and will soon be fused to a global repository including populations from all continents.
Bercovitch FB, Widdig A, Trefilov A, Kessler MJ, Berard JD, Schmidtke J, Nürnberg P, Krawczak M.
A longitudinal study of age-specific reproductive output and body condition among male rhesus macaques, Macaca mulatta.Naturwissenschaften,
90 (2003), 309-12.
[abstract]
Abstract:
In many mammalian species, male reproductive success appears to climb sharply at young adulthood, form a brief plateau during prime ages, and decline among older animals, a pattern often attributed to reduced physical condition with ageing. However, solid evidence to either substantiate or refute this profile among nonhuman primates is lacking. Here, we combine a decade of genetic analysis of paternity among free-ranging rhesus macaques, Macaca mulatta, with information about body condition in order to evaluate how changes in morphology might govern age-specific reproduction among males. We show that age-specific reproductive success traverses the same life history profile as found in other mammals, but reductions in reproductive output with advanced age were associated with reduced chances of survivorship rather than accompanied by diminished body condition. We demonstrate that variance in male age at onset of reproduction is three times greater than variance in female age at onset of reproduction. We provide the first evidence from primates that age-specific reproductive output among males is not a consequence of age-related changes in body condition, but reflects social and demographic factors.
Gusmão L, Krawczak M, Sánchez-Diz P, Alves C, Lopes A, Beleza S, Carracedo A, Amorim A.
Bimodal allele frequency distribution at Y-STR loci DYS392 and DYS438: no evidence for a deviation from the stepwise mutation model.Int J Legal Med,
117 (2003), 287-90.
[abstract]
Abstract:
A deviation from the stepwise mutation model (SMM) has been suggested for the trinucleotide Y-STR locus DYS392, based upon its bimodal allele frequency distribution in various populations. The same type of distribution is also observed for the pentanucleotide Y-STR DYS438. In order to verify whether a departure from an SMM is likely for these two loci, we studied a large number of Portuguese male DNA samples typed for the two loci and in addition, for the Y-STR loci DYS19, DYS389I/II, DYS390, DYS391 and DYS393. The compatibility of the observed allele frequency spectrum with an SMM was assessed by an apportionment of the molecular variance among, and consideration of the molecular distances between, haplotype groups defined according to their allelic state at each of the two markers of interest. For haplotypes carrying either modal alleles 11 or 13 of DYS392, 18.6% of the molecular variance of the remaining Y-STR background could be attributed to variation between the two groups. When all pairwise Phi(st) values between haplotype groups were compared, group 12 was found to be closer to 11 than to 13, and group 14 was much closer to 13 than to 12 and 11. It may therefore be concluded that DYS392 allele 13 represents an evolutionary lineage with little or no relationship to 11 and 12. Furthermore, allele 14 is a one-step neighbour of 13 and is therefore likely to represent an offshoot from group 13. For haplotypes carrying either modal allele 10 or modal allele 12 of DYS438, 27.7% of the molecular variance of the Y-STR background was found to be due to variation between the two groups. Comparison of the other pairwise Phi(st) values indicated that group 10 was closer to 9 and 11 than to 12, and that group 12 was closer to 11 and 13 than to 10. The lineages defined by the two modal alleles of DYS438 therefore also seem to be phylogenetically distant. When the two loci were analysed in combination, using the standardised linkage disequilibrium measure (D'), a strong association was noted between alleles DYS392*11 and DYS438*10 (D'=0.70) and between DYS392*13 and DYS438*12 (D'=0.72). Taken together, these results show that the bimodal allele frequency distributions of DYS392 and DYS438 are explicable in terms of (probably the same) historical and demographic causes, rather than a mutational mechanism other than SMM. The loci do therefore not appear to warrant any special attention when applied in population genetic or forensic studies.
Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN.
Human Gene Mutation Database (HGMD): 2003 update.Hum Mutat,
21 (2003), 577-81.
[abstract]
Abstract:
The Human Gene Mutation Database (HGMD) constitutes a comprehensive core collection of data on germ-line mutations in nuclear genes underlying or associated with human inherited disease (www.hgmd.org). Data catalogued includes: single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation is entered into HGMD only once in order to avoid confusion between recurrent and identical-by-descent lesions. By March 2003, the database contained in excess of 39,415 different lesions detected in 1,516 different nuclear genes, with new entries currently accumulating at a rate exceeding 5,000 per annum. Since its inception, HGMD has been expanded to include cDNA reference sequences for more than 87% of listed genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. Although HGMD has recently entered into a licensing agreement with Celera Genomics (Rockville, MD), mutation data will continue to be made freely available via the Internet.
Szibor R, Krawczak M, Hering S, Edelmann J, Kuhlisch E, Krause D.
Use of X-linked markers for forensic purposes.Int J Legal Med,
117 (2003), 67-74.
[abstract]
Abstract:
In forensic science, X-chromosomal short tandem repeats (ChrX STRs) bear the potential to efficiently complement the analysis of other genetic markers (autosomal, Y-chromosomal or mitochondrial). We review the population genetic properties and forensic utility of selected ChrX markers, and discuss the problems and limitations arising with their practical use. Formulae required to assess the evidential power of individual markers in different contexts are summarised and applied to ChrX STRs of interest. Since linkage and linkage disequilibrium between markers affect the inferential interpretation of genotype data, practically relevant information regarding the co-localisation and haplotypic association of ChrX STRs is provided. Finally, two examples of complex kinship testing are presented which serve to highlight the particular importance of ChrX STRs for solving deficiency cases and cases involving blood relatives.
Hampe J, Heymann K, Krawczak M, Schreiber S.
Association of inflammatory bowel disease with indicators for childhood antigen and infection exposure.Int J Colorectal Dis,
18 (2003), 413-7.
[abstract]
Abstract:
BACKGROUND AND AIMS: Genetic susceptibility plays an important role in the predisposition to inflammatory bowel disease (IBD), but genetics alone cannot explain the six- to eightfold rise in incidence accompanying postwar socioeconomic changes in developed countries. It is presently unclear how environmental factors either trigger or modify the risk for and course of IBD in the presence of genetic susceptibility. PATIENTS AND METHODS: We evaluated 2,351 consecutive responses from IBD patients and from 3,364 of their unaffected first-degree relatives (parents/siblings) who completed a multi-item questionnaire with their physicians as part of a study of IBD genetics. All single-patient families were excluded from the analysis to avoid ascertainment bias, resulting in 120-133 independent cases for the analysis of environmental factors and 1,685 patients to be included in the analysis of birth rank. RESULTS: No statistically significant association was observed between the presence of IBD and the availability of either (warm) tap water, water toilets, or central heating during childhood. However, higher birth rank (> or =3) was significantly associated with a lower risk of IBD (odds ratio 0.68). CONCLUSION: Lower birth rank as a possible indicator of increased childhood infection exposure was associated with a higher risk for IBD. Future studies need to address the interaction of known genetic variations (e.g., in the NOD2 gene) with environmental factors potentially mediating this effect.
Millar DS, Lewis MD, Horan M, Newsway V, Easter TE, Gregory JW, Fryklund L, Norin M, Crowne EC, Davies SJ, Edwards P, Kirk J, Waldron K, Smith PJ, Phillips JA, Scanlon MF, Krawczak M, Cooper DN, Procter AM.
Novel mutations of the growth hormone 1 (GH1) gene disclosed by modulation of the clinical selection criteria for individuals with short stature.Hum Mutat,
21 (2003), 424-40.
[abstract]
Abstract:
Subtle mutations in the growth hormone 1 (GH1) gene have been regarded as a comparatively rare cause of short stature. Such lesions were sought in a group of 41 individuals selected for short stature, reduced height velocity, and bone age delay; a group of 11 individuals with short stature and idiopathic growth hormone deficiency (IGHD); and a group of 154 controls. Heterozygous mutations were identified in all three groups but disproportionately in the individuals with short stature, both with (odds ratio 25.2; 95% CI, 5.1-132.2) and without (odds ratio 3.6; 95% CI, 1.0-12.9) IGHD. Twenty-four novel GH1 gene lesions were found. Thirteen novel missense mutations were characterized by assaying the signal transduction activity of in vitro expressed variants; six (T27I, K41R, N47D, S71F, S108R, and T175A) exhibited a reduced ability to activate the JAK/STAT pathway. Molecular modeling suggested that both K41R and T175A might compromise GH receptor binding. Seven GH variants (R16C, K41R, S71F, E74K, Q91L, S108C, and a functional polymorphism, V110I) manifested reduced secretion in rat pituitary cells after allowance had been made for the level of expression attributable to the associated GH1 proximal promoter haplotype. A further leader peptide variant (L-11P) was not secreted. Eleven novel mutations in the GH1 gene promoter were assessed by reporter gene assay but only two, including a GH2 gene-templated gene conversion, were found to be associated with a significantly reduced level of expression. Finally, a novel intron 2 acceptor splice-site mutation, detected in a family with autosomal dominant type II IGHD, was shown to lead to the skipping of exon 3 from the GH1 transcript. A total of 15 novel GH1 gene mutations were thus considered to be of probable phenotypic significance. Such lesions are more prevalent than previously recognized and although most may be insufficient on their own to account for the observed clinical phenotype, they are nevertheless likely to play a contributory role in the etiology of short stature.
Krawczak M, Zschocke J.
A role for overdominant selection in phenylketonuria? Evidence from molecular data.Hum Mutat,
21 (2003), 394-7.
[abstract]
Abstract:
To date, the reason is unknown for the high prevalence of phenylalanine hydroxylase (PAH) mutations causing phenylketonuria (PKU) in extant European populations. However, molecular genetic data generated over the last decade suggest that the concomitant excess of (unaffected) PKU carriers is at least in part the result of overdominant selection ("heterozygous advantage"). Such selection would have acted upon several different mutations in different historical populations. The exact nature of the underlying selective mechanism is unknown; its elucidation requires further investigation.
Turic D, Robinson L, Duke M, Morris DW, Webb V, Hamshere M, Milham C, Hopkin E, Pound K, Fernando S, Grierson A, Easton M, Williams N, Van Den Bree M, Chowdhury R, Gruen J, Stevenson J, Krawczak M, Owen MJ, Williams J.
Linkage disequilibrium mapping provides further evidence of a gene for reading disability on chromosome 6p21.3-22.Mol Psychiatry,
8 (2003), 176-85.
[abstract]
Abstract:
Linkage disequilibrium (LD) mapping was used to follow up reports of linkage between reading disability (RD) and an 18 cM region of chromosome 6p21.3-22. Using a two-stage approach, we tested for association between RD and 22 microsatellite markers in two independent samples of 101 (Stage 1) and 77 (Stage 2) parent/proband trios in which RD was rigorously defined. The most significant replicated associations were observed between combinations of markers D6S109/422/1665 (Stage 1, P=0.002 (adjusted for multiple testing); Stage 2, P=0.0001) and D6S506/1029/1660 (Stage 1, P=0.02 (adjusted), Stage 2, P=0.0001). The only two-marker association observed in both samples was with D6S422/1665 (P=0.01, 0.04). No single marker showed replicated association but D6S506 produced values of P=0.01 and 0.08 which were significant when combined (P=0.02). We observed weaker and less consistent evidence of association in a region of confirmed linkage to RD in previous studies. The most consistently significant haplotypic association D6S109/422/1665, showed association with single-word reading, spelling, phonological awareness, phonological decoding, orthographic accuracy and random automised naming, but not with vocabulary or Attention Deficit Hyperactivity Disorder. Our findings strongly support the presence of a gene contributing to RD in a region of chromosome 6 between markers D6S109 and D6S1260, but do not rule out the presence of a gene between D6S1556 and MOG.
Chuzhanova NA, Anassis EJ, Ball EV, Krawczak M, Cooper DN.
Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity.Hum Mutat,
21 (2003), 28-44.
[abstract]
Abstract:
A relatively rare type of mutation causing human genetic disease is the indel, a complex lesion that appears to represent a combination of micro-deletion and micro-insertion. In the absence of meta-analytical studies of indels, the mutational mechanisms underlying indel formation remain unclear. Data from the Human Gene Mutation Database (HGMD) were therefore used to compare and contrast 211 different indels underlying genetic disease in an attempt to deduce the processes responsible for their genesis. Each indel was treated as if it were the result of a two-step insertion/deletion process and was assessed in the context of 10 base-pairs DNA sequence flanking the lesion on either side. Several indel hotspots were noted and a GTAAGT motif was found to be significantly over-represented in the vicinity of the indels studied. Previously postulated mechanisms underlying micro-deletions and micro-insertions were initially explored in terms of local DNA sequence regularity as measured by its complexity. The change in complexity consequent to a mutation was found to be indicative of the type of repeat sequence involved in mediating the event, thereby providing clues as to the underlying mutational mechanism. Complexity analysis was then employed to examine the possible intermediates through which each indel could have occurred and to propose likely mechanisms and pathways for indel generation on an individual basis. Manual analysis served to confirm that the majority of indels (>90%) are explicable in terms of a two-step process involving established mutational mechanisms. Indels equivalent to double base-pair substitutions (22% of the total) were found to be mechanistically indistinguishable from the remainder and may therefore be regarded as a special type of indel. The observed correspondence between changes in local DNA sequence complexity and the involvement of specific mutational mechanisms in the insertion/deletion process, and the ability of generated models to account for both the number and identity of the bases deleted and/or inserted, makes this approach invaluable not only for the analysis of indel formation, but also for the study of other types of complex lesion.
Upadhyaya M, Majounie E, Thompson P, Han S, Consoli C, Krawczak M, Cordeiro I, Cooper DN.
Three different pathological lesions in the NF1 gene originating de novo in a family with neurofibromatosis type 1.Hum Genet,
112 (2003), 12-7.
[abstract]
Abstract:
Three members of a Portuguese family, who exhibited clinical evidence of neurofibromatosis type 1 (NF1), were found to possess different heritable and pathological mutations in their NF1 genes: a 1.5-Mb deletion spanning the entire NF1 gene, a truncating CGA-->TGA transition in exon 22 (R1241X), and a frameshift mutation in exon 29 (5406insT). All three lesions occurred de novo and are likely to have been generated by different mutational mechanisms. At least two of the mutations occurred on different chromosomal backgrounds. The probability of finding three non-identical NF1 gene lesions arising de novo in a family with NF1 is very remote, too low to be readily accepted as mere coincidence. A number of possible explanations for this unique finding were therefore explored, but none were found to be wholly convincing. This report nevertheless serves as a reminder that it is unwise, even in the case of an autosomal dominant condition, to extrapolate from the detection of a single mutation in a specific individual to assuming an identical molecular genetic aetiology in other clinically affected members of the same family.
Cooper DN, Horan M, Millar DS, Hedderich J, Lewis G, Newsway V, Mo N, Fryklund L, Procter AM, Krawczak M.
Human growth hormone I gene expression is influenced in a complex haplotype-dependent fashion by polymorphic variation in both the proximal promoter and the locus control region.J Pediatr Endocrinol Metab,
15 Suppl 5 (2002), 1429.
Wieland I, Jakubiczka S, Muschke P, Wolf A, Gerlach L, Krawczak M, Wieacker P.
Mapping of a further locus for X-linked craniofrontonasal syndrome.Cytogenet Genome Res,
99 (2002), 285-8.
[abstract]
Abstract:
Craniofrontonasal syndrome is a rare dysostosis syndrome with an unusual pattern of X-linked inheritance, because males are usually not or less severely affected than females. Previously, a CFNS locus has been localised in Xp22. We report on a haplotype analysis in a German CFNS family, mapping the CFNS locus to the pericentromeric region of the X chromosome. This discrepancy can be explained by locus heterogeneity. Furthermore, random X inactivation could be demonstrated in affected females. The most plausible interpretation for this unusual pattern of X-linked inheritance is metabolic interference. Consequently, we propose that the CFNS gene escapes X inactivation.
Williams NM, Spurlock G, Norton N, Williams HJ, Hamshere ML, Krawczak M, Kirov G, Nikolov I, Georgieva L, Jones S, Cardno AG, Owen MJ.
Mutation screening and LD mapping in the VCFS deleted region of chromosome 22q11 in schizophrenia using a novel DNA pooling approach.Mol Psychiatry,
7 (2002), 1092-100.
[abstract]
Abstract:
We examined whether variation within six genes from the VCFS critical region at 22q11 (DGSC, Stk22A1, DGSI, Gscl, Slc25A1 and Znf74) confers susceptibility to schizophrenia. We screened the exons and flanking intronic sequence of each gene for mutations in 14 individuals with DSM-IV schizophrenia using DHPLC. All polymorphisms identified were characterised and genotyped in a sample of 184 schizophrenics and matched controls, using novel DNA pooling methods. Of the polymorphisms identified, 17 were located within exons, six were within coding sequence, and two were non-synonymous. Pooled genotyping revealed no differences in the allele frequencies for any polymorphism between cases and controls that met our pre-defined criterion (P < or = 0.1). In a complementary approach we also attempted to define the location of a schizophrenia susceptibility locus more precisely by performing association mapping using seven microsatellites spanning the VCFS region with an average inter-marker distance of 450 kb. Conventional chi(2) analysis of genotypes in 368 cases and 368 controls revealed that none of the markers was significantly associated (P < 0.05) with schizophrenia. However, evidence for significant association (P = 0.003) was obtained for D22S944 when alleles were combined. TDT analysis of D22S944 genotyped in a further 278 cases of schizophrenia and their parents failed to find any overall allele-wise significant transmission disequilibrium (chi(2) = 18.3, P = 0.17). However, individual analysis of the alleles revealed that allele 12 was excessively non-transmitted and that this almost reached significance when corrected for multiple alleles (chi(2) = 7.35, P = 0.006, P = 0.078 corrected for 13 alleles).
McEntagart M, Parsons G, Buj-Bello A, Biancalana V, Fenton I, Little M, Krawczak M, Thomas N, Herman G, Clarke A, Wallgren-Pettersson C.
Genotype-phenotype correlations in X-linked myotubular myopathy.Neuromuscul Disord,
12 (2002), 939-46.
[abstract]
Abstract:
X-linked myotubular myopathy is a severe congenital myopathy that presents in the neonatal period with profound hypotonia and an inability to establish spontaneous respiration. Usually death occurs in infancy from respiratory failure. However, there is phenotypic variability; a number of affected boys have achieved respiratory independence and become ambulatory. Disease-causing mutations have been identified throughout the MTM1 gene on Xq28. MTM1 encodes the protein myotubularin, which is expressed ubiquitously. The main objectives of this study were to establish whether the nature or site of the mutation in the MTM1 gene could predict severity of the disease and to investigate whether early intensive clinical intervention facilitated survival until spontaneous improvement occurred. An association was demonstrated between the presence of a non-truncating mutation of the MTM1 gene and the mild phenotype. However, many non-truncating mutations were also seen in association with the severe phenotype and these were not confined to recognized functional domains of the protein. This suggests that the use of mutation analysis to predict prognosis in the early period following diagnosis is limited. Unexpectedly, over 50 patients surviving for more than 1 year were identified in this study. Further information obtained on 40 of these cases revealed that 50% were receiving 24-h ventilatory support, while 27% were ventilated at night only. The high survival rate for this disorder therefore reflects intensive medical intervention without which the majority of these boys would not survive.
Mühl T, Krawczak M, Ten Haaft P, Hunsmann G, Sauermann U.
MHC class I alleles influence set-point viral load and survival time in simian immunodeficiency virus-infected rhesus monkeys.J Immunol,
169 (2002), 3438-46.
[abstract]
Abstract:
In HIV-infected humans and SIV-infected rhesus macaques, host genes influence viral containment and hence the duration of the disease-free latency period. Our knowledge of the rhesus monkey immunogenetics, however, is limited. In this study, we describe partial cDNA sequences of five newly discovered rhesus macaque (Mamu) class I alleles and PCR-based typing techniques for the novel and previously published Mhc class I alleles. Using 15 primer pairs for PCR-based typing and DNA sequence analysis, we identified at least 21 Mhc class I alleles in a cohort of 91 SIV-infected macaques. The results confirm the presence of multiple class I genes in rhesus macaques. Of these alleles, Mamu-A*01 was significantly associated with lower set-point viral load and prolonged survival time. Mamu-A*1303 was associated with longer survival and a "novel" Mhc class I allele with lower set-point viral load. The alleles are frequent in rhesus macaques of Indian origin (12-22%). In addition, survival probability of individual SIV-infected rhesus monkeys increased with their number of alleles considered to be associated with longer survival. The results contribute to improve the interpretation and quality of preclinical studies in rhesus monkeys.
Terp BN, Cooper DN, Christensen IT, Jørgensen FS, Bross P, Gregersen N, Krawczak M.
Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease.Hum Mutat,
20 (2002), 98-109.
[abstract]
Abstract:
The inclusion of a mutation in a pathology-based database such as the Human Gene Mutation Database (HGMD) is a two-stage process: first, the mutation must occur at the DNA level, then it must cause a clinically detectable disease state. The likelihood of the latter step, termed the relative clinical observation likelihood (RCOL), can be regarded as a function of the structural/functional consequences of a mutation at the protein level. Following this paradigm, we modeled in silico all amino acid replacements that could potentially have arisen from an inherited single base pair substitution in five human genes encoding arylsulphatase A (ARSA), antithrombin III (SERPINC1), protein C (PROC), phenylalanine hydroxylase (PAH), and transthyretin (TTR). These proteins were chosen on the basis of 1) the availability of a crystallographic structure, and 2) a sufficiently large number of amino acid replacements being logged in HGMD. A total of 9,795 possible mutant structures were modeled and 20 different biophysical parameters assessed. Together with the HGMD-derived spectra of clinically detected mutations, these data allowed maximum likelihood estimation of RCOL profiles for the 20 parameters studied. Nine parameters (including energy difference between wild-type and mutant structures, accessibility of the mutated residue, and distance from the binding/active site) exhibited statistically significant variability in their RCOL profiles, indicating that mutation-associated changes affected protein function. As yet, however, a biological meaning could only be attributed to the RCOL profiles of solvent accessibility and, for three proteins, local energy change, disturbed geometry, and distance from the active center. The limited ability of the biophysical properties of mutations to explain clinical consequences is probably due to our current lack of understanding as to which amino acid residues are critical for protein folding. However, since the proteins examined here were unrelated, and our findings consistent, it may nevertheless prove possible to extrapolate to other proteins whose dysfunction underlies inherited disease.
Norton N, Kirov G, Zammit S, Jones G, Jones S, Owen R, Krawczak M, Williams NM, Owen MJ.
Schizophrenia and functional polymorphisms in the MAOA and COMT genes: no evidence for association or epistasis.Am J Med Genet,
114 (2002), 491-6.
[abstract]
Abstract:
Several lines of evidence suggest that psychosis is associated with altered dopaminergic neurotransmission. Dopamine is catabolized by monoamine oxidase (MAO) and catechol-O-methyl transferase (COMT). We hypothesized that the genes encoding MAOA and COMT might contain genetic variation conferring increased risk to schizophrenia. In order to test this hypothesis, we genotyped the 941T > G and the promoter VNTR polymorphisms in the MAOA gene and the V158M COMT polymorphism in 346 DSMIV schizophrenics and 334 controls. We also genotyped the-287A > G COMT promoter polymorphism in 177 schizophrenics and 173 controls. No significant differences were found in allele or genotype frequencies between affecteds and controls for any of the polymorphisms. As both genes are involved in degrading catecholamines, we also sought evidence for additive and epistatic effects but none was observed. Our data, therefore, do not support the hypothesis that genetic variation in MAOA and COMT is involved individually or in combination in the etiology of schizophrenia.
Mascheretti S, Hampe J, Kühbacher T, Herfarth H, Krawczak M, Fölsch UR, Schreiber S.
Pharmacogenetic investigation of the TNF/TNF-receptor system in patients with chronic active Crohn's disease treated with infliximab.Pharmacogenomics J,
2 (2002), 127-36.
[abstract]
Abstract:
Infliximab (anti-TNF-alpha monoclonal antibody) induces remission in 30-40% of Crohn's disease patients. Treatment response is a stable trait. Two cohorts from independent, prospective clinical trials of infliximab in Crohn's disease were studied. Hypotheses were generated in an exploratory cohort (n = 90) and then tested in a confirmatory cohort (n = 444), using a statistical design, which is stable against type 1 and type 2 errors. In the exploratory cohort, the mutant 196Arg allele of TNFR-II (exon 6 polymorphism) and a novel silent polymorphism in exon 2 of TNFR-II were associated with lack of response to infliximab (83.3% in homozygote mutant 196 Arg patients vs 36.9% in heterozygotes and wild-type homozygotes (P = 0.036) and 85.7% in homozygote mutant exon 2 patients vs 36.1% (P = 0.01), respectively). None of the homozygote mutant individuals (0/6) achieved clinical remission, whereas the remission rate was 35.7% (30/84) in wild-type homozygotes and heterozygotes. In the large second cohort, the observed genotype-phenotype associations were not replicated. Other polymorphisms (TNF-alpha promoter -238, -308, -376, -857, -1031, TNF-R-I -609, +36 (exon 1), TNF-R-II 1663, 1690 (3'-UTR)) were not associated with treatment response in both cohorts (P > 0.5). None of the polymorphisms was associated with refractory Crohn's disease itself when compared to healthy controls. In a two-cohort study, a series of polymorphisms in the TNF, the TNF-R-I and in the TNF-R-II genes could be thoroughly excluded as pharmacogenetic markers for a treatment response to infliximab and as etiologic factors for Crohn's disease, respectively. The discrepancy between the two cohorts observed for the TNF-R-II exon 6 and exon 2 polymorphism may point to a weak effect on treatment response but also serves to illustrate the need for a sequential exploratory/confirmatory design in pharmacogenetic studies.
Hampe J, Grebe J, Nikolaus S, Solberg C, Croucher PJ, Mascheretti S, Jahnsen J, Moum B, Klump B, Krawczak M, Mirza MM, Foelsch UR, Vatn M, Schreiber S.
Association of NOD2 (CARD 15) genotype with clinical course of Crohn's disease: a cohort study.Lancet,
359 (2002), 1661-5.
[abstract]
Abstract:
BACKGROUND: Crohn's disease is a heterogeneous disorder for which NOD2 (CARD 15) has been identified as a susceptibility gene. We investigate the relation between NOD2 genotype and phenotypic characteristics of patients with Crohn's disease. METHODS: Hypotheses about the relation between NOD2 genotype and Crohn's disease phenotype were generated retrospectively from a group of 446 German patients with this disorder. Positive findings (p<0.10) were verified in prospectively established cohorts of 106 German and 55 Norwegian patients with Crohn's disease. All patients were genotyped for the main coding mutations in NOD2, denoted SNP8, SNP12, and SNP13, with Taqman technology. FINDINGS: In the retrospective cohort, six clinical characteristics showed noteworthy haplotype association: fistulising, ileal, left colonic and right colonic disease, stenosis, and resection. In the German prospective cohort, these haplotype associations could be replicated for ileal (p=0.006) and right colonic disease (p < or =0.001). A similar trend was noted in the Norwegian patients. INTERPRETATION: We recorded a distinct relation between NOD2 genotype and phenotype of Crohn's disease. Test strategies with NOD2 variations to predict the clinical course of Crohn's disease could lead to the development of new therapeutic paradigms.
Bercovitch FB, Widdig A, Berard JD, Nürnberg P, Kessler MJ, Schmidtke J, Trefilov A, Krawczak M.
Multiple sirehood in free-ranging twin rhesus macaques (Macaca mulatta).Am J Primatol,
57 (2002), 31-4.
[abstract]
Abstract:
Rhesus macaque females regularly copulate with a number of partners, and produce a single offspring per reproductive cycle in over 99% of cases. We used genotyping of 10 STR markers to determine paternity in the Cayo Santiago population of rhesus macaques. About 1,500 monkeys have been analyzed to date, with their marker genotypes entered into a computerized database. These data enable us to report the first documented case in any cercopithecine nonhuman primate species of the production of twin offspring sired by different males.
Cooper DN, Nussbaum RL, Krawczak M.
Proposed guidelines for papers describing DNA polymorphism-disease associations.Hum Genet,
110 (2002), 207-8.
[abstract]
Abstract:
Studies reporting DNA polymorphism-disease associations represent an important source of information on disease gene candidacy. Such studies are, however, extremely variable in terms of their design and of the statistical methodology employed. Guidelines are therefore proposed that are intended to promote the publication of scientifically meaningful disease association studies through the introduction of sensible methodological standards.
Chuzhanova NA, Krawczak M, Thomas N, Nemytikova LA, Gusev VD, Cooper DN.
The evolution of the vertebrate beta-globin gene promoter.Evolution Int J Org Evolution,
56 (2002), 224-32.
[abstract]
Abstract:
Complexity analysis is capable of highlighting those gross evolutionary changes in gene promoter regions (loosely termed "promoter shuffling") that are undetectable by conventional DNA sequence alignment. Complexity analysis was therefore used here to identify the modular components (blocks) of the orthologous beta-globin gene promoter sequences of 22 vertebrate species, from zebrafish to humans. Considerable variation between the beta-globin gene promoters was apparent in terms of block presence/absence, copy number, and relative location. Some sequence blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Block similarities were also evident between the promoters of the paralogous human beta-like globin genes. It may be inferred that a wide variety of different mutational mechanisms have operated upon the beta-globin gene promoter over evolutionary time. Because these include gross changes such as deletion, duplication, amplification, elongation, contraction, and fusion, as well as the steady accumulation of single base-pair substitutions, it is clear that some redefinition of the term "promoter shuffling" is required. This notwithstanding, and as previously described for the vertebrate growth hormone gene promoter, the modular structure of the beta-globin promoter region and those of its paralogous counterparts have continually been rearranged into new combinations through the alteration, or shuffling, of preexisting blocks. Some of these changes may have had no influence on promoter function, but others could have altered either the level of gene expression or the responsiveness of the promoter to external stimuli. The comparative study of vertebrate beta-globin gene promoter regions described here confirms the generality of the phenomenon of sequence block shuffling and thus supports the view that it could have played an important role in the evolution of differential gene expression.
Cheadle JP, Krawczak M, Thomas MW, Hodges AK, Al-Tassan N, Fleming N, Sampson JR.
Different combinations of biallelic APC mutation confer different growth advantages in colorectal tumours.Cancer Res,
62 (2002), 363-6.
[abstract]
Abstract:
New facets to Knudson's [corrected] "two-hit" hypothesis have been proposed recently in relation to adenomatous polyposis coli (APC): protein inactivation may be selected weakly, and the two hits may be interdependent. We reviewed published data on 165 sporadic and 102 familial adenomatous polyposis-associated colorectal tumors with two characterized mutations. Using a Poisson model, we redefined the mutation cluster region (MCR) to residues 1281-1556 and confirmed that the locations of pairs of APC mutations are interdependent (P < 0.0001). A mathematical model, based on the data for sporadic tumors, implied different growth advantages for different combinations of APC mutations: genotype I/I (I: mutation inside MCR) was 3.9 times more likely to be selected than IO or IL (O: mutation outside MCR, L: allelic loss), which were 27.8 times more likely to be selected than OO or OL.
Hampe J, Frenzel H, Mirza MM, Croucher PJ, Cuthbert A, Mascheretti S, Huse K, Platzer M, Bridger S, Meyer B, Nürnberg P, Stokkers P, Krawczak M, Mathew CG, Curran M, Schreiber S.
Evidence for a NOD2-independent susceptibility locus for inflammatory bowel disease on chromosome 16p.Proc Natl Acad Sci U S A,
99 (2002), 321-6.
[abstract]
Abstract:
Heritable predisposition to inflammatory bowel disease (IBD) has been demonstrated by epidemiological and genetic analysis. Linkage of IBD to broad regions of chromosome 16 has been established by analysis of multiple populations. NOD2, located on proximal 16q, was recently identified as an IBD gene. As the linkage regions on chromosome 16 are large, we have investigated the possibility that NOD2 is not the only IBD gene located on this chromosome. A high-density experiment using 39 microsatellite markers was performed to identify additional regions of association, and to indicate areas of interest for further investigation. A triple-peaked configuration of the linkage curve with peak logarithm of odds (lod) scores of 2.7, 3.2, and 3.1 was observed on proximal 16p, proximal 16q, and central 16q, respectively. The cohort was stratified by coding individuals carrying the NOD2 single nucleotide polymorphism (SNP)8 and SNP13 "unknown." Significance at the central peak, corresponding to the genomic location of NOD2, then decreased from 3.2 to 1.2. The maximal lod scores on the proximal p-arm (lod = 2.1) and central q-arm (lod = 2.6) changed only moderately. An exploratory association analysis (TRANSMIT) yielded a strong lead at D16S3068 (P = 0.00028). The region around this marker was further investigated by using anonymous SNPs. An associated haplotype containing three SNPs was identified (peak significance P = 0.00027, IBD phenotype). On stratification based on NOD2 genotype, this significance increased to P = 0.0001. These results confirm the importance of NOD2 and provide evidence for a second IBD gene located on chromosome 16p.
Al-Jader LN, Harper PS, Krawczak M, Palmer SR.
The frequency of inherited disorders database: prevalence of Huntington disease.Community Genet,
4 (2001), 148-57.
[abstract]
Abstract:
A database of the frequency of human inherited disorders is being established for use in a clinical context, in medical research, for epidemiological studies, and in the planning of genetic services. Each entry includes the disease name categorized by organ system, an Online Mendelian Inheritance in Man (OMIM) number, the mode of inheritance, the population origin, a prevalence and/or incidence rate and a literature reference. The Frequency of Inherited Disorders Database (FIDD) currently contains 1,580 entries relating to 280 different Mendelian disorders. FIDD will be prospectively maintained and can be accessed at http://www.uwcm.ac.uk/uwcm/mg/fidd/. A more refined and systematic literature search that will serve to expand the size, scope and scale of the database is currently in progress. The coverage of neurological and neuromuscular disorders is however considered to be nearly complete. In this first description of FIDD, Huntington disease was used to illustrate the structure and scope of the database as well as its potential scientific utility. A total of 100 published articles on the prevalence of Huntington disease were appraised. Prevalence and incidence rates varied between different ethnic groups and between different countries. Possible reasons for this variation are discussed.
Krawczak M.
ASP--a simulation-based power calculator for genetic linkage studies of qualitative traits, using sib-pairs.Hum Genet,
109 (2001), 675-7.
[abstract]
Abstract:
An easy-to-use, simulation-based power calculator (ASP) for linkage analysis using sib-pair designs (concordant or discordant) has been developed and made publicly available via the Internet. The program employs a diallelic model for the trait locus, at which parental/offspring genotypes are simulated, assuming Hardy-Weinberg equilibrium in the parental generation. Genotypes at a linked multiallelic marker locus are simulated conditional upon the inheritance pattern at the trait locus, allowing for recombination. Marker genotypes are tested for non-Mendelian identity-by-descent sharing, using both an unrestricted and a restricted likelihood ratio test, the latter representing an extension of the "mean test" from fully to partially informative families. The power of user-defined datasets is estimated by the number of simulations giving significant results at varying type I error levels.
Gill P, Brenner C, Brinkmann B, Budowle B, Carracedo A, Jobling MA, de Knijff P, Kayser M, Krawczak M, Mayr WR, Morling N, Olaisen B, Pascali V, Prinz M, Roewer L, Schneider PM, Sajantila A, Tyler-Smith C.
DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs.Forensic Sci Int,
124 (2001), 5-10.
[abstract]
Abstract:
During the past few years, the DNA Commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area - namely, Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods.
Widdig A, Nürnberg P, Krawczak M, Streich WJ, Bercovitch FB.
Paternal relatedness and age proximity regulate social relationships among adult female rhesus macaques.Proc Natl Acad Sci U S A,
98 (2001), 13769-73.
[abstract]
Abstract:
Kin selection promotes the evolution of social behavior that increases the survival and reproductive success of close relatives. Among primates, maternal kinship frequently coincides with a higher frequency of grooming and agonistic aiding, but the extent to which paternal kinship influences adult female social relationships has not yet been investigated. Here, we examine the effect of both maternal and paternal kinship, as well as age proximity, on affiliative interactions among semifree-ranging adult female rhesus macaques, Macaca mulatta. Kinship was assessed by using both microsatellites and DNA-fingerprinting. Our study confirms that the closest affiliative relationships characterize maternal half-sisters. We provide evidence that adult females are significantly more affiliative with paternal half-sisters than with nonkin. Furthermore, paternal kin discrimination was more pronounced among peers than among nonpeers, indicating that age proximity has an additional regulatory effect on affiliative interactions. We propose that kin discrimination among cercopithecine primates emerges from ontogenetic processes that involve phenotype matching based on shared behavioral traits, such as inherited personality profiles, rather than physiological or physical characteristics.
Gill P, Brenner C, Brinkmann B, Budowle B, Carracedo A, Jobling MA, de Knijff P, Kayser M, Krawczak M, Mayr WR, Morling N, Olaisen B, Pascali V, Prinz M, Roewer L, Schneider PM, Sajantila A, Tyler-Smith C.
DNA commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs.Int J Legal Med,
114 (2001), 305-9.
[abstract]
Abstract:
During the past few years the DNA commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area, namely Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods.
Krawczak M, Cooper DN, Schmidtke J.
Estimating the efficacy and efficiency of cascade genetic screening.Am J Hum Genet,
69 (2001), 361-70.
[abstract]
Abstract:
Screening for genetic variants that predispose individuals or their offspring to disease may be performed at the general population level or may instead be targeted at the relatives of previously identified carriers. The latter strategy has come to be known as "cascade genetic screening." Since the carrier risk of close relatives of known carriers is generally higher than the population risk, cascade screening is more efficient than population screening, in the sense that fewer individuals have to be genotyped per detected carrier. The efficacy of cascade screening, as measured by the overall proportion of carriers detected in a given population, is, however, lower than that of population-wide screening, and the respective inclusion rates vary according to the population frequency and mode of inheritance of the predisposing variants. For dominant mutations, we have developed equations that allow the inclusion rates of cascade screening to be calculated in an iterative fashion, depending upon screening depth and penetrance. For recessive mutations, we derived only equations for the screening of siblings and the children of patients. Owing to their mathematical complexity, it was necessary to study more extended screening strategies by simulation. Cascade screening turned out to result in low inclusion rates (<1%) when aimed at the identification of heterozygous carriers of rare recessive variants. Considerably higher rates are achievable, however, when screening is performed to detect covert homozygotes for frequent recessive mutations with reduced penetrance. This situation is exemplified by hereditary hemochromatosis, for which up to 40% of at-risk individuals may be identifiable through screening of first- to third-degree relatives of overt carriers (i.e., patients); the efficiency of this screening strategy was found to be approximately 50 times higher than that of population-wide screening. For dominant mutations, inclusion rates of cascade screening were estimated to be higher than for recessive variants. Thus, some 80% of all carriers of the factor V Leiden mutation would be detected if screening were to be targeted specifically at first- to third-degree relatives of patients with venous thrombosis. The relative cost efficiency of cascade as compared with population-wide screening (i.e., the overall savings in the extra managerial cost of the condition) is also likely to be higher for dominant than for recessive mutations. This notwithstanding, once screening has become cost-effective at the population level, it can be expected that cascade screening would only transiently represent an economically viable option.
Hampe J, Cuthbert A, Croucher PJ, Mirza MM, Mascheretti S, Fisher S, Frenzel H, King K, Hasselmeyer A, MacPherson AJ, Bridger S, van Deventer S, Forbes A, Nikolaus S, Lennard-Jones JE, Foelsch UR, Krawczak M, Lewis C, Schreiber S, Mathew CG.
Association between insertion mutation in NOD2 gene and Crohn's disease in German and British populations.Lancet,
357 (2001), 1925-8.
[abstract]
Abstract:
Background Genetic predisposition to inflammatory bowel disease (IBD) has been shown by epidemiological and linkage studies. Genetic linkage of IBD to chromosome 16 has been previously observed and replicated in independent populations. The recently identified NOD2 gene is a good positional and functional candidate gene since it is located in the region of linkage on chromosome 16q12, and activates nuclear factor (NF) kappaB in response to bacterial lipopolysaccharides.Methods We sequenced the coding region of the NOD2 gene and genotyped an insertion polymorphism affecting the leucine-rich region of the protein product in 512 individuals with IBD from 309 German or British families, 369 German trios (ie, German patients with sporadic IBD and their unaffected parents), and 272 normal controls. We then tested for association with Crohn's disease and ulcerative colitis.Findings Family-based association analyses were consistently positive in 95 British and 99 German affected sibling pairs with Crohn's disease (combined p<0.0001); the association was confirmed in the 304 German trios with Crohn's disease. No association was seen in the 115 sibling pairs and 65 trios with ulcerative colitis. The genotype-specific disease risks conferred by heterozygous and homozygous mutant genotypes were 2.6 (95% CI 1.5-4.5) and 42.1 (4.3-infinity), respectively.Interpretation The insertion mutation in the NOD2 gene confers a substantially increased susceptibility to Crohn's disease but not to ulcerative colitis.
Sauermann U, Nürnberg P, Bercovitch FB, Berard JD, Trefilov A, Widdig A, Kessler M, Schmidtke J, Krawczak M.
Increased reproductive success of MHC class II heterozygous males among free-ranging rhesus macaques.Hum Genet,
108 (2001), 249-54.
[abstract]
Abstract:
Gene conversion and balancing selection have been invoked to explain the ubiquitous diversity of the antigen-presenting proteins encoded in the vertebrate major histocompatibility complex (MHC). In the present study, direct evidence for over-dominant selection promoting MHC diversity in primates is provided by the observation that, in a large free-ranging population of rhesus macaques, males heterozygous at MHC class II locus Mamu-DQB1 sired significantly more offspring than homozygotes (the male-specific selection coefficient s equals 0.34). This heterozygote advantage appeared to be independent of the actual male Mamu-DQB1 genotype. No similar effect emerged for a captive group of monkeys of similar genetic background but under veterinary care.
Lessig R, Edelmann J, Krawczak M.
Population genetics of Y-chromosomal microsatellites in Baltic males.Forensic Sci Int,
118 (2001), 153-7.
[abstract]
Abstract:
Y-chromosomal microsatellites (STRs) are potentially useful in forensic practice but, in contrast to autosomal systems, large and diverse population databases are required in order to facilitate the statistical evaluation of donor-stain matches. Since appropriate data from the Baltic region have so far been lacking, blood samples were obtained from 430 males originating from one of the three Baltic states and these samples were genotyped using a previously described "extended core set" of nine Y-STR marker systems. Allele frequency distributions and discrimination indices were calculated, and the three populations were tested for genetic differences by means of analysis of molecular variance (AMOVA). A larger genetic difference became apparent between Estonian and both Lithuanian and Latvian males than between the latter two, non-Finno-Ugric speaking populations. The haplotype data reported here have been included into the Y-STR database maintained at the Institute of Legal Medicine, Humboldt University, Berlin.
Krawczak M.
Forensic evaluation of Y-STR haplotype matches: a comment.Forensic Sci Int,
118 (2001), 114-5.
Roewer L, Krawczak M, Willuweit S, Nagy M, Alves C, Amorim A, Anslinger K, Augustin C, Betz A, Bosch E, Cagliá A, Carracedo A, Corach D, Dekairelle AF, Dobosz T, Dupuy BM, Füredi S, Gehrig C, Gusmaõ L, Henke J, Henke L, Hidding M, Hohoff C, Hoste B, Jobling MA, Kärgel HJ, de Knijff P, Lessig R, Liebeherr E, Lorente M, Martínez-Jarreta B, Nievas P, Nowak M, Parson W, Pascali VL, Penacino G, Ploski R, Rolf B, Sala A, Schmidt U, Schmitt C, Schneider PM, Szibor R, Teifel-Greding J, Kayser M.
Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.Forensic Sci Int,
118 (2001), 106-13.
[abstract]
Abstract:
The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.
Kayser M, Krawczak M, Excoffier L, Dieltjes P, Corach D, Pascali V, Gehrig C, Bernini LF, Jespersen J, Bakker E, Roewer L, de Knijff P.
An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations.Am J Hum Genet,
68 (2001), 990-1018.
[abstract]
Abstract:
The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were.86-.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, phi(ST) statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure.
Al-Jader LN, Harper PS, Krawczak M, Palmer SR, Johansen BN, Cooper DN.
The Frequency of Inherited Disorders Database.Hum Genet,
108 (2001), 72-4.
Winter H, Langbein L, Krawczak M, Cooper DN, Jave-Suarez LF, Rogers MA, Praetzel S, Heidt PJ, Schweizer J.
Human type I hair keratin pseudogene phihHaA has functional orthologs in the chimpanzee and gorilla: evidence for recent inactivation of the human gene after the Pan-Homo divergence.Hum Genet,
108 (2001), 37-42.
[abstract]
Abstract:
In addition to nine functional genes, the human type I hair keratin gene cluster contains a pseudogene, phihHaA (KRTHAP1), which is thought to have been inactivated by a single base-pair substitution that introduced a premature TGA termination codon into exon 4. Large-scale genotyping of human, chimpanzee, and gorilla DNAs revealed the homozygous presence of the phihHaA nonsense mutation in humans of different ethnic backgrounds, but its absence in the functional orthologous chimpanzee (cHaA) and gorilla (gHaA) genes. Expression analyses of the encoded cHaA and gHaA hair keratins served to highlight dramatic differences between the hair keratin phenotypes of contemporary humans and the great apes. The relative numbers of synonymous and non-synonymous substitutions in the phihHaA and cHaA genes, as inferred by using the gHaA gene as an outgroup, suggest that the human hHaA gene was inactivated only recently, viz., less than 240,000 years ago. This implies that the hair keratin phenotype of hominids prior to this date, and after the Pan-Homo divergence some 5.5 million years ago, could have been identical to that of the great apes. In addition, the homozygous presence of the phihHaA exon 4 nonsense mutation in some of the earliest branching lineages among extant human populations lends strong support to the "single African origin" hypothesis of modern humans.
Martín MA, Rubio JC, García A, Fernández MA, Campos Y, Krawczak M, Cooper DN, Arenas J.
Resolution of a mispaired secondary structure intermediate could account for a novel micro-insertion/deletion (387 insA/del 8 bp) in the PYGM gene causing McArdle's disease.Clin Genet,
59 (2001), 48-51.
[abstract]
Abstract:
We report two siblings with McArdle's disease who are both compound heterozygotes for two non-identical frameshift mutations in the PYGM gene; a previously reported 753 delA in exon 18 and a novel 387 insA/del 8 bp in exon 10. The novel mutation is predicted to result in premature termination of translation 33 amino acids downstream of the site of mutation, potentially encoding a severely truncated protein of 419 amino acids instead of 841 amino acids. The complete lack of myophosphorylase activity observed in muscle derived from one sibling suggests that this mutation has deleterious functional consequences. The underlying mechanism of mutagenesis may have been slipped mispairing mediated by the formation of a Moebius loop-like secondary intermediate.
Antonarakis SE, Krawczak M, Cooper DN.
Disease-causing mutations in the human genome.Eur J Pediatr,
159 Suppl 3 (2000), S173-8.
[abstract]
Abstract:
A considerable number of gene mutations has now been reported in a total of more than 1000 different human genes. Data on these mutations and their associated phenotypes have been collated and are available online through two major databases: Online Mendelian Inheritance in Man in Baltimore and the Human Gene Mutation Database in Cardiff. Since the non-randomness of mutation is determined largely by the local DNA sequence environment, the study of mutation may not only yield information on underlying mechanisms but also lead to the optimization of mutation search strategies. CONCLUSION: There is a high frequency of CG to TG or CA mutations in the human genome due to deamination of 5' methyl-cytosine. The second most common type of mutations in human disorders is short deletions or insertions of less than 20 nucleotides.
Trefilov A, Berard J, Krawczak M, Schmidtke J.
Natal dispersal in rhesus macaques is related to serotonin transporter gene promoter variation.Behav Genet,
30 (2000), 295-301.
[abstract]
Abstract:
A VNTR polymorphism previously characterized in the promoter region of the human serotonin transporter (SLC6A4) gene was also found to segregate two major alleles (l and s) among the free-ranging rhesus macaques of Cayo Santiago, Puerto Rico. When VNTR genotypes were related to age at male natal dispersal on Cayo Santiago, ss homozygotes (43 of 532 males tested) were found to have left their natal groups significantly earlier (age 57.1 +/- 2.6 months) than carriers of the l allele (ll age, 71.5 +/- 2.1 months; ls age, 63.5 +/- 1.5 months; P = 0.0001). Since migration implies reproductive costs and benefits that change with age at dispersal, migration at an intermediate age might have conferred a heterozygote advantage serving to maintain the VNTR polymorphism via overdominant selection.
Schubert S, Dechend F, Skawran B, Krawczak M, Schmidtke J.
Molecular evolution of the murine tspy genes.Cytogenet Cell Genet,
91 (2000), 239-42.
[abstract]
Abstract:
Molecular aspects of murine evolution were studied by sequencing, and subsequently comparing, introns of the Y-chromosomal tspy genes from Apodemus agrarius, A. sylvaticus, A. flavicollis, Mus platythrix (subgenus Pyromys), M. booduga (subgenus Leggada), and from species of the subgenus Mus, including M. cervicolor, M. macedonicus and M. spretus. Estimates of nucleotide substitution rates in these lineages were in perfect agreement with phylogenetic data previously published by She et al. (1990), Catzeflis et al. (1992; 1993), and Lyon et al. (1996). The only exception was provided by a comparatively late divergence of M. spretus and M. macedonicus. Our data also suggest that M. booduga diverged from the subgenus Mus about 3 Myr ago.
Dechend F, Williams G, Skawran B, Schubert S, Krawczak M, Tyler-Smith C, Schmidtke J.
TSPY variants in six loci on the human Y chromosome.Cytogenet Cell Genet,
91 (2000), 67-71.
[abstract]
Abstract:
We have studied the structure, organization, and evolution of the human TSPY gene family by mapping three sequence variants identified through RT-PCR analysis onto genomic clones derived from two different YAC contigs. TSPY gene family members occur in at least six locations on the human Y chromosome, and each cluster contains a unique combination of variants. Our data further suggest that an 18-bp tandem duplication found in TSPY exon 1 originated from an unequal sister chromatid exchange between two tandemly arranged TSPY clusters.
Krawczak M, Chuzhanova NA, Stenson PD, Johansen BN, Ball EV, Cooper DN.
Changes in primary DNA sequence complexity influence the phenotypic consequences of mutations in human gene regulatory regions.Hum Genet,
107 (2000), 362-5.
[abstract]
Abstract:
No general rules have been proposed to account for the functional consequences of gene regulatory mutations. In a first attempt to establish the nature of such rules, an analysis was performed of the DNA sequence context of 153 different single base-pair substitutions in the regulatory regions of 65 different human genes underlying inherited disease. Use of a recently proposed measure of DNA sequence complexity (taking into account the level of structural repetitiveness of a DNA sequence, rather than simply the oligonucleotide composition) has served to demonstrate that the concomitant change in local DNA sequence complexity surrounding a substituted nucleotide is related to the likelihood of a regulatory mutation coming to clinical attention. Mutations that led to an increase in complexity exhibited higher odds ratios in favour of pathological consequences than mutations that led to a decrease or left complexity unchanged. This relationship, however, was discernible only for pyrimidine-to-purine transversions. Odds ratios for other types of substitution were not found to be significantly associated with local changes in sequence complexity, even though a trend similar to that observed for Y-->R transversions was also apparent for transitions. These findings suggest that the maintenance of a defined level of DNA sequence complexity, or at least the avoidance of an increase in sequence complexity, is a critical prerequisite for the function of gene regulatory regions.
Millar DS, Kemball-Cook G, McVey JH, Tuddenham EG, Mumford AD, Attock GB, Reverter JC, Lanir N, Parapia LA, Reynaud J, Meili E, von Felton A, Martinowitz U, Prangnell DR, Krawczak M, Cooper DN.
Molecular analysis of the genotype-phenotype relationship in factor VII deficiency.Hum Genet,
107 (2000), 327-42.
[abstract]
Abstract:
Factor VII (FVII) deficiency is a rare haemorrhagic condition, normally inherited as an autosomal recessive trait, in which clinical presentation is highly variable and correlates poorly with laboratory phenotype. The FVII (F7) gene was sequenced in 48 unrelated individuals with FVII deficiency, yielding a total of 23 novel lesions including 15 missense mutations, 2 micro-deletions, 5 splice junction mutations and a single base-pair substitution in the 5' untranslated region. Family studies were performed in order to distinguish the contributions of individual mutant F7 alleles to the clinical and laboratory phenotypes. Specific missense mutations were evaluated by molecular modelling in the context of the FVIIa-tissue factor crystal structure. Single base-pair substitutions in splice sites and the 5' untranslated region were studied by in vitro splicing assay and luciferase reporter gene assay, respectively. All probands were also typed for four previously reported F7 polymorphisms. In the majority of cases of FVII deficiency studied here, consideration of both mutational and polymorphism data permitted the derivation of plausible explanations for the FVII activity and antigen levels measured in the laboratory. Inter-familial variation in FVII activity and the antigen levels of heterozygous relatives of probands was found to be significantly higher than intra-familial variation, consistent with the view that the nature of the F7 gene lesion(s) segregating in a given family is a prime determinant of laboratory phenotype. Although no relationship could be discerned between laboratory phenotype and polymorphism genotype, the frequencies of the A2 and M2 polymorphic alleles were significantly higher in the FVII-deficient individuals tested than in controls. This suggests that the presence of these alleles may have served to increase the likelihood of pathological F7 gene lesions coming to clinical attention.
Chuzhanova NA, Krawczak M, Nemytikova LA, Gusev VD, Cooper DN.
Promoter shuffling has occurred during the evolution of the vertebrate growth hormone gene.Gene,
254 (2000), 9-18.
[abstract]
Abstract:
Comparative studies of vertebrate gene promoter regions seldom detect gross rearrangements ('promoter shuffling') since such analyses usually employ relatively similar DNA sequences. Conversely, attempts to compare evolutionarily more divergent promoter sequences have been largely unsuccessful owing to the inability of conventional alignment procedures to deal with gross rearrangements. These limitations have been circumvented in the present study by using the novel technique of complexity analysis to identify modular components ('blocks') in the growth hormone (GH) gene promoter sequences of some 22 vertebrate species, from salmon to human. Significant rearrangement of blocks was found to have occurred, indicating that they have evolved as independent units. Some blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Considerable variation between orthologous GH gene promoters was apparent in terms of block length, copy number and relative location. It may be inferred that a wide variety of different mutational mechanisms have operated upon the GH gene promoter over evolutionary time. These include gross changes such as deletion, duplication, amplification, elongation, contraction, transposition, inversion and fusion, as well as the slow, steady accumulation of single base-pair substitutions. Thus the patchwork structure of the modular GH promoter region, and those of its paralogous GH2 and prolactin (PRL) counterparts, have continually been shuffled into new combinations through the rearrangement of pre-existing blocks. Although some of these changes may have had no influence on promoter function, others could have served to alter either the level of gene expression or the responsiveness of the promoter to external stimuli.
Sauermann U, Stahl-Hennig C, Stolte N, Mühl T, Krawczak M, Spring M, Fuchs D, Kaup FJ, Hunsmann G, Sopper S.
Homozygosity for a conserved Mhc class II DQ-DRB haplotype is associated with rapid disease progression in simian immunodeficiency virus-infected macaques: results from a prospective study.J Infect Dis,
182 (2000), 716-24.
[abstract]
Abstract:
In human immunodeficiency virus type 1 (HIV-1)-infected individuals, disease progression varies considerably. This is also observed after experimental infection of macaques with simian immunodeficiency virus (SIV). Major histocompatibility complex (MHC) genes may influence disease progression in both species. Homozygosity for Mhc-Mamu (Macaca mulatta)-DQB1*0601 was previously identified to be associated with rapid disease progression in SIV-infected macaques. To validate the association of this genotype with disease progression, a prospective study was carried out. Six unrelated monkeys homozygous for Mamu-DQB1*0601 and DRB1*0309-DRB*W201 and 6 heterozygous monkeys were infected with SIVmac. Five of the homozygous and only 1 of the heterozygous monkeys died rapidly after infection, with manifestations of AIDS. These results were validated by a retrospective survival analysis of 71 SIV-infected monkeys. The identified DQ-DRB genotype is frequent among monkeys of different breeding colonies and allows a fairly reliable selection before infection of monkeys predisposed for rapid disease progression.
Roewer L, Kayser M, de Knijff P, Anslinger K, Betz A, Caglià A, Corach D, Füredi S, Henke L, Hidding M, Kärgel HJ, Lessig R, Nagy M, Pascali VL, Parson W, Rolf B, Schmitt C, Szibor R, Teifel-Greding J, Krawczak M.
A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males.Forensic Sci Int,
114 (2000), 31-43.
[abstract]
Abstract:
A 9-locus microsatellite framework (minimal haplotype), previously developed for forensic purposes so as to facilitate stain analysis, personal identification and kinship testing, has been adopted for the establishment of a large reference database of male European Y-chromosomal haplotypes. The extent of population stratification pertaining to this database, an issue crucial for its practical forensic application, was assessed through analysis of molecular variance (AMOVA) of the 20 regional samples included. Despite the notion of some significant haplotype frequency differences, which were found to correlate with known demographic and historic features of Europeans, AMOVA generally revealed a high level of genetic homogeneity among the populations analyzed. Owing to their high diversity, however, accurate frequency estimation is difficult for Y-STR haplotypes when realistic (i.e. moderately sized) datasets are being used. As expected, strong pair-wise and higher order allelic associations were found to exist between all markers studied, implying that haplotype frequencies cannot be estimated as products of allele frequencies. A new extrapolation method was therefore developed which treats haplotype frequencies as random variables and generates estimates of the underlying distribution functions on the basis of closely related haplotypes. This approach, termed frequency 'surveying', is based upon standard population genetics theory and can in principle be applied to any combination of markers located on the Y-chromosome or in the mitochondrial genome. Application of the method to the quality assured reference Y-STR haplotype database described herein will prove very useful for the evaluation of positive trace-donor matches in forensic casework.
Tischkowitz M, Wheeler D, France E, Chapman C, Lucassen A, Sampson J, Harper P, Krawczak M, Gray J.
A comparison of methods currently used in clinical practice to estimate familial breast cancer risks.Ann Oncol,
11 (2000), 451-4.
[abstract]
Abstract:
BACKGROUND: With the identification of genes predisposing to hereditary breast cancer, the accurate and consistent estimation of a woman's risk of developing breast cancer based on her family history is of paramount importance if national service guidelines are to be developed. PATIENTS AND METHODS: The residual lifetime risk of developing breast cancer was estimated for 200 women attending a breast cancer genetic assessment clinic by three different methods currently in use in the UK. Risks were computed on the basis of the Cancer and Steroid Hormone (CASH) study data and were classified as 'low/moderate' (<20%) or 'high' (>20%). These risk categories are representative of those currently used to allocate surveillance and genetic testing. Risks were then compared to estimates derived by other methods used in current clinical practice, including those of Houlston and Murday. RESULTS: The CASH data-based method ascribed 27% to the high risk category, as compared to 53% for the combined Houlston and Murday methods. A method based on the number of affected relatives alone ascribed only 14% to the high risk category. Overall, 108 (54%) women were placed in the same risk category by all three methods. CONCLUSIONS: This study demonstrates that there is a significant degree of variability between methods currently used to estimate breast cancer risk which has serious implications for individual patient management, service provision and multicentre studies evaluating the benefits of genetic testing for breast cancer susceptibility.
Cheadle JP, Gill H, Fleming N, Maynard J, Kerr A, Leonard H, Krawczak M, Cooper DN, Lynch S, Thomas N, Hughes H, Hulten M, Ravine D, Sampson JR, Clarke A.
Long-read sequence analysis of the MECP2 gene in Rett syndrome patients: correlation of disease severity with mutation type and location.Hum Mol Genet,
9 (2000), 1119-29.
[abstract]
Abstract:
Mutations in the methyl-CpG-binding protein gene MECP2 at Xq28 cause Rett syndrome (RTT), an X-linked dominant neurodevelopmental disorder characterized by a period of stagnation followed by regression in the development of young girls. Mutations were sought in MECP2 in 48 females with classical sporadic RTT, seven families with possible familial RTT and five sporadic females with features suggestive, but not diagnostic of RTT. Long distance PCR coupled with long-read direct sequencing was employed to sequence the entire MECP2 gene coding region in all cases. Mutations were identified in 44/55 (80%) unrelated classical sporadic and familial RTT patients, but only 1/5 (20%) sporadic cases with suggestive but non-diagnostic features of RTT. Twenty-one different mutations were identified (12 missense, four nonsense and five frame-shift mutations); 14 of these were novel. All missense mutations were located either in the methyl-CpG-binding domain or in the transcription repression domain. Nine recurrent mutations were characterized in a total of 33 unrelated cases (73% of all cases with MECP2 mutations). Significantly milder disease was noted in patients carrying missense mutations as compared with those with truncating mutations ( P = 0. 0023), and milder disease was associated with late as compared with early truncating mutations ( P = 0.0190).
Kayser M, Roewer L, Hedman M, Henke L, Henke J, Brauer S, Krüger C, Krawczak M, Nagy M, Dobosz T, Szibor R, de Knijff P, Stoneking M, Sajantila A.
Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs.Am J Hum Genet,
66 (2000), 1580-8.
[abstract]
Abstract:
A number of applications of analysis of human Y-chromosome microsatellite loci to human evolution and forensic science require reliable estimates of the mutation rate and knowledge of the mutational mechanism. We therefore screened a total of 4,999 meioses from father/son pairs with confirmed paternity (probability >/=99. 9%) at 15 Y-chromosomal microsatellite loci and identified 14 mutations. The locus-specific mutation-rate estimates were 0-8. 58x10-3, and the average mutation rate estimates were 3.17x10-3 (95% confidence interval [CI] 1.89-4.94x10-3) across 8 tetranucleotide microsatellites and 2.80x10-3 (95% CI 1.72-4.27x10-3) across all 15 Y-chromosomal microsatellites studied. Our data show a mutational bias toward length increase, on the basis of observation of more repeat gains than losses (10:4). The data are in almost complete agreement with the stepwise-mutation model, with 13 single-repeat changes and 1 double-repeat change. Sequence analysis revealed that all mutations occurred in uninterrupted homogenous arrays of >/=11 repeats. We conclude that mutation rates and characteristics of human Y-chromosomal microsatellites are consistent with those of autosomal microsatellites. This indicates that the general mutational mechanism of microsatellites is independent of recombination.
Hateboer N, Veldhuisen B, Peters D, Breuning MH, San-Millán JL, Bogdanova N, Coto E, van Dijk MA, Afzal AR, Jeffery S, Saggar-Malik AK, Torra R, Dimitrakov D, Martinez I, de Castro SS, Krawczak M, Ravine D.
Location of mutations within the PKD2 gene influences clinical outcome.Kidney Int,
57 (2000), 1444-51.
[abstract]
Abstract:
BACKGROUND: Since the cloning of the gene for autosomal dominant polycystic kidney disease type 2 (PKD2), approximately 40 different mutations of that gene have been reported to be associated with the disease. The relationship between the PKD2 genotype and phenotype, however, remains unclear. METHODS: Detailed clinical information was collected for PKD2 families in which the underlying mutation had been identified. Logistic regression analysis was employed to assess the influence of age and sex on hypertension, hematuria, renal calculi, and urinary tract infections, and a clinical phenotype score was computed. Patients were then grouped according to the relative location of their mutation within the cDNA sequence, and differences in the mean phenotypic score between groups were tested for statistical significance by means of a multiple pairwise t-test. RESULTS: While phenotypic scores for each mutational group revealed a considerable degree of intragroup variability, the variability in phenotypic scores was significantly higher between mutational groups than within groups. A group-wise comparison of the mean phenotypic scores confirmed the observation of significant nonlinear variation in disease severity, with high- and low-scoring mutational groups interspersed along the gene sequence. CONCLUSION: The identification of groups of mutations in the PKD2 gene, which differ significantly with respect to clinical outcome, is to our knowledge the first description of a genotype/phenotype correlation in autosomal dominant polycystic kidney disease. It also provides evidence against complete loss of function of the mutant PKD2 gene product.
Morris DW, Robinson L, Turic D, Duke M, Webb V, Milham C, Hopkin E, Pound K, Fernando S, Easton M, Hamshere M, Williams N, McGuffin P, Stevenson J, Krawczak M, Owen MJ, Williams J.
Family-based association mapping provides evidence for a gene for reading disability on chromosome 15q.Hum Mol Genet,
9 (2000), 843-8.
[abstract]
Abstract:
Family-based association mapping was used to follow up reports of linkage between reading disability (RD) and a genomic region on chromosome 15q. Using a two-stage approach, we ascertained 101 (stage 1) and 77 (stage 2) parent-proband trios, in which RD was characterized rigorously. In stage 1, a set of eight microsatellite markers spanning the region of putative linkage was used and a highly significant association was detected between RD and a three-marker haplotype (D15S994/D15S214/D15S146: P and empirical P < 0.001). A significant association with the same three-marker haplotype was also observed in the second-stage sample (P = 0.009, empirical P = 0.006). Our data therefore provide strong evidence for one or more genes contributing to RD being located in the vicinity of the region including D15S146 and D15S994. In addition, our results provide support for association analysis being a useful method to map susceptibility loci for complex disorders.
Millar DS, Elliston L, Deex P, Krawczak M, Wacey AI, Reynaud J, Nieuwenhuis HK, Bolton-Maggs P, Mannucci PM, Reverter JC, Cachia P, Pasi KJ, Layton DM, Cooper DN.
Molecular analysis of the genotype-phenotype relationship in factor X deficiency.Hum Genet,
106 (2000), 249-57.
[abstract]
Abstract:
Factor X deficiency is a rare haemorrhagic condition, normally inherited as an autosomal recessive trait, in which a variable clinical presentation correlates poorly with laboratory phenotype. The factor X (F10) genes of 14 unrelated individuals with factor X deficiency (12 familial and two sporadic cases) were sequenced yielding a total of 13 novel mutations. Family studies were performed in order to distinguish the contributions of individual mutant F10 alleles to the clinical and laboratory phenotypes. Missense mutations were studied by means of molecular modelling, whereas single basepair substitutions in splice sites and the 5' flanking region were examined by in vitro splicing assay and luciferase reporter gene assay respectively. The deletion allele of a novel hexanucleotide insertion/deletion polymorphism in the F10 gene promoter region was shown by reporter gene assay, to reduce promoter activity by approximately 20%. One family manifesting an autosomal dominant pattern of inheritance possessed three clinically affected members who were heterozygous for a splice-site mutation that was predicted to lead to the production of a truncated protein product. A model which accounts for the dominant negative effect of this lesion is presented. Variation in the antigen level of heterozygous relatives of probands was found to be significantly higher between families than within families, consistent with the view that the nature of the F10 lesion(s) segregating in a given family is a prime determinant of the laboratory phenotype. By contrast, no such relationship could be discerned between laboratory phenotype and polymorphism genotype.
Krawczak M, Ball EV, Fenton I, Stenson PD, Abeysinghe S, Thomas N, Cooper DN.
Human gene mutation database-a biomedical information and research resource.Hum Mutat,
15 (2000), 45-51.
[abstract]
Abstract:
Although 20 years have elapsed since the first single basepair substitution underlying an inherited disease in humans was characterised at the DNA level, the initiative has only recently been taken to establish central database resources for pathological genetic variants. Disease-associated gene lesions are currently collected and publicised by the Human Gene Mutation Database (HGMD) in Cardiff, locus-specific mutation databases, and to some extent also by the Genome Database (GDB) and Online Mendelian Inheritance in Man (OMIM). To date, HGMD represents the only comprehensive and publicly available database of gene lesions underlying human inherited disease. By July 1999, HGMD contained over 18,000 different mutations from some 900 human genes, the majority being single basepair substitutions. In addition to its potential as an information resource for clinicians and genetic counsellors, HGMD has allowed molecular geneticists to address a variety of biological questions through meta-analysis of the collated data. HGMD also promises to assist research workers in optimising mutation search strategies for a given gene. A questionnaire sent out to, and answered by, the editors of 20 key journals revealed that human genetics journals are increasingly reluctant to publish mutation reports. Electronic data submission and publication facilities are therefore urgently required. The World Wide Web (WWW) provides an excellent medium within which to combine the centralised management of basic mutation data, including rigorous quality control, with the possibility of publishing additional mutation-related information. In response to these needs, HGMD has both instituted a collaboration with Springer-Verlag GmbH, Heidelberg, to potentiate free online submission and electronic publication of human gene mutation data and developed links with the curators of locus-specific mutation databases.
Krawczak M, Chuzhanova NA, Cooper DN.
Evolution of the proximal promoter region of the mammalian growth hormone gene.Gene,
237 (1999), 143-51.
[abstract]
Abstract:
The evolutionary relationship between the proximal growth hormone (GH) gene promoter sequences of 12 mammalian species was explored by comparison of their trinucleotide composition and by multiple sequence alignment. Both approaches yielded results that were consistent with the known fossil record-based phylogeny of the analysed sequences, suggesting that the two methods of tree reconstruction might be equally efficient and reliable. The pattern of evolution inferred for the mammalian GH gene promoters was found to vary both temporally and spatially. Thus, two distinct regions devoid of any evolutionary changes exist in primates, but only one of these 'gaps' is also observed in rodents, and neither is seen in ruminants. Furthermore, different evolutionary rates must have prevailed during different periods of evolutionary time and in different lineages, with a dramatic increase in evolutionary rate apparent in primates. Since a similar pattern of discontinuity has been previously noted for the evolution of the GH-coding regions, it may reflect the action of positive selection operating upon the GH gene as a single cohesive unit. Strong evidence for the action of gene conversion between primate GH gene promoters is provided by the fact that the human GH1 and GH2 sequences, which are thought to have diverged before the divergence of Old World monkeys from great apes, are more similar to one another than either is to the rhesus monkey GH2 promoter. Finally, it was noted that a number of nucleotide positions in the GH1 gene promoter that are polymorphic in humans appear to be highly conserved in mammals. This apparent conundrum, which could represent a caveat for the interpretation of phylogenetic footprinting studies, is potentially explicable in terms either of reduced genetic diversity in highly inbred animal species or insufficient population data from non-human species.
Trefilov A, Krawczak M, Berard J, Schmidtke J.
DNA sequence polymorphisms in genes involved in the regulation of dopamine and serotonin metabolism in rhesus macaques.Electrophoresis,
20 (1999), 1771-7.
[abstract]
Abstract:
A systematic search was performed for DNA sequence variation in genes regulating neurotransmitter metabolism in rhesus macaque (Macaca mulatta). These genes included dopamine and serotonin receptors and transporters, and tyrosine hydroxylase. A total of 13 single nucleotide polymorphisms in five different genes were identified, namely: DRD1 (-244T->G), q = 0.45; DRD1 (-179C->T), q = 0.19; DRD1 (-127G->A), q = 0.25; DRD1(-11T->G), q = 0.08; DRD1(-81C->T), q = 0.19; DRD3 (248G->A), q= 0.08; DRD3(341G->C), q = 0.11; DRD3(377A->G), q = 0.19; DRD3 (403C->T; A59V), q= 0.11; DRD4(2608G->A), q= 0.48; HTR1D(-506G->T), q = 0.47; HTR1D(-173C->T), q = 0.47; and HTT(340G->A), q = 0.39. The nucleotide positions listed correspond to the human homologs.
Krawczak M.
Informativity assessment for biallelic single nucleotide polymorphisms.Electrophoresis,
20 (1999), 1676-81.
[abstract]
Abstract:
Common single nucleotide polymorphisms (SNPs) have the potential to provide a widely used means of simple and robust kinship testing. Suitable measures of polymorphism informativity are therefore required in order to guide the search for the most efficient combinations of SNPs. In the context of kinship testing, such measures should preferably be related to Z, the power of excluding false paternity in trios comprising mother, child and alleged father. Since the bulk of SNPs is expected to be biallelic, a Z-related measure of informativity can be defined for SNPs in a particularly elegant manner: allele frequency vectors of sets of n biallelic SNPs that give rise to the same Z value approximate to an n-dimensional sphere around (1/2,...,1/2). Owing to this relationship, it can be shown that the number N of maximally informative SNPs (i.e., of SNPs with allele frequencies 1/2), providing the same Z value as a given set of n SNPs, approximates to 2n times the average gene diversity of the latter. Linear regression analysis of a large number of simulated SNP sets reveals that only a minor linear correction of Nis required for large n. Since Z= 1-(13/16)N, Ncan also be calculated easily for multiallelic markers with known Z. The "equivalent number of maximally informative SNPs", N, is therefore suggested as a measure of marker informativity in the context of kinship testing.
Hagelberg E, Kayser M, Nagy M, Roewer L, Zimdahl H, Krawczak M, Lió P, Schiefenhövel W.
Molecular genetic evidence for the human settlement of the Pacific: analysis of mitochondrial DNA, Y chromosome and HLA markers.Philos Trans R Soc Lond B Biol Sci,
354 (1999), 141-52.
[abstract]
Abstract:
Present-day Pacific islanders are thought to be the descendants of Neolithic agriculturalists who expanded from island South-east Asia several thousand years ago. They speak languages belonging to the Austronesian language family, spoken today in an area spanning half of the circumference of the world, from Madagascar to Easter Island, and from Taiwan to New Zealand. To investigate the genetic affinities of the Austronesian-speaking peoples, we analysed mitochondrial DNA, HLA and Y-chromosome polymorphisms in individuals from eight geographical locations in Asia and the Pacific (China, Taiwan, Java, New Guinea highlands, New Guinea coast, Trobriand Islands, New Britain and Western Samoa). Our results show that the demographic expansion of the Austronesians has left a genetic footprint. However, there is no simple correlation between languages and genes in the Pacific.
Wacey AI, Cooper DN, Liney D, Hovig E, Krawczak M.
Disentangling the perturbational effects of amino acid substitutions in the DNA-binding domain of p53.Hum Genet,
104 (1999), 15-22.
[abstract]
Abstract:
The spectrum of somatic cancer-associated missense mutations in the human TP53 gene was studied in order to assess the potential structural and functional importance of various intra-molecular properties associated with these substitutions. Relating the observed frequency of particular amino acid substitutions in the p53 DNA-binding domain to their expected frequency, as calculated from DNA sequence-dependent mutation rates, yielded estimates of their relative clinical observation likelihood (RCOL). Several biophysical properties were found to display significant covariation with RCOL values. Thus RCOL values were observed to decrease with increasing solvent accessibility of the substituted residue and with increasing distance from the p53 DNA-binding and Zn2+ -binding sites. The number of adverse steric interactions introduced by an amino acid replacement was found to be positively correlated with its RCOL value, irrespective of the magnitude of the interactions. A gain in hydrogen bond number was found to be only half as likely to come to clinical attention as mutations involving either a reduction or no change in hydrogen bond number. When the difference in potential energy between the wild-type and mutant DNA-binding domains was considered, RCOL values exhibited a minimum around changes of zero. Finally, classification of mutated residues in terms of their protein/solvent environment yielded, for somatic p53 mutations, RCOL values that resembled those previously determined for inherited mutations of human factor IX causing haemophilia B, suggesting that similar mechanisms may be responsible for the mutation-related perturbation of biological function in different protein folds.
Kehoe P, Krawczak M, Harper PS, Owen MJ, Jones AL.
Age of onset in Huntington disease: sex specific influence of apolipoprotein E genotype and normal CAG repeat length.J Med Genet,
36 (1999), 108-11.
[abstract]
Abstract:
Age of onset (AO) of Huntington disease (HD) is known to be correlated with the length of an expanded CAG repeat in the HD gene. Apolipoprotein E (APOE) genotype, in turn, is known to influence AO in Alzheimer disease, rendering the APOE gene a likely candidate to affect AO in other neurological diseases too. We therefore determined APOE genotype and normal CAG repeat length in the HD gene for 138 HD patients who were previously analysed with respect to CAG repeat length. Genotyping for APOE was performed blind to clinical information. In addition to highlighting the effect of the normal repeat length upon AO in maternally inherited HD and in male patients, we show that the APOE epsilon2epsilon3 genotype is associated with significantly earlier AO in males than in females. Such a sex difference in AO was not apparent for any of the other APOE genotypes. Our findings suggest that subtle differences in the course of the neurodegeneration in HD may allow interacting genes to exert gender specific effects upon AO.
Millar DS, Krawczak M, Cooper DN.
Variation of site-specific methylation patterns in the factor VIII (F8C) gene in human sperm DNA.Hum Genet,
103 (1998), 228-33.
[abstract]
Abstract:
The methylation status of 12 CpG sites in three exons of the human factor VIII (F8C) gene was examined by bisulphite genomic sequencing of human sperm DNA from 14 European Caucasians and Asians. Different CpG sites were found to vary in their methylation status both within and between individuals. Strand differences in methylation status were also detected at certain sites, a finding that could reflect hemi-methylation. No evidence for systematic deviations in methylation status were found between the two ethnic groups. Only a limited correlation was observed between the level of methylation of specific CpG sites in sperm DNA and their mutability, a finding that is probably attributable to the pattern of methylation observed in mature spermatocytes not being representative of that of the germline.
Krawczak M, Cooper DN.
p53 mutations, benzo[a]pyrene and lung cancer.Mutagenesis,
13 (1998), 319-20.
Krawczak M, Ball EV, Cooper DN.
Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes.Am J Hum Genet,
63 (1998), 474-88.
[abstract]
Abstract:
The spectrum of single-base-pair substitutions logged in The Human Gene Mutation Database (HGMD), comprising 7,271 different lesions in the coding regions of 547 different human genes, was analyzed for nearest-neighbor effects on relative mutation rates. Owing to its retrospective nature, HGMD allows mutation rates to be estimated only in relative terms. Therefore, a novel methodology was devised in order to obtain these estimates in iterative fashion, correcting, at the same time, for the confounding effects of differential codon usage and for the fact that different types of amino acid replacement come to clinical attention with different probabilities. Over and above the hypermutability of CpG dinucleotides, reflected in transition rates five times the base mutation rate, only a subtle and locally confined influence of the surrounding DNA sequence on relative single-base-pair substitution rates was observed, which extended no farther than 2 bp from the substitution site. A disparity between the two DNA strands was evidenced by the fact that, when substitution rates were estimated conditional on the 5' and 3' flanking nucleotides, a significant rate difference emerged for 10 of 96 possible pairs of complementary substitutional events. Mutational bias, favoring substitutions toward flanking bases, a phenomenon reminiscent of misalignment mutagenesis, was apparent and exhibited both directionality and reading-frame sensitivity. No specific preponderance of repeat-sequence motifs was observed in the vicinity of nucleotide substitutions, but a moderate correlation between the relative mutability and thermodynamic stability of DNA triplets emerged, suggesting either inefficient DNA replication in regions of high stability or the transient stabilization of misaligned intermediates.
Upadhyaya M, Ruggieri M, Maynard J, Osborn M, Hartog C, Mudd S, Penttinen M, Cordeiro I, Ponder M, Ponder BA, Krawczak M, Cooper DN.
Gross deletions of the neurofibromatosis type 1 (NF1) gene are predominantly of maternal origin and commonly associated with a learning disability, dysmorphic features and developmental delay.Hum Genet,
102 (1998), 591-7.
[abstract]
Abstract:
Mutation screening in neurofibromatosis type 1 (NF1) families has long been hampered by the complexity of the NF1 gene. By using a novel multi-track screening strategy, 67 NF1 families (54 two-generation, 13 three-generation) with a de novo mutation in the germline of the first generation were studied with two extragenic and 11 intragenic markers. The pathological lesion was identified in 31 cases. Loss of heterozygosity (LOH) in the affected individual revealed a gross gene deletion in 15 of the two-generation families; in 12 (80%) of them, the deletion was maternally derived. Eleven patients with a gross deletion exhibited developmental delay, ten had dysmorphic features and six manifested a learning disability. No gross deletion was apparent in any of the 13 three-generation families, suggesting that such lesions are subject to more intense selection. In these families, the new mutation was of paternal origin in 11 kindreds and the underlying mutational event could be characterised in three of them.
Hughes HE, Alderman JK, Krawczak M, Rogers C.
Contracting for clinical genetic services: the Welsh model.J Med Genet,
35 (1998), 309-13.
[abstract]
Abstract:
In a time of increasing competition for clinical services resources, it is imperative that health professionals actively participate in the commissioning process in order to ensure that established clinical standards are not compromised. Introduction of the NHS reforms in the UK in the early 1990s highlighted the difficulties in contracting for a specialised service such as clinical genetics, especially in the absence of a consensus regarding the contract currency. An average block contract price for each new family referred was introduced in Wales in 1992, and data from the subsequent five years show that this charging system is economically feasible and has the advantages of (1) recognising the contribution to care of non-medical personnel on the genetics team, (2) covering follow up including the counselling of relatives, (3) protecting the service from loss of income owing to non-attendance, and (4) providing a basis for negotiation when new services are being proposed to purchasers. Activity data show that while the majority of conditions incur below average cost, the mean cost is influenced by a small number of autosomal dominant and X linked disorders. The cost risk to the provider for seeing families over an extended period is minimal, as the data establish that family files experience an exponential decrease in activation probability over the early years, but this becomes constant later on. The robustness of the system is dependent on accurate baseline data on referral patterns to the service, recording of activity, and staff costs.
Cooper DN, Ball EV, Krawczak M.
The human gene mutation database.Nucleic Acids Res,
26 (1998), 285-7.
[abstract]
Abstract:
The Human Gene Mutation Database (HGMD) represents a comprehensive core collection of data on published germline mutations in nuclear genes underlying human inherited disease. By September 1997, the database contained nearly 12 000 different lesions in a total of 636 different genes, with new entries currently accumulating at a rate of over 2000 per annum. Although originally established for the scientific study of mutational mechanisms in human genes, HGMD has acquired a much broader utility to researchers, physicians and genetic counsellors so that it was made publicly available at http://uwcm.ac.uk/uwcm/mg/hgmd0.html in April 1996. Mutation data in HGMD are accessible on the basis of every gene being allocated one web page per mutation type, if data of that type are present. Meaningful integration with phenotypic, structural and mapping information has been accomplished through bi-directional links between HGMD and both the Genome Database (GDB) and Online Mendelian Inheritance in Man (OMIM), Baltimore, USA. Hypertext links have also been established to Medline abstracts through Entrez , and to a collection of 458 reference cDNA sequences also used for data checking. Being both comprehensive and fully integrated into the existing bioinformatics structures relevant to human genetics, HGMD has established itself as the central core database of inherited human gene mutations.
Nürnberg P, Sauermann U, Kayser M, Lanfer C, Manz E, Widdig A, Berard J, Bercovitch FB, Kessler M, Schmidtke J, Krawczak M.
Paternity assessment in rhesus macaques (Macaca mulatta): multilocus DNA fingerprinting and PCR marker typing.Am J Primatol,
44 (1998), 1-18.
[abstract]
Abstract:
Establishing kinship relations in primates using modern molecular genetic techniques has enhanced the ability to scrutinize a number of fundamental biological issues. We screened 51 human short tandem repeats (STRs) for cross-species PCR amplification in rhesus macaques (Macaca mulatta) and identified 11 polymorphic loci with heterozygosity rates of at least 0.6. These markers were used for paternity testing in three social groups (M, R, and S) of rhesus macaques from Cayo Santiago, Puerto Rico. Several consecutive birth cohorts were analyzed in which approximately 200 males were tested for paternity against more than 100 mother/ infant pairs. Despite a combined exclusion rate of more than 99.9% in all three groups, some cases could not be solved unequivocally with the STR markers and additional testing of the MHC-associated DQB1 polymorphism. A final decision became possible through multilocus DNA fingerprinting with one or more of the oligonucleotide probes (GATA)4, (CA)8, and (CAC)5. Paternity assessment by multilocus DNA analysis with probe (CAC)5 alone was found to have limitations in rhesus macaques as regards the number of potential sires which might be involved in a given case. Multilocus DNA fingerprinting requires large amounts of DNA, and the ensuing autoradiographic patterns present difficulties in comparisons across gels and even within the same gel across remote lanes. Computer-assisted image analysis was incapable of eliminating this problem. Therefore, a dual approach to DNA typing has been adopted, using STR markers to reduce the number of potential sires to a level where all remaining candidates can be tested by multilocus DNA fingerprinting on a single gel, preferably in lanes adjacent to the mother/infant pair.
Wacey AI, Krawczak M, Kemball-Cook G, Cooper DN.
Homology modelling of the catalytic domain of early mammalian protein C: evolution of structural features.Hum Genet,
101 (1997), 37-42.
[abstract]
Abstract:
By means of a novel cDNA-based strategy employing the maximum parsimony principle, we have previously deduced probable amino acid sequences for the catalytic domains of the early mammalian ancestors of each of the five extant vitamin K-dependent serine proteases of coagulation, and for their common ancestor from a still earlier stage of vertebrate evolution. In the present study, we employed one of these sequences to construct a molecular model of the catalytic domain of early mammalian protein C and to explore its functional architecture. Following the domain's progression from the common ancestor of the vitamin K-dependent serine proteases toward extant human protein C, this novel application of homology modelling to a reconstructed amino acid sequence has allowed us to trace the evolution of structural features in a vital coagulation protein.
Schmucker B, Krawczak M.
Meiotic microdeletion breakpoints in the BRCA1 gene are significantly associated with symmetric DNA-sequence elements.Am J Hum Genet,
61 (1997), 1454-6.
Wirth B, Schmidt T, Hahnen E, Rudnik-Schöneborn S, Krawczak M, Müller-Myhsok B, Schönling J, Zerres K.
De novo rearrangements found in 2% of index patients with spinal muscular atrophy: mutational mechanisms, parental origin, mutation rate, and implications for genetic counseling.Am J Hum Genet,
61 (1997), 1102-11.
[abstract]
Abstract:
Spinal muscular atrophy (SMA) is a relatively common autosomal recessive neuromuscular disorder. We have identified de novo rearrangements in 7 (approximately 2%) index patients from 340 informative SMA families. In each, the rearrangements resulted in the absence of the telomeric copy of the survival motor neuron (SMN) gene (telSMN), in two cases accompanied by the loss of the neuronal apoptosis-inhibitory protein gene . Haplotype analysis revealed unequal recombination in four cases, with loss of markers Ag1-CA and C212, which are near the 5' ends of the SMN genes. In one case, an interchromosomal rearrangement involving both the SMN genes and a regrouping of Ag1-CA and C212 alleles must have occurred, suggesting either interchromosomal gene conversion or double recombination. In two cases, no such rearrangement was observed, but loss of telSMN plus Ag1-CA and C212 alleles in one case suggested intrachromosomal deletion or gene conversion. In six of the seven cases, the de novo rearrangement had occurred during paternal meiosis. Direct detection of de novo SMA mutations by molecular genetic means has allowed us to estimate for the first time the mutation rate for a recessive disorder in humans. The sex-averaged rate of 1.1 x 10(-4), arrived at in a proband-based approach, compares well with the rate of 0.9 x 10(-4) expected under a mutation-selection equilibrium for SMA. These findings have important implications for genetic counseling and prenatal diagnosis in that they emphasize the relevance of indirect genotype analysis in combination with direct SMN-gene deletion testing in SMA families.
Jones AC, Daniells CE, Snell RG, Tachataki M, Idziaszczyk SA, Krawczak M, Sampson JR, Cheadle JP.
Molecular genetic and phenotypic analysis reveals differences between TSC1 and TSC2 associated familial and sporadic tuberous sclerosis.Hum Mol Genet,
6 (1997), 2155-61.
[abstract]
Abstract:
Tuberous sclerosis (TSC) is an autosomal dominant disorder characterised by the development of hamartomatous growths in many organs. Sixty to seventy percent of cases are sporadic and appear to represent new mutations. TSC exhibits locus heterogeneity: the TSC2 gene is located at 16p13.3 whilst the TSC1 gene, predicted to encode a novel protein termed hamartin, has recently been cloned from 9q34. With the exception of a contiguous gene deletion syndrome involving TSC2 and PKD1 , TSC1 and TSC2 phenotypes have been considered identical. We have now comprehensively defined the TSC1 mutational spectrum in 171 sequentially ascertained, unrelated TSC patients by single strand conformation polymorphism and heteroduplex analysis of all 21 coding exons, and by assaying a restriction fragment spanning the whole locus. Mutations were identified in 9/24 familial cases, but in only 13/147 sporadic cases. In contrast, a limited screen revealed TSC2 mutations in two of the familial cases and in 45 of the sporadic cases. Thus TSC1 mutations were significantly under-represented among sporadic cases (Fisher's exact p -value = 3.12 x 10(-4)). Both large deletions and missense mutations were common at the TSC2 locus whereas most TSC1 mutations were small truncating lesions. Mental retardation was significantly less frequent among carriers of TSC1 than TSC2 mutations (odds ratio 5.54 for sporadic cases only, 6.78 +/- 1.54 when a single randomly selected patient per multigeneration family was also included). No correlation between mental retardation and the type of mutation was found. We conclude that there is a reduced risk of mental retardation in TSC1 as opposed to TSC2 disease and that consequent ascertainment bias, at least in part, explains the relative paucity of TSC1 mutations in sporadic TSC.
Kayser M, de Knijff P, Dieltjes P, Krawczak M, Nagy M, Zerjal T, Pandya A, Tyler-Smith C, Roewer L.
Applications of microsatellite-based Y chromosome haplotyping.Electrophoresis,
18 (1997), 1602-7.
[abstract]
Abstract:
Y-chromosomal microsatellites have been investigated for the purposes of application to male identification, population genetics and population history. With nine markers, every male in a German population sample (n = 70) could be identified by an individual-specific Y microsatellite haplotype. The analysis of 474 unrelated males of nine human populations with seven markers revealed 301 different Y haplotypes. The analysis of molecular variance (AMOVA) approach was used to detect male population characteristics of Y microsatellite haplotypes. With pairwise comparisons of inter-population variance, most of the populations could be distinguished significantly. Sixty individuals from different male populations in Asia and Northern Europe carrying a novel Y-chromosomal T-->C transition show reduced microsatellite variability together with haplotype similarities. Microsatellite data suggest that the mutation occurred recently in Asia, supporting the hypothesis of Asian ancestry of some northern European populations.
Kühnau W, Böhm I, Krawczak M, Schmidtke J.
A paternity case with apparently conflicting multilocus and single-locus DNA typing results.Electrophoresis,
18 (1997), 1598-601.
[abstract]
Abstract:
A paternity case is presented in which DNA typing with thirteen variable number of tandem repeat (VNTR) systems was in apparent conflict with an initial multilocus DNA analysis using oligonucleotide probe (CAC)5. A dual approach was necessary, because the multilocus analysis yielded a proportion of aberrant nonmaternal offspring bands far too small and level of band-sharing too high for non-paternity. The case could finally be solved by reference to the joint likelihood ratio combining both approaches. Arguments are presented that summation of log likelihoods is indeed valid even if no information is available regarding linkage between the VNTR loci and the loci contributing to a multilocus DNA fingerprint.
Sauermann U, Krawczak M, Hunsmann G, Stahl-Hennig C.
Identification of Mhc-Mamu-DQB1 allele combinations associated with rapid disease progression in rhesus macaques infected with simian immunodeficiency virus.AIDS,
11 (1997), 1196-8.
Maynard J, Krawczak M, Upadhyaya M.
Characterization and significance of nine novel mutations in exon 16 of the neurofibromatosis type 1 (NF1) gene.Hum Genet,
99 (1997), 674-6.
[abstract]
Abstract:
Nine novel mutations have been characterized as the result of screening exon 16 of the human NF1 gene in 465 unrelated neurofibromatosis type 1 patients. These lesions include three nonsense and two missense mutations, two deletions, one duplication, and one mutation in the 5' splice site of intron 16. Although exon 16 is the largest NF1 exon, no mutations have so far been reported in this region. This apparent paucity of lesions may be due either to a reduced functional importance of exon 16 or a screening bias or both. However, consideration of the mutability of exon 16 in comparison with other exons suggests that, at least for single base pair substitutions, no such factors need be invoked. Any previous lack of exon 16 mutations in this category would be explicable in terms of a lower propensity to mutate for codons in this gene region.
Macek M, Macek M, Krebsová A, Nash E, Hamosh A, Reis A, Varon-Mateeva R, Schmidtke J, Maestri NE, Sperling K, Krawczak M, Cutting GR.
Possible association of the allele status of the CS.7/HhaI polymorphism 5' of the CFTR gene with postnatal female survival.Hum Genet,
99 (1997), 565-72.
[abstract]
Abstract:
Cystic fibrosis (CF) patients show a high degree of linkage disequilibrium between the CF transmembrane conductance regulator (CFTR) gene and polymorphisms 5' of that gene. To determine whether the region 5' of CFTR contains biologically important sequences, the allele frequencies of six CFTR-linked polymorphisms (metH/MspI, XV-2c/TaqI, CS.7/HhaI, KM19/PstI, MP6d9/MspI, J44/XbaI) were determined in 417 randomly selected elderly individuals (over 75 years of age) from the Czech population. The elderly individuals were considered "escapees" of strong selective pressures that had operated during their lifetime, prior to the introduction of modern health care since 1950. The pooled allele frequencies of the analyzed marker polymorphisms in the elderly did not significantly differ from published data. However, when analyzed by ex, the allele frequencies of markers CS.7/HhaI and KM19/PstI differed significantly (P < 0.05) between elderly females and males. The allele frequencies of the six polymorphisms were then determined in 646 newborns and 345 young adults of reproductive age; these individuals were selected in a similar manner and drawn from the same population. In these control groups, the studied marker polymorphisms exhibited no statistically significant differences between sexes and/or between individuals of the same sex, only between different age groups. A gradual relative increase in the frequency of allele "2" of marker CS.7/HhaI was observed from newborn females to elderly women, the overall difference in allele frequencies of this marker polymorphism between newborn females and elderly women reaching statistical significance (P < 0.05). Interestingly, allele "2" is the major constituent of the extended "B-haplotype", which is in strong linkage disequilibrium with common CF alleles. Taken together, our data suggest that the region spanning markers CS.7 and KM19 is associated with a genetic factor that influences postnatal female survival, providing a possible mechanism for increasing the frequency of particular mutations in the adjacent CFTR gene.
Krawczak M, Cooper DN.
The human gene mutation database.Trends Genet,
13 (1997), 121-2.
de Knijff P, Kayser M, Caglià A, Corach D, Fretwell N, Gehrig C, Graziosi G, Heidorn F, Herrmann S, Herzog B, Hidding M, Honda K, Jobling M, Krawczak M, Leim K, Meuser S, Meyer E, Oesterreich W, Pandya A, Parson W, Penacino G, Perez-Lezaun A, Piccinini A, Prinz M, Roewer L.
Chromosome Y microsatellites: population genetic and evolutionary aspects.Int J Legal Med,
110 (1997), 134-49.
[abstract]
Abstract:
By means of a multicenter study, a large number of males have been characterized for Y-chromosome specific short tandem repeats (STRs) or microsatellites. A complete summary of the allele frequency distributions for these Y-STRs is presented in the Appendix. This manuscript describes in more detail some of the population genetic and evolutionary aspects for a restricted set of seven chromosome Y STRs in a selected number of population samples. For all the chromosome Y STRs markedly different region-specific allele frequency distributions were observed, also when closely related populations were compared. Haplotype analyses using AMOVA showed that when four different European male groups (Germans, Dutch, Swiss, Italians) were compared, less than 10% of the total genetic variability was due to differences between these populations. Nevertheless, these pairwise comparisons revealed significant differences between most population pairs. Assuming a step-wise mutation model and a mutation frequency of 0.21%, it was estimated that chromosome Y STR-based evolutionary lines of descent can be reliably inferred over a time-span of only 1950 generations (or about 49,000 years). This reduces the reliability of the inference of population affinities to a historical, rather than evolutionary time scale. This is best illustrated by the construction of a human evolutionary tree based on chromosome Y STRs in which most of the branches connect in a markedly different way compared with trees based on classical protein polymorphisms and/or mtDNA sequence variation. Thus, the chromosome Y STRs seem to be very useful in comparing closely related populations which cannot probably be separated by e.g. autosomal STRs. However, in order to be used in an evolutionary context they need to be combined with more stable Y-polymorphisms e.g. base-substitutions.
Kayser M, Caglià A, Corach D, Fretwell N, Gehrig C, Graziosi G, Heidorn F, Herrmann S, Herzog B, Hidding M, Honda K, Jobling M, Krawczak M, Leim K, Meuser S, Meyer E, Oesterreich W, Pandya A, Parson W, Penacino G, Perez-Lezaun A, Piccinini A, Prinz M, Schmitt C, Roewer L.
Evaluation of Y-chromosomal STRs: a multicenter study.Int J Legal Med,
110 (1997), 125-33, 141-9.
[abstract]
Abstract:
A multicenter study has been carried out to characterize 13 polymorphic short tandem repeat (STR) systems located on the male specific part of the human Y chromosome (DYS19, DYS288, DYS385, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, YCAI, YCAII, YCAIII, DXYS156Y). Amplification parameters and electrophoresis protocols including multiplex approaches were compiled. The typing of non-recombining Y loci with uniparental inheritance requires special attention to population substructuring due to prevalent male lineages. To assess the extent of these subheterogeneities up to 3825 unrelated males were typed in up to 48 population samples for the respective loci. A consistent repeat based nomenclature for most of the loci has been introduced. Moreover we have estimated the average mutation rate for DYS19 in 626 confirmed fatherson pairs as 3.2 x 10(-3) (95% confidence interval limits of 0.00041-0.00677), a value which can also be expected for other Y-STR loci with similar repeat structure. Recommendations are given for the forensic application of a basic set of 7 STRs (DYS19, DYS3891, DYS389II, DYS390, DYS391, DYS392, DYS393) for standard Y-haplotyping in forensic and paternity casework. We recommend further the inclusion of the highly polymorphic bilocal Y-STRs DYS385, YCAII, YCAIII for a nearly complete individualisation of almost any given unrelated male individual. Together, these results suggest that Y-STR loci are useful markers to identify males and male lineages in forensic practice.
Cooper DN, Krawczak M.
Human Gene Mutation Database.Hum Genet,
98 (1996), 629.
Krawczak M, Wacey A, Cooper DN.
Molecular reconstruction and homology modelling of the catalytic domain of the common ancestor of the haemostatic vitamin-K-dependent serine proteinases.Hum Genet,
98 (1996), 351-70.
[abstract]
Abstract:
The vitamin-K-dependent serine proteinases of coagulation have evolved by a process of gene duplication and divergence, acquiring along the way a considerable degree of functional diversity that has equipped them for their different roles in haemostasis. The cDNA sequences encoding the catalytic domains of the early mammalian ancestors of five vitamin-K-dependent factors (factors VII, IX and X, protein C and prothrombin) were reconstructed by employing cDNA sequence data from a range of extant mammals and by using established phylogenies. The cDNA sequence of the putative common ancestor of these early mammalian proteins was then reconstructed from the five sequences by using a deduced phylogeny that was different in a number of respects from those previously proposed. Factor IX is proposed to have branched off early on, followed by protein C and prothrombin and finally factors VII and X. Significant differences in mutation rates were observed between proteins within a species; factor IX exhibited a lower mutation rate than the other proteins, consistent with its early emergence. Differences in mutation rates were also observed between species for a given protein and these exhibited an inverse correlation with generation time. A biophysically plausible structure for the ancestral vitamin-K-dependent factor protein was constructed by comparative methods. Studies of the functional architecture of this model provide new insights into the evolution of protein-binding specificity in this family of proteins.
Roewer L, Kayser M, Dieltjes P, Nagy M, Bakker E, Krawczak M, de Knijff P.
Analysis of molecular variance (AMOVA) of Y-chromosome-specific microsatellites in two closely related human populations.Hum Mol Genet,
5 (1996), 1029-33.
[abstract]
Abstract:
The analysis of seven Y-chromosome-specific microsatellite loci revealed a high level of polymorphism in two closely related human populations (Dutch, n = 89, and German, n = 70). Four of these loci were found to generate at least 77 different haplotypes, only 15 of which were shared by the two populations. These results demonstrate that highly informative PCR-based DNA typing of the Y chromosome is now feasible. Assuming a stepwise mutation model, a network comprising all minimum spanning evolutionary trees connecting the haplotypes was constructed. Analysis of molecular variance based upon this network indicated that the within-population heterogeneity with respect to haplotype descent was significantly smaller than the between-population heterogeneity, suggesting that males were more closely related to males from their own population as opposed to males from the other population. These findings suggest that Y-chromosomal microsatellites might be very useful not only for forensic purposes but also in association studies of multifactorial traits, allowing the characterization of the level of genetic distinctiveness of supposedly inbred or isolated populations and discrimination even between closely related populations.
Badens C, Thuret I, Michel G, Krawczak M, Mattei JF, Lena-Russo D, Labie D, Elion J.
Novel and unusual deletion-insertion thalassemic mutation in exon 1 of the beta-globin gene.Hum Mutat,
8 (1996), 89-92.
Krawczak M, Cooper DN.
Single base-pair substitutions in pathology and evolution: two sides to the same coin.Hum Mutat,
8 (1996), 23-31.
[abstract]
Abstract:
Relative single base-pair substitution rates in human genes, derived from a collection of > 2,700 point mutations causing human genetic disease, were related to the results of an evolutionary gene/pseudogene comparison. At the mononucleotide level, notable differences between the two datasets were confined to C-to-T and G-to-A transitions, both being rarer in gene/pseudogene alignments than among disease-associated lesions. Relative nearest neighbour-dependent substitution rates were found to be similar in the two datasets, indicating the long-term stability of these parameters during human genome evolution. Allowing for the 5' and 3' nucleotides flanking mutated sites, the primary likelihood of mutation generation could be demonstrated to be biased toward the avoidance of replacements that: (1) change the chemical characteristics of the encoded amino acid residue substantially, and (2) have a high chance of resulting in genetic disease in humans. A similar bias is also reflected in the evolutionary history of human and rodent proteins: amino acid replacements that currently exhibit a high likelihood of coming to clinical attention have been less likely to be accepted during protein evolution.
Winter PC, Scopes DA, Berg LP, Millar DS, Kakkar VV, Mayne EE, Krawczak M, Cooper DN.
Functional analysis of an unusual length polymorphism in the human antithrombin III (AT3) gene promoter.Blood Coagul Fibrinolysis,
6 (1995), 659-64.
[abstract]
Abstract:
The prevalence of the alternative alleles of an unusual length polymorphism in the promoter of the human antithrombin III (AT3) gene was determined in a sample of 155 unrelated individuals from the Northern Irish population. The 108bp L allele and the 32bp S allele occurred at frequencies of 0.21 and 0.79 respectively. Some homology was noted between the L-specific sequence and the region immediately downstream. Residual homology was also evident between the L and S sequences, suggesting that the S allele was derived from the L allele during evolution by partial deletion followed by sequence divergence. The functional significance of the polymorphism was investigated by transient transfection of AT3 promoter/luciferase reporter gene constructs into two human hepatoma cell lines in vitro. The promoter strength of the L allele was found to be 1.6-fold higher than the S allele in HepG2 cells whereas in Hep3B cells, the strength of the S allele was 1.7-fold higher than that of the L allele. In order to evaluate the phenotypic consequences of the AT3 promoter polymorphism in vivo, plasma samples from the 155 control individuals were assayed for antithrombin III (ATIII) activity. Mean activities of the different promoter polymorphism genotypes (SS, LL, SL) were not significantly different. These results suggest that the AT3 promoter polymorphism does not contribute to the variation in plasma ATIII activity that occurs in the general population.
Krawczak M.
Locus homogeneity for cartilage-hair hypoplasia proven?.Hum Genet,
96 (1995), 371-2.
Krawczak M, Reitsma PH, Cooper DN.
The mutational demography of protein C deficiency.Hum Genet,
96 (1995), 142-6.
[abstract]
Abstract:
The geographical distribution and prevalence of 256 single base-pair substitutions (105 of them being different) within the coding region of the human protein C (PROC) gene were correlated with their initial likelihoods of generation. A significant positive correlation was observed between these "mutational likelihoods" and the geographical dispersal of the PROC gene lesions within and between 16 different countries. This relationship could be attributed to the fact that, with few exceptions, high dispersal was only exhibited by CG-->TG and CG-->CA transitions, i.e. those substitutions that are known to arise de novo at the highest frequency. The statistical distribution of mutational likelihoods was as predicted on the basis of the PROC cDNA sequence alone, allowing however for the redundancy of the genetic code. These findings suggest (1) that genetic drift and lesion-specific selection have been of relatively minor importance in determining the mutational spectrum observed in the PROC gene and (2) that most multiple reports of particular substitutions in different geographical locations appear to reflect recurrent mutation rather than identity-by-descent.
Varon R, Magdorf K, Staab D, Wahn HU, Krawczak M, Sperling K, Reis A.
Recurrent nasal polyps as a monosymptomatic form of cystic fibrosis associated with a novel in-frame deletion (591del18) in the CFTR gene.Hum Mol Genet,
4 (1995), 1463-4.
Hallam PJ, Millar DS, Krawczak M, Kakkar VV, Cooper DN.
Population differences in the frequency of the factor V Leiden variant among people with clinically symptomatic protein C deficiency.J Med Genet,
32 (1995), 543-5.
[abstract]
Abstract:
The factor V Leiden variant, responsible for the phenomenon of activated protein C resistance, was found to be less frequent among British (0.06) and Swedish/Danish (0.15) protein C deficiency patients than previously reported in a Dutch study (0.19). In the Swedish population, a significantly increased frequency of the factor V Leiden allele was apparent in protein C deficiency patients as compared to healthy controls. However, this was not found in the British population. Coinheritance of the factor V Leiden variant is therefore unlikely to be the sole determinant of whether a person with protein C deficiency will come to clinical attention. Nevertheless, when patient data were analysed by type of protein C deficiency, it was noted that the frequency of the factor V Leiden variant was 2.8-fold higher in type II patients compared to type I patients. A possible explanation of this disparity is discussed.
Scopes D, Berg LP, Krawczak M, Kakkar VV, Cooper DN.
Polymorphic variation in the human protein C (PROC) gene promoter can influence transcriptional efficiency in vitro.Blood Coagul Fibrinolysis,
6 (1995), 317-21.
[abstract]
Abstract:
The haplotype frequencies of two closely linked diallelic polymorphisms in the protein C(PROC) gene promoter were determined in the British population. In principle, differences in transcription efficiency between PROC promoter haplotypes could represent an additional risk factor in determining whether or not an individual already predisposed to venous thrombosis will come to clinical attention. In order to explore this postulate, transient transfection of human hepatoma cells with PROC promoter-luciferase reporter gene constructs was performed in vitro. In HepG2 cells, the T.....A haplotype exhibited at least a two-fold higher transcription efficiency than the C.....G haplotype. A sample of British protein C deficiency patients with recurrent venous thrombosis was then allelotyped by a combination of oligonucleotide discriminant hybridization and DNA sequencing. The frequency of the low expressing C.....G haplotype was found to be slightly yet not significantly higher in these patients (0.43) than in controls (0.35).
Reitsma PH, Bernardi F, Doig RG, Gandrille S, Greengard JS, Ireland H, Krawczak M, Lind B, Long GL, Poort SR.
Protein C deficiency: a database of mutations, 1995 update. On behalf of the Subcommittee on Plasma Coagulation Inhibitors of the Scientific and Standardization Committee of the ISTH.Thromb Haemost,
73 (1995), 876-89.
Hallam PJ, Wacey AI, Mannucci PM, Legnani C, Kühnau W, Krawczak M, Kakkar VV, Cooper DN.
A novel missense mutation (Thr176-->Ile) at the putative hinge of the neo N-terminus of activated protein C.Hum Genet,
95 (1995), 447-50.
[abstract]
Abstract:
We describe the detection of a novel missense mutation (Thr176-->Ile) that is located at the neo N-terminus of activated protein C. The Thr176-->Ile substitution leads to a type 1 deficiency state. Evidence is presented suggesting that this residue plays a role in pivoting the N-terminus of protein C to fold into the oxyanion hole.
Krawczak M, Cooper DN.
Core database.Nature,
374 (1995), 402.
Krawczak M, Lubjuhn T.
An informativity index for multilocus DNA fingerprints.Electrophoresis,
16 (1995), 16-21.
[abstract]
Abstract:
An informativity index for multilocus DNA fingerprints, r, was developed. It is based upon the Shannon information that a paternal DNA fingerprint conveys about the offspring phenotype pattern. Both simulation and empirical data reveal that the index r is strongly correlated with the mean log likelihood ratio (paternity vs. nonpaternity) expected in trio cases of true paternity. Since r can be estimated from DNA fingerprints of unrelated individuals in advance, it will provide an easy means to assess the potential utility of a given probe/enzyme combination in kinship testing.
Krawczak M, Smith-Sorensen B, Schmidtke J, Kakkar VV, Cooper DN, Hovig E.
Somatic spectrum of cancer-associated single basepair substitutions in the TP53 gene is determined mainly by endogenous mechanisms of mutation and by selection.Hum Mutat,
5 (1995), 48-57.
[abstract]
Abstract:
The spectrum of somatic TP53 single basepair substitutions detected in 955 cancers was compared with that of 2,224 different germline mutations in 279 different human genes (other than TP53), reported as the cause of inherited disease. This comparison reveals that, disregarding a relatively small subset (12%) of TP53 mutations that probably result from the action of exogenous mutagens, both the relative rates and the nearest-neighbor spectra of single basepair substitutions are similar in the two datasets. This spectral resemblance suggests that a substantial proportion of cancer-associated somatic TP53 mutations result from endogenous cellular mechanisms. The likelihood of clinical observation of a particular mutation type differs, however, between tumors and genetic diseases, when the chemical properties of the resulting amino acid substitutions are considered. Together with a sixfold higher observation likelihood for mutations at evolutionarily conserved residues, this finding argues that selection is a critical factor in determining which TP53 mutations are found to be associated with human cancer.
Wacey AI, Krawczak M, Kakkar VV, Cooper DN.
Determinants of the factor IX mutational spectrum in haemophilia B: an analysis of missense mutations using a multi-domain molecular model of the activated protein.Hum Genet,
94 (1994), 594-608.
[abstract]
Abstract:
A multi-domain molecular model of factor IXa was constructed by comparative methods. The quaternary structure of the protein was assembled by docking individual domains through consideration of their shape complementarity, polaric properties and the location of cross-reacting material positive/negative (CRM+/-) variants on domain surfaces. Some 217 different missense mutations in the factor IX (F9) gene were then selected for study. Using maximum likelihood analysis, missense mutations affecting highly conserved amino acid residues of factor IX were shown to be 15-20 times more likely to result in haemophilia B than those affecting non-conserved residues. However, about one quarter of this increase in likelihood of clinical observation could be attributed to the magnitude of the amino acid exchange. Missense mutations in structurally conserved residues were found to be 2.1-fold more likely to come to clinical attention than those in structurally variable residues. Missense mutations in residues whose side chains were inwardly pointing were 3.6-fold more likely to be observed than those in surface residues. These observations imply a complex hierarchy of sequence/structure conservation in the protein. The severity of the clinical phenotype correlated with both the extent of the evolutionary sequence conservation of the residue at the site of mutation and the magnitude of the amino acid exchange. Further, the substitution of residues exhibiting minimal side chain solvent accessibility was associated disproportionately with severe haemophilia compared with that of surface residues. Clusters of CRM+ mutations were observed at factor IX-specific residues on the surface of the molecule. These clusters may reflect factor IX-specific docking interactions. The likelihood that a given factor IX mutation will come to clinical attention is therefore a complex function of the sequence characteristics of the F9 gene, the nature of the amino acid substitution, its precise location and immediate environment within the protein molecule, and its resulting effects on the structure and function of the protein.
Mertes G, Ludwig M, Finkelnburg B, Krawczak M, Schwaab R, Brackmann HH, Olek K.
A G+3-to-T donor splice site mutation leads to skipping of exon 50 in von Willebrand factor mRNA.Genomics,
24 (1994), 190-1.
Krawczak M, Schmidtke J, Epplen JT, Hansmann I, Thies U.
A multilocus DNA fingerprint with built-in security devices.Med Sci Law,
34 (1994), 256-62.
[abstract]
Abstract:
An unusual case of paternity testing is reported in which determination of paternity was an essential part of a genetic diagnosis. A Y-chromosomal abnormality, observed in a 33-year-old male whose wife had experienced a series of spontaneous abortions, was not found in his alleged father. DNA fingerprinting with the oligonucleotide multilocus probe (CAC)5 yielded two aberrant bands for the proband, i.e. bands exhibited by neither parent. This finding resulted in a comparatively low paternity probability of 0.02934 which is suggestive of, but does not unequivocally prove, false paternity. Subsequent analysis with other multi- and single-locus systems, however, failed to confirm this preliminary result. The paternity probability computed on the basis of the single-locus systems was 0.99997, providing compelling evidence in favour of true paternity. The present case thus demonstrates that even when two mutations turn up in a DNA fingerprint, these may be readily recognized as such.
Krawczak M.
Multilocus DNA fingerprinting: the independence problem in quantitative paternity testing.Electrophoresis,
15 (1994), 165-9.
[abstract]
Abstract:
A simulation study was performed in order to determine whether or not the assumption of independence, made in the quantitative analysis of multilocus DNA fingerprints, represents an inadmissible over-simplification. A total of 10,000 cases of true and false paternity, respectively, were simulated in twenty replicas of various genetic models. Log-likelihood ratios (paternity vs. non-paternity; LR) were calculated using published likelihood formulae and assuming position-wise independence. The resulting LR distributions were compared to (i) the results of a classical analysis of the underlying genotype data, and (ii) the distributions expected from the likelihood model employed in the LR calculations. Although considerable discrepancies were observed between these distributions, decision making about paternity appeared to be only marginally affected, especially when only a fraction of each multilocus DNA fingerprint was analyzed.
Dörk T, Will K, Grade K, Krawczak M, Tümmler B.
A 32-bp deletion (2991del32) in the cystic fibrosis gene associated with CFTR mRNA reduction.Hum Mutat,
4 (1994), 65-70.
[abstract]
Abstract:
Cystic fibrosis, a common recessive disorder of exocrine glands, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We describe the identification of a 32-bp deletion within the coding region of CFTR that involves the nucleotides 2991-3022 in exon 15 (2991del32). This unusual frameshift mutation was confirmed in three unrelated German families, accounting for a frequency of 0.3% in 1,028 CF chromosomes. All identified patients are compound heterozygotes for 2991del32 and for the most frequent cystic fibrosis mutation, delta F508. The evaluation of clinical data revealed typical symptoms of cystic fibrosis, including pancreatic insufficiency, in all three index cases. To characterize further the mutation in the CFTR transcript, we analysed RNA from lymphocytes by reverse transcription and PCR amplification. 2991del32 transcripts were detectable neither in the RNA sample from a patient compound heterozygous delta F508/2991del32 nor in the parental sample heterozygous wild-type/2991del32. These data indicate that the 32-bp deletion causes a pancreas insufficient cystic fibrosis phenotype by a severe reduction of CFTR mRNA.
Bartels I, Bockel B, Caesar J, Krawczak M, Thiele M, Rauskolb R.
Risk of fetal Down's syndrome based on maternal age and varying combinations of maternal serum markers.Arch Gynecol Obstet,
255 (1994), 57-64.
[abstract]
Abstract:
Serum samples from 320 women with chromosomally normal fetuses and from 50 women with fetuses affected by Down's syndrome were assayed retrospectively for human chorionic gonadotropin (hCG), pregnancy-specific beta 1 glycoprotein (SP1), alpha fetoprotein (AFP), and unconjugated estriol (uE3) between 14 and 21 weeks of gestation. Nonparametric discriminant analysis was applied to calculate Down syndrome risks on the basis of various combinations of serum parameters. At a risk threshold that falsely identifies 5% of controls as being affected, 46 to 48% of Down syndrome pregnancies were detected by combinations of hCG/AFP, hCG/AFP/uE3, and hCG/AFP/uE3/SP1 respectively. HCG, AFP, and uE3 were assayed in 652 serum samples from women who underwent amniocentesis because of maternal age (> or equal to 35 years in this prospective study). 49% of women with euploid fetal karyotype, 8 of 10 pregnancies with Down's syndrome, and 3 pregnancies with sex chromosomal anomalies were identified as being at an increased risk (> 1:380).
Krawczak M, Böhm I, Nürnberg P, Hampe J, Hundrieser J, Pöche H, Peters C, Slomski R, Kwiatkowska J, Nagy M.
Paternity testing with oligonucleotide multilocus probe (CAC)5/(GTG)5: a multicenter study.Forensic Sci Int,
59 (1993), 101-17.
[abstract]
Abstract:
The statistical analysis is reported of 256 paternity cases referred to seven different German laboratories for multilocus DNA fingerprinting with oligonucleotide probe (CAC)5/(GTG)5 and restriction enzyme HinfI. All parameters characteristic of multilocus DNA fingerprints were found to differ significantly between the contributing centres: the number of analyzed gel positions, the number of bands scored per individual, the probability of occurrence of a band at a particular position, and the band-sharing probabilities between the mother and both child and alleged father. Despite these differences, paternity cases could be divided clearly into two distinct subgroups on the basis of (i) offspring bands that could not be assigned to either the mother or the alleged father and (ii) the extent of band-sharing between child and alleged father. This partitioning, which is likely to correspond to true and false paternity, confirms previous findings for other multilocus probes. A goodness-of-fit test on the normalized number of bands scored per individual revealed no systematic deviations from commonly adopted analytical models regarding electrophoretic bands as independent entities. Log10-likelihood ratios of paternity vs. non-paternity were calculated utilizing one of these models, and a clear-cut partitioning was again obtained which coincides with that mentioned before. Only one case could not be decided unambiguously, and was either due to two independent mutations or to a close relative of the alleged father being the true father.
Nürnberg P, Berard JD, Bercovitch F, Epplen JT, Schmidtke J, Krawczak M.
Oligonucleotide fingerprinting of free-ranging and captive rhesus macaques from Cayo Santiago: paternity assignment and comparison of heterozygosity.EXS,
67 (1993), 445-51.
[abstract]
Abstract:
Multilocus DNA fingerprinting with oligonucleotide probes (GTG)5, (GATA)4, and (CA)8 was applied in order to determine paternity in one birth cohort (15 infants) of social group (S) from the free-ranging colony of rhesus macaques (Macaca mulatta) on Cayo Santiago. While sires could be identified in 11 cases, all males tested (N = 19) could be excluded from paternity for the remaining four infants. Data revealed marked discrepancies between actual paternity and paternity as inferred from the observation of copulation behavior. Thus, a dominant social rank does not appear to be strongly associated with reproductive success. Furthermore, alternative reproductive strategies were found to yield comparable net benefits in reproduction. A second group of animals (M) was translocated from Cayo Santiago to the Sabana Seca Field Station in 1984. They have continuously resided together in a large outdoor enclosure since then. Here paternity assessment was seriously impeded by a reduced number of discriminating bands, i.e. offspring bands which were unequivocally derived from the sires. This was initially held to be indicative of a smaller degree of heterozygosity in Group M, and was attributed to inbreeding due to a lack of male immigration or extra-group fertilizations. However, a comparison of the DNA fingerprint patterns obtained in Group S and Group M lends only partial support to this idea.
Böhm I, Krawczak M, Nürnberg P, Hampe J, Hundrieser J, Pöche H, Peters C, Slomski R, Kwiatkowska J, Nagy M.
Oligonucleotide DNA fingerprinting: results of a multi-center study on reliability and validity.EXS,
67 (1993), 257-60.
[abstract]
Abstract:
We report the results of an empirical study of 256 paternity cases referred to 7 different German laboratories for DNA fingerprinting with oligonucleotide probe (CAC)5/(GTG)5. All parameters characteristic of such multilocus DNA fingerprints were found to differ significantly between the contributing centres. Despite these differences, clear-cut decisions between paternity and non-paternity could be made in all but one case. Furthermore, we found no systematic deviation of the gel-phenotype distribution among trios from random expectation as derived from commonly adopted analytical models. Thus, we conclude that oligonucleotide DNA fingerprinting is a robust and reliable means for the resolution of paternity cases.
Krawczak M, Bockel B.
The formal analysis of multilocus DNA fingerprints.EXS,
67 (1993), 249-55.
[abstract]
Abstract:
A description is given of a novel method for the formal analysis of multilocus DNA fingerprints, the so-called 'genetic factor model'. Using this model, multilocus DNA fingerprints can be shown to be a robust means for both paternity testing and pedigree reconstruction.
Krawczak M, Reiss J, Cooper DN.
The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences.Hum Genet,
90 (1992 Sep-Oct), 41-54.
[abstract]
Abstract:
A total of 101 different examples of point mutations, which lie in the vicinity of mRNA splice junctions, and which have been held to be responsible for a human genetic disease by altering the accuracy of efficiency of mRNA splicing, have been collated. These data comprise 62 mutations at 5' splice sites, 26 at 3' splice sites and 13 that result in the creation of novel splice sites. It is estimated that up to 15% of all point mutations causing human genetic disease result in an mRNA splicing defect. Of the 5' splice site mutations, 60% involved the invariant GT dinucleotide; mutations were found to be non-randomly distributed with an excess over expectation at positions +1 and +2, and apparent deficiencies at positions -1 and -2. Of the 3' splice site mutations, 87% involved the invariant AG dinucleotide; an excess of mutations over expectation was noted at position -2. This non-randomness of mutation reflects the evolutionary conservation apparent in splice site consensus sequences drawn up previously from primate genes, and is most probably attributable to detection bias resulting from the differing phenotypic severity of specific lesions. The spectrum of point mutations was also drastically skewed: purines were significantly over-represented as substituting nucleotides, perhaps because of steric hindrance (e.g. in U1 snRNA binding at 5' splice sites). Furthermore, splice sites affected by point mutations resulting in human genetic disease were markedly different from the splice site consensus sequences. When similarity was quantified by a 'consensus value', both extremely low and extremely high values were notably absent from the wild-type sequences of the mutated splice sites. Splice sites of intermediate similarity to the consensus sequence may thus be more prone to the deleterious effects of mutation. Regarding the phenotypic effects of mutations on mRNA splicing, exon skipping occurred more frequently than cryptic splice site usage. Evidence is presented that indicates that, at least for 5' splice site mutations, cryptic splice site usage is favoured under conditions where (1) a number of such sites are present in the immediate vicinity and (2) these sites exhibit sufficient homology to the splice site consensus sequence for them to be able to compete successfully with the mutated splice site. The novel concept of a "potential for cryptic splice site usage" value was introduced in order to quantify these characteristics, and to predict the relative proportion of exon skipping vs cryptic splice site utilization consequent to the introduction of a mutation at a normal splice site.
Krawczak M, Bockel B.
A genetic factor model for the statistical analysis of multilocus DNA fingerprints.Electrophoresis,
13 (1992 Jan-Feb), 10-7.
[abstract]
Abstract:
A novel concept is described for the statistical analysis of multilocus DNA fingerprints. Utilizing this method, it is shown by simulation that the application of multilocus DNA fingerprints to paternity testing is robust against deviations from idealistic assumptions made about underlying models and parameters. Partial homozygosity, allelism and linkage at the DNA loci involved, as well as variations in estimates of band-sharing probabilities were studied for effects on the resulting paternity probabilities. None of the above-mentioned phenomena appear to change these values to an extent relevant for decision making in paternity cases.
Krawczak M, Schmidtke J.
The decision theory of paternity disputes: optimization considerations applied to multilocus DNA fingerprinting.J Forensic Sci,
37 (1992), 1525-33.
[abstract]
Abstract:
The solution of paternity disputes using results from scientific analyses is studied from a decision-theoretical viewpoint. Two alternative approaches to decision making, the so-called 'Bayes' and 'Minimax' strategies, are described and discussed. If prior probabilities of paternity are exactly known, then Bayes decisions are (a) independent of the source of evidence and (b) optimal with respect to average losses caused by wrong decisions. However, it is concluded that Minimax decisions, which depend upon the employed test system but not upon prior probabilities, are more appropriate in paternity cases if equal prior good will towards disclaimed children and alleged fathers is demanded. It is further demonstrated that, when major evidence about paternity comes from multilocus DNA fingerprinting, prior probabilities must be known quite accurately for Bayes decisions to be superior with respect to average losses. Finally, we are able to show that 'quasi' Bayes decision making, that is, adopting a neutral prior probability of 0.5 but leaving thresholds for decision making unchanged, coincides with Minimax decision making if multilocus DNA fingerprinting is employed.
Bockel B, Nürnberg P, Krawczak M.
Likelihoods of multilocus DNA fingerprints in extended families.Am J Hum Genet,
51 (1992), 554-61.
[abstract]
Abstract:
A concept for the application of complex pedigree analysis to multilocus DNA fingerprinting is described. By following this approach, the extent to which the DNA fingerprints of grandparents influence the phenotype likelihoods of their offspring was determined. It was demonstrated by simulation that approximately 90% of paternity disputes can be solved if mother, child, and paternal grandparents, instead of the putative father, are tested. If only phenotype information on a single paternal sib is allowed for, true paternity will be detected with reasonable persuasive power in up to 64% of cases. Exclusion of false paternity remains possible for 40% of cases. Finally, the analysis concept is modified by reducing the number of genotype variations considered in likelihood computations. This time-saving procedure is shown to yield sufficiently accurate likelihoods in the analysis of both simulation data and multilocus DNA fingerprints obtained in two large families.
Krawczak M, Bockel B.
Does the omission of missing information bias the estimates of age-at-onset distributions?.Am J Hum Genet,
50 (1992), 652-4.
Grundy CB, Schulman S, Krawczak M, Kobosko J, Kakkar VV, Cooper DN.
Protein C deficiency and thromboembolism: recurrent mutation at Arg 306 in the protein C gene.Hum Genet,
88 (1992), 586-8.
[abstract]
Abstract:
A CGA----TGA transition in the protein C gene, resulting in an Arg306----Term substitution, was detected in a Swedish kindred with thrombotic disease whose members exhibit plasma protein C activity/antigen levels consistent with type I protein C deficiency. Although an identical lesion has been reported previously in several Dutch families, RFLP typing indicated that the Dutch and Swedish mutations were unlikely to be identical by descent and probably arose by recurrent mutation.
Dörk T, Neumann T, Wulbrand U, Wulf B, Kälin N, Maass G, Krawczak M, Guillermit H, Ferec C, Horn G.
Intra- and extragenic marker haplotypes of CFTR mutations in cystic fibrosis families.Hum Genet,
88 (1992), 417-25.
[abstract]
Abstract:
In order to facilitate the screening for the less common mutations in the cystic fibrosis (CF) gene viz., the CF transmembrane conductance regulator gene (CFTR), marker haplotypes were determined for German non-CF (N) and CF chromosomes by polymerase chain reaction analysis of four polymorphisms upstream of the CF gene (XV-2c, KM.19, MP6-D9, J44) and six intragenic polymorphisms (GATT, TUB9, M470V, T854T, TUB18, TUB20) that span the CFTR gene from exon 6 through exon 21. Novel informative sequence variants of CFTR were detected in front of exons 10 (1525-61 A or G), 19 (3601-65 C or A), and 21 (4006-200 A or G). The CF locus exhibits strong long-range marker-marker linkage disequilibrium with breakpoints of recombination between XV-2c and KM.19, and between exons 10 and 19 of CFTR. Marker alleles of GATT-TUB9 and TUB18-TUB20 were found to be in absolute linkage disequilibrium. Four major haplotypes encompass more than 90% of German N and CF chromosomes. Fifteen CFTR mutations detected on 421 out of 500 CF chromosomes were each identified on one of these four predominant 7-marker haplotypes. Whereas all analysed delta F508 chromosomes carried the same KM.19-D9-J44-GATT-TUB9-M470V-T854T haplotype, another frequent mutation in Germany, R553X, was identified on two different major haplotypes. Hence, a priori haplotyping cannot exclude a particular CF mutation, but in combination with population genetic data, enables mutations to be ranked by decreasing probability.
Krawczak M, Bockel B, Sandkuijl L, Thies U, Fenton I, Harper PS.
Covariate-dependent age-at-onset distributions for Huntington disease.Am J Hum Genet,
49 (1991), 735-45.
[abstract]
Abstract:
A combined logistic regression and life-table analysis is presented on age-at-onset data for Huntington disease. Covariates included in the analysis were sex of the at-risk individual, parental age at onset, and sex of transmitting parent. Parental age at onset and parental sex were found to be significant covariates for age at onset in the offspring, and the appropriate logistic regression functions are calculated by maximum likelihood methods. These regression functions permit a more precise evaluation of carrier risks and likelihoods than hitherto was possible by simple computational means. We further introduce a novel method to account for sibship correlations in the significance assessment, using log-likelihood differences between different models.
Krawczak M, Bockel B.
DNA-fingerprinting: a short note on mutation rates.Hum Genet,
87 (1991), 632-3.
Grundy CB, Thomas F, Millar DS, Krawczak M, Melissari E, Lindo V, Moffat E, Kakkar VV, Cooper DN.
Recurrent deletion in the human antithrombin III gene.Blood,
78 (1991), 1027-32.
[abstract]
Abstract:
Eight unrelated patients with recurrent thromboembolism, a family history of thrombosis, and plasma antithrombin III (ATIII) activity/antigen levels consistent with a diagnosis of heterozygous type I ATIII deficiency were studied by polymerase chain reaction/direct sequencing of ATIII gene exon-coding regions. Frameshift mutations of one base and two bases, respectively, were found to have occurred in two unrelated patients at the same GAG codon (Glu 245) within exon 4 of the ATIII gene. A literature search showed six further hitherto unrecognized deletion "hotspots" in four other human genes. These deletion-prone sites exhibited sufficient sequence homology with each other to derive a consensus sequence (T G A/G A/G G A/C), suggesting that deletion in human genes may not only be non-random but also sequence-directed.
Reiss J, Cooper DN, Bal J, Slomski R, Cutting GR, Krawczak M.
Discrimination between recurrent mutation and identity by descent: application to point mutations in exon 11 of the cystic fibrosis (CFTR) gene.Hum Genet,
87 (1991), 457-61.
[abstract]
Abstract:
A total of 75 non-delta F508 chromosomes from 59 German cystic fibrosis patients was screened for mutations in exon 11 of the cystic fibrosis (CFTR) gene. These Caucasian patients were found to possess an identical haplotype background for two common mutations (G551D, R553X) consistent with their being identical by descent. However, a different R553X associated haplotype found in American black patients was suggestive of recurrent mutation, a postulate supported by the location of the R553X alteration in a hypermutable CpG dinucleotide. Likelihood estimates for recurrent mutation and identity by descent were compared and strongly supported the hypothesis of recurrent R553X mutation. The ability to distinguish between these two alternatives provides an indication of whether or not the search for mutations should be restricted to chromosomes with similar haplotypes.
Cooper DN, Krawczak M.
Mechanisms of insertional mutagenesis in human genes causing genetic disease.Hum Genet,
87 (1991), 409-15.
[abstract]
Abstract:
Examples of the insertion of less than 10 bp of DNA sequence into human gene-coding regions causing genetic disease were collated in order to study the underlying causative mechanisms. The nature of these insertions was found to be consistent with several mechanisms of mutagenesis including: (1) slipped mispairing mediated by direct repeats or runs of identical bases and (2) the templated misincorporation of bases by secondary-structure intermediates whose formation is facilitated by palindromic (inverted repeat) sequences, quasi-palindromic sequences or symmetric elements. Both the size and position of insertions were found to be non-random and highly dependent upon the surrounding DNA sequence. Inferred mechanisms of insertional mutagenesis thus appear to be very similar to those involved in the causation of gene deletions.
Günther E, Kiesel U, Kolb H, Krawczak M, Rothermel E, Wurst W.
Genetic analysis of susceptibility to diabetes mellitus in F2-hybrids between diabetes-prone BB and various MHC-recombinant congenic rat strains.J Autoimmun,
4 (1991), 543-51.
[abstract]
Abstract:
The occurrence of diabetes mellitus was analysed in F2 hybrids bred from diabetic BB male rats and females of congenic rat strains carrying different major histocompatibility (RT1) haplotypes on the common LEW strain genetic background. Permissiveness for the disease in BB rats is probably determined by class II genes of the RT1 complex, which are also present in normal rats. Class I and class III genes, notably the Hsp70 genes in the class III region, do not appear to be involved. Among the diabetic F2 hybrids, about 90% are shown by DNA analysis to be homozygous for the class II genes of the permissive RT1 haplotype. The segregation patterns are in accord with the action of two independent recessive genes, one of them being RT1-linked.
Bürger J, Macek M, Stuhrmann M, Reis A, Krawczak M, Schmidtke J.
Genetic influences in the formation of nasal polyps.Lancet,
337 (1991), 974.
Wulbrand U, Dörk T, Tümmler B, Krawczak M.
Genetic determinants in cystic fibrosis.Lancet,
337 (1991), 623.
Krawczak M, Cooper DN.
Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment.Hum Genet,
86 (1991), 425-41.
[abstract]
Abstract:
Reports describing short (less than 20 bp) gene deletions causing human genetic disease were collated in order to study underlying causative mechanisms. Deletion breakpoint junction regions were found to be non-random both at the nucleotide and dinucleotide sequence levels, an observation consistent with an endogenous sequence-directed mechanism of mutagenesis. Direct repeats of between 2bp and 8bp were found in the immediate vicinity of all but one of the 60 deletions analysed. Direct repeats are a feature of a number of recombination, replication or repair-based models of deletion mutagenesis and the possible contribution of each to the spectrum of mutations examined was assessed. The influence of parameters such as repeat length and length of DNA between repeats was studied in relation to the frequency, location and extent of these deletions. Findings were broadly consistent with a slipped mispairing model but the predicted deletion of one whole repeat copy was found only rarely. A modified version of the slipped mispairing hypothesis was therefore proposed and was shown to possess considerable explanatory value for approximately 25% of deletions examined. Whereas the frequency of inverted repeats in the vicinity of gene deletions was not significantly elevated, these elements may nevertheless promote instability by facilitating the formation of secondary structure intermediates. A significant excess of symmetrical sequence elements was however found at sites of single base deletions. A new model to explain the involvement of symmetric elements in frameshift mutagenesis was devised, which successfully accounted for a majority of the single base deletions examined. In general, the loss of one or a few base pairs of DNA was found to be more compatible with a replication-based model of mutagenesis than with a recombination or repair hypothesis. Seven hitherto unrecognized hotspots for deletion were noted in five genes (AT3, F8, HBA, HBB and HPRT). Considerable sequence homology was found between these different sites, and a consensus sequence (TGA/GA/GG/TA/C) was drawn up. Sequences fitting this consensus (i) were noted in the immediate vicinity of 41% of the other (sporadic) gene deletions, (ii) were found frequently at sites of spontaneous deletion in the hamster APRT gene, (iii) were found to be associated with many larger human gene deletions/translocations, (iv) act as arrest sites for human polymerase alpha during DNA replication and (v) have been shown by in vitro studies of human polymerase alpha to be especially prone to frameshift mutation.(ABSTRACT TRUNCATED AT 400 WORDS)
Macek M, Vavrova V, Boehm I, Stuhrmann M, Reis A, Macek M, Duspisova R, Jelinkova E, Sperling K, Krawczak M.
Frequency of the delta-F508 mutation and flanking marker haplotypes at the cystic fibrosis locus from 167 Czech families.Adv Exp Med Biol,
290 (1991), 373-5.
Bal J, Maciejko D, Mazurczak T, Potocka A, Krawczak M, Reiss J.
Frequency of the cystic fibrosis mutation delta F508 in Poland.Hum Genet,
86 (1991), 329.
Stuhrmann M, Dörk T, Krawczak M, Dueck M, Banholzer U, Domagk J, Hoffknecht N, Posselt HG, Reis A, Schlösser M.
Genotype-phenotype correlations in cystic fibrosis patients.Adv Exp Med Biol,
290 (1991), 97-101; discussion 102-3.
[abstract]
Abstract:
Genetic and biomedical data from 346 cystic fibrosis patients of German origin have been evaluated. We demonstrated an age dependent distribution of CFTR genotypes, and confirmed the previously reported association between the dF508 mutation in the CFTR gene and pancreatic insufficiency. However 3 out of 22 pancreatic sufficient patients were dF508 homozygous. When patients were grouped with respect to height development, significant differences were seen in the distribution of J3.11-MspI alleles. We conclude that genetic determinants in and around the CFTR gene contribute to the variability in the clinical course of the disease.
Macek M, Vavrová V, Böhm I, Stuhrmann M, Reis A, Duspivová R, Macek M, Sperling K, Krawczak M, Schmidtke J.
Frequency of the delta F508 mutation and flanking marker haplotypes at the CF locus from 167 Czech families.Hum Genet,
85 (1990), 417-8.
[abstract]
Abstract:
This study analyses distribution patterns of the delta F508 mutation of the cystic fibrosis transmembrane conductance regulator gene (CFTR) gene and the cystic fibrosis (CF)-linked marker loci MET, D7S23, D7S399, and D7S8 in a sample of 167 (116 complete) CF families from Bohemia and Moravia (Czechoslovakia). DNA typing was performed by polymerase chain reaction amplification, restriction analysis, and agarose or polyacrylamide gel electrophoresis. The frequency of the delta F508 mutation in this sample is 67% and the frequency of the B haplotype is 77.6% on CF chromosomes. Linkage disequilibrium was found between delta F508 and all markers tested.
Reiss J, Schlösser M, Wagner M, Lenz U, Krawczak M, Ammann G, Klösser S, Böwing B.
[Direct genetic diagnosis in cystic fibrosis].Monatsschr Kinderheilkd,
138 (1990), 434-7.
[abstract]
Abstract:
The recent cloning of the cystic fibrosis gene and the simultaneous identification of the predominant mutation enabled direct gene diagnosis in the majority of all CF families. We demonstrate the superiority of now available direct genotyping in five individual cases.
Cooper DN, Krawczak M.
The mutational spectrum of single base-pair substitutions causing human genetic disease: patterns and predictions.Hum Genet,
85 (1990), 55-74.
[abstract]
Abstract:
Reports of single base-pair substitutions that cause human genetic disease and that have been located and characterized in an unbiased fashion were collated; 32% of point mutations were CG----TG or CG----CA transitions consistent with a chemical model of mutation via methylation-mediated deamination. This represents a 12-fold higher frequency than that predicted from random expectation, confirming that CG dinucleotides are indeed hotspots of mutation causing human genetic disease. However, since CG also appears hypermutable irrespective of methylation-mediated deamination, a second mechanism may also be involved in generating CG mutations. The spectrum of point mutations occurring outwith CG dinucleotides is also non-random, at both the mono- and dinucleotide, levels. An intrinsic bias in clinical detection was excluded since frequencies of specific amino acid substitutions did not correlate with the 'chemical difference' between the amino acids exchanged. Instead, a strong correlation was observed with the mutational spectrum predicted from the experimentally measured mispairing frequencies of vertebrate DNA polymerases alpha and beta in vitro. This correlation appears to be independent of any difference in the efficiency of enzymatic proofreading/mismatch-repair mechanisms but is consistent with a physical model of mutation through nucleotide misincorporation as a result of transient misalignment of bases at the replication fork. This model is further supported by an observed correlation between dinucleotide mutability and stability, possibly because transient misalignment must be stabilized long enough for misincorporation to occur. Since point mutations in human genes causing genetic disease neither arise by random error nor are independent of their local sequence environment, predictive models may be considered. We present a computer model (MUTPRED) based upon empirical data; it is designed to predict the location of point mutations within gene coding regions causing human genetic disease. The mutational spectrum predicted for the human factor IX gene was shown to resemble closely the observed spectrum of point mutations causing haemophilia B. Further, the model was able to predict successfully the rank order of disease prevalence and/or mutation rates associated with various human autosomal dominant and sex-linked recessive conditions. Although still imperfect, this model nevertheless represents an initial attempt to relate the variable prevalence of human genetic disease to the mutability inherent in the nucleotide sequences of the underlying genes.
Stuhrmann M, Macek M, Reis A, Schmidtke J, Tümmler B, Dörk T, Vavrova V, Macek M, Krawczak M.
Genotype analysis of cystic fibrosis patients in relation to pancreatic sufficiency.Lancet,
335 (1990), 738-9.
Reiss J, Krawczak M, Schloesser M, Wagner M, Cooper DN.
The effect of replication errors on the mismatch analysis of PCR-amplified DNA.Nucleic Acids Res,
18 (1990), 973-8.
[abstract]
Abstract:
The mismatch analysis of PCR-amplified DNA has generally assumed the absence of artificially introduced base substitutions in a significant proportion of the amplification product. This technique, however, differs from the direct sequencing of amplified DNA in that non-specific substitutions will render a molecule useless in analysis. The expected signal-to-noise ratio is heavily influenced by several parameters viz. initial template copy number, number of replication cycles, eventual product yield and the type of experimental system adopted. Mathematical modelling can be used to optimize fragment length with respect to the method applied and suggests as yet undescribed improvements such as partial modification or cleavage to optimize signal detection.
Jakubiczka S, Arnemann J, Cooke HJ, Krawczak M, Schmidtke J.
A search for restriction fragment length polymorphism on the human Y chromosome.Hum Genet,
84 (1989), 86-8.
[abstract]
Abstract:
A systematic search for restriction fragment length polymorphisms (RFLPs) on the human Y chromosome was performed. DNA samples from 16-34 individuals were screened with five restriction enzymes and 12 Y-chromosomal probes, 3 of which detect lowly repetitive sequences and 9 of which are apparently single copy in genomic DNA. None of the single-copy probes revealed any variation. The repetitive sequence probe p21A1 (DYZ?) revealed a TaqI RFLP with q = 0.05. The frequency of fixed point mutations in Y-chromosomal DNA outside the pseudoautosomal region is probably less than 1 in 18,000 bp.
Cooper DN, Krawczak M.
Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes.Hum Genet,
83 (1989), 181-8.
[abstract]
Abstract:
The dinucleotide CpG is a "hotspot" for mutation in the human genome as a result of (1) the modification of the 5' cytosine by cellular DNA methyltransferases and (2) the consequent high frequency of spontaneous deamination of 5-methyl cytosine (5mC) to thymidine. DNA methylation thus contributes significantly, albeit indirectly, to the incidence of human genetic disease. We have attempted to estimate for the first time the in vivo rate of deamination of 5mC from the measured rate of 5mC deamination in vitro and the known error frequency of the cellular G/T mismatch-repair system. The accuracy and utility of this estimate (md) was then assessed by comparison with clinical data, and an improved estimate of md (1.66 X 10(-16) s-1) was derived. Comparison of the CpG mutation rates exhibited by globin gene and pseudogene sequences from human, chimpanzee and macaque provided further estimates of md, all of which were consistent with the first. Use of this value in a mathematical model then permitted the estimation of the length of time required to produce the level of "CpG suppression" currently found in the "bulk DNA" of vertebrate genomes. This time span, approximately 450 million years, corresponds closely to the estimated time since the emergence and adaptive radiation of the vertebrates and thus coincides with the probable advent of heavily methylated genomes. An accurate estimate of the 5mC deamination rate is important not only for clinical medicine but also for studies of gene evolution. Our data suggest both that patterns of vertebrate gene methylation may be comparatively stable over relatively long periods of evolutionary time, and that the rate of CpG deamination can, under certain limited conditions, serve as a "molecular clock".
Reiss J, Krawczak M, Gal A, Zerres K, Kaiser R, Weber J.
[An at-risk pregnancy of a carrier of cystic fibrosis (mucoviscidosis) with a new partner].Monatsschr Kinderheilkd,
137 (1989), 451-3.
[abstract]
Abstract:
The mother of a girl affected by CF was pregnant in her second marriage with a new partner. We determined the fetal risk of being affected by means of enzyme testing, segregation analysis and haplotype association.
Wiedeking K, Schmidtke J, Krawczak M.
[Genetic counseling--not a short process. Gene diagnosis and the fate of the family--cystic fibrosis as an example].Fortschr Med,
107 (1989), 435-6.
Krawczak M, Reis A, Schmidtke J.
[Molecular genetics and diagnostic certainty--the example of cystic fibrosis].Dtsch Med Wochenschr,
114 (1989), 929-30.
Trefz FK, Lichter-Konecki U, Krawczak M, Schmidtke J, Dueck M, Nützenadel W, Konecki DS.
[DNA diagnosis of monogene hereditary diseases exemplified by phenylketonuria and mucoviscidosis].Monatsschr Kinderheilkd,
137 (1989), 201-7.
[abstract]
Abstract:
In 170 inherited diseases there exists the possibility for diagnosis at the DNA level. Using phenylketonuria (PKU) and cystic fibrosis (CF) as examples we demonstrate the capability of direct and indirect DNA-diagnosis through the use of DNA markers and allelespecific oligonucleotide hybridization respectively. In 88% of our PKU-patients and in 98% of the CF-patients DNA linkage analysis and therefore prenatal diagnosis on the DNA level can be carried out in affected families. The reliability of DNA-diagnosis is 99.0% for PKU and between 96.0-99.99% for CF depending on where the DNA-markers are localized. In contrast to CF, the PKU gene has been isolated and distinct mutations within the phenylalanine hydroxylase gene have been characterized. There is evidence for a correlation between genotype and clinical and biochemical phenotype. Also in CF it is indicated that certain DNA haplotypes correlate with the severity of the disease: less frequent haplotypes seem to be more often associated with a milder course than haplotype "B/B" which represents 85% of the CF chromosomes. Therefore DNA diagnostic methods not only make a major contribution to improved genetic counseling but also offer the possibility for a better future understanding of the heterogeneity of genetic diseases.
Krawczak M, Reiss J, Schmidtke J, Rösler U.
Polymerase chain reaction: replication errors and reliability of gene diagnosis.Nucleic Acids Res,
17 (1989), 2197-201.
[abstract]
Abstract:
The impact of replication errors on the reliability of polymerase chain reaction (PCR) data is studied theoretically. Practical applications of our results to RFLP analysis and oligonucleotide probing confirm that for practical purposes replication errors can be neglected if a large number of starting templates (e.g. 100,000) is being used. For single locus analysis in single cells, however, the probability of false diagnosis due to such errors is of the order of 1 percent.
Schmidtke J, Krawczak M.
Sex difference in D7S8 marker allele distribution in adult cystic fibrosis patients.Lancet,
1 (1989), 393.
Schwartz M, Super M, Schmidtke J, Buys C, Farrall M, Halley D, Krawczak M, Poncin JE, Loukopoulos D, Devoto M.
Prenatal diagnosis of cystic fibrosis using linked DNA probes.Prenat Diagn,
8 (1988), 619-24.
[abstract]
Abstract:
This paper presents data collected in Europe on 107 prenatal diagnoses of cystic fibrosis (CF) using linked DNA markers. To date, 38 children have been born without CF, as predicted, demonstrating the present rapid move from research to clinical genetic service.
Krawczak M.
Algorithms for the restriction-site mapping of DNA molecules.Proc Natl Acad Sci U S A,
85 (1988), 7298-301.
[abstract]
Abstract:
Two algorithms are described that rapidly construct restriction maps of DNA molecules from single- and double-digest data. The implementation of these algorithms into the Pascal programs AMAPK and AMARD allows such mapping to be done on microcomputers.
Krawczak M, Konecki DS, Schmidtke J, Dück M, Engel W, Nützenadel W, Trefz FK.
Allelic association of the cystic fibrosis locus and two DNA markers, XV2c and KM19, in 55 German families.Hum Genet,
80 (1988), 78-80.
[abstract]
Abstract:
Allelic association between cystic fibrosis and two linked markers is demonstrated in a sample of 55 German families. It is shown by example how these observations can be used for genetic risk calculation.
Gellert G, Peterson J, Krawczak M, Zoll B.
Linkage relationship between retinoschisis and four marker loci.Hum Genet,
79 (1988), 382-4.
[abstract]
Abstract:
The linkage relationship between the locus for juvenile retinoschisis (RS) and four X-chromosomal marker loci DXS9 (RC8), DXS16 (XUT23), DXS41 (99-6), and DXS43 (D2) has been studied in six families showing a history of this disease. Recombination with RS was found for all marker loci except DXS9. The maximum lod score is zeta = 2.66 for RS vs. DXS9 at a recombination fraction of theta = 0.0. Multipoint linkage analysis was performed and the locus order best supported by our data is: RS - DXS9 - DXS43 - DXS16 - DXS41.
Schmidtke J, Krawczak M.
[Prenatal diagnosis of cystic fibrosis with molecular genetic methods].Gynakologe,
21 (1988), 119-24.
Böhm D, Krawczak M, Schmidtke J.
Linkage of the DNA-segment D7S13 (pB79a) with the cystic fibrosis locus.Hum Genet,
78 (1988), 186-7.
[abstract]
Abstract:
A map distance of 2.9 cM between D7S13 (pB79a) and the cystic fibrosis (CF) locus was obtained from the analysis of 13 informative families with a history of CF. This result is based solely on the HindIII restriction fragment length polymorphism (HindIII-RFLP) at D7S13, since the interpretation of the MspI-RFLP at this locus was found to be unreliable.
Schmidtke J, Krawczak M.
[Prenatal diagnosis of cystic fibrosis with recombinant DNA methods].Monatsschr Kinderheilkd,
135 (1987), 805-10.
[abstract]
Abstract:
Cystic fibrosis is one of the commonest genetic disorders with about 1 in 3000 newborns being affected. The molecular etiology of the disease is still not known. In spite of improved therapy the life expectancy is markedly reduced. Many parents of a child affected by CF request a prenatal diagnosis, when a further child is expected. By using molecular genetic methods the prenatal detection of CF is possible now with great accuracy in most families. This review describes the principles of the genetics and the diagnosis of the disease. Case reports illustrate risk figure ascertainment. Preconditions for performing the diagnosis in individual cases are outlined, and a guide to the practical approach is given.
Schmidtke J, Krawczak M, Schwartz M, Alkan M, Bonduelle M, Bühler E, Chemke M, Darnedde T, Domagk J, Engel W.
Linkage relationships and allelic associations of the cystic fibrosis locus and four marker loci.Hum Genet,
76 (1987), 337-43.
[abstract]
Abstract:
The linkage relationships between the cystic fibrosis (CF) locus and four marker loci (MET-H, MET-D, D7S8 and D7S16), allelic associations between these loci and the extent of informativity at these marker loci were investigated in a sample of 206 families with at least one child affected by CF. The data were contributed by 11 laboratories from Europe and Israel. The maximum lod scores and recombination frequency estimates (luminal diameter) (and confidence limits of luminal diameter) were: 18.3 at luminal diameter = 0.007 (0.001-0.038) for CF vs. MET, 11.0 at luminal diameter = 0.016 (0.001-0.068) for CF vs. D7S8, and 5.7 at luminal diameter = 0.0 (0.0-0.064) for CF vs. D7S16. A gene order of CF-MET-D7S8 was best supported by the data, but its preference to the order D7S8-CF-MET is mainly based on one single family. There are significant allelic associations between CF, MET, D7S8 and D7S16; these allelic associations affect the risk of random individuals to be carriers of CF.
Krawczak M.
Genetic risk and recombination fraction--an example of non-monotonic dependency.Hum Genet,
75 (1987), 189-90.
[abstract]
Abstract:
The carrier risk for a monogenic disease is not generally monotonously dependent on the recombination fraction between the disease locus and a single marker locus.
Wilichowski E, Krawczak M, Seemanova E, Hanefeld F, Schmidtke J.
Genetic linkage study between the loci for Duchenne and Becker muscular dystrophy and nine X-chromosomal DNA markers.Hum Genet,
75 (1987), 32-40.
[abstract]
Abstract:
A set of nine polymorphic loci defined by DNA probes was studied for linkage with the disease locus in ten families with a history of Duchenne muscular dystrophy (DMD), and three families with a history of Becker muscular dystrophy (BMD). The results confirm DMD and BMD linkage to all marker loci and suggest closer linkage of several probes than hitherto detected. This will be of practical interest for risk calculations in affected families.
Schmidtke J, Krawczak M, Cooper DN.
Human gene cloning: the storm before the lull?.Nature,
322 (1986 Jul 10-16), 119.
Zoll B, Arnemann J, Krawczak M, Cooper DN, Pescia G, Wahli W, Steinbach P, Schmidtke J.
Evidence against close linkage of the loci for fraXq of Martin-Bell syndrome and for factor IX.Hum Genet,
71 (1985), 122-6.
[abstract]
Abstract:
Linkage between the loci for fraXq of Martin-Bell syndrome and factor IX was studied in nine families exhibiting this syndrome by means of a restriction fragment length polymorphism at the factor IX locus. Computer analysis of the data indicates there to be no evidence for close linkage between the syndrome and the factor IX locus.
