Publikationen von Michael Nothnagel
Rubin D, Helwig U, Pfeuffer M, Auinger A, Ruether A, Matusch D, Darabaneanu S, Freitag-Wolf S, Nothnagel M, Schreiber S, Schrezenmeir J.
The effect of FABP2 promoter haplotype on response to a diet with medium-chain triacylglycerols.Genes Nutr,
(2012).
[abstract]
Abstract:
The fatty-acid-binding protein-2 (FABP2) gene has been proposed as a candidate gene for diabetes because the encoded protein is involved in fatty acid absorption and therefore may affect insulin sensitivity and glucose metabolism. The rare haplotype (B) of its promoter was shown to be associated with a lower risk for type 2 diabetes. The aim of this study was to investigate whether a polymorphism in the FABP2 promoter does affect the metabolic response to either an medium-chain triacylglycerol (MCT) or an long-chain triacylglycerol (LCT) diet, which were suggested to differ in transport mechanisms, in affinity to FABP2, in activating transcription factors binding to the FABP2 promoter and in their effects on insulin sensitivity. We studied 82 healthy male subjects varying in the FABP2 promoter (42 homozygous for common haplotype (A), 40 homozygous for the rare haplotype (B)) in an interventional study with either an MCT or LCT diet over 2 weeks to examine gene-nutrient interaction. The saturation grade of MCT was adjusted to that of the LCT fat. We determined glucose, insulin, triacylglycerols (TGs), chylomicron triacylglycerols and cholesterol before and after a standardised mixed meal before and after the intervention. HDL cholesterol increased in all groups, which was most pronounced in subjects homozygous for the common promoter haplotype A who received MCT diet (P = 0.001), but not significant in homozygous rare haplotype B subjects who received MCT fat. Subjects homozygous for FABP2 haplotype A showed a significant decrease in fasting and postprandial glucose (P = 0.01, 0.04, respectively) and a decrease in insulin resistance (HOMA-IR, P = 0.04) during LCT diet. After correction for multiple testing, those effects did not remain significant. Fasting and postprandial triacylglycerols, LDL cholesterol, chylomicron TGs and cholesterol were not affected by genotype or diet. MCT diet increased HDL cholesterol dependent on the FABP2 promoter haplotype. The effects of the promoter haplotype B could be mediated by PPARγ, which is upregulated by medium-chain fatty acids.
Ellinghaus D, Ellinghaus E, Nair RP, Stuart PE, Esko T, Metspalu A, Debrus S, Raelson JV, Tejasvi T, Belouchi M, West SL, Barker JN, Kõks S, Kingo K, Balschun T, Palmieri O, Annese V, Gieger C, Wichmann HE, Kabesch M, Trembath RC, Mathew CG, Abecasis GR, Weidinger S, Nikolaus S, Schreiber S, Elder JT, Weichenthal M, Nothnagel M, Franke A.
Combined Analysis of Genome-wide Association Studies for Crohn Disease and Psoriasis Identifies Seven Shared Susceptibility Loci.Am J Hum Genet,
90 (2012), 636-47.
[abstract]
Abstract:
Psoriasis (PS) and Crohn disease (CD) have been shown to be epidemiologically, pathologically, and therapeutically connected, but little is known about their shared genetic causes. We performed meta-analyses of five published genome-wide association studies on PS (2,529 cases and 4,955 controls) and CD (2,142 cases and 5,505 controls), followed up 20 loci that showed strongest evidence for shared disease association and, furthermore, tested cross-disease associations for previously reported PS and CD risk alleles in additional 6,115 PS cases, 4,073 CD cases, and 10,100 controls. We identified seven susceptibility loci outside the human leukocyte antigen region (9p24 near JAK2, 10q22 at ZMIZ1, 11q13 near PRDX5, 16p13 near SOCS1, 17q21 at STAT3, 19p13 near FUT2, and 22q11 at YDJC) shared between PS and CD with genome-wide significance (p < 5 × 10(-8)) and confirmed four already established PS and CD risk loci (IL23R, IL12B, REL, and TYK2). Three of the shared loci are also genome-wide significantly associated with PS alone (10q22 at ZMIZ1, p(rs1250544) = 3.53 × 10(-8), 11q13 near PRDX5, p(rs694739) = 3.71 × 10(-09), 22q11 at YDJC, p(rs181359) = 8.02 × 10(-10)). In addition, we identified one susceptibility locus for CD (16p13 near SOCS1, p(rs4780355) = 4.99 × 10(-8)). Refinement of association signals identified shared genome-wide significant associations for exonic SNPs at 10q22 (ZMIZ1) and in silico expression quantitative trait locus analyses revealed that the associations at ZMIZ1 and near SOCS1 have a potential functional effect on gene expression. Our results show the usefulness of joint analyses of clinically distinct immune-mediated diseases and enlarge the map of shared genetic risk loci.
Nothnagel M, Szibor R, Vollrath O, Augustin C, Edelmann J, Geppert M, Alves C, Gusmão L, Vennemann M, Hou Y, Immel UD, Inturri S, Luo H, Lutz-Bonengel S, Robino C, Roewer L, Rolf B, Sanft J, Shin KJ, Sim JE, Wiegand P, Winkler C, Krawczak M, Hering S.
Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome.Forensic Sci Int Genet,
(2012).
[abstract]
Abstract:
A large number of short tandem repeat (STR) markers spanning the entire human X chromosome have been described and established for use in forensic genetic testing. Due to their particular mode of inheritance, X-STRs often allow easy and informative haplotyping in kinship analyses. Moreover, some X-STRs are known to be tightly linked so that, in combination, they constitute even more complex genetic markers than each STR taken individually. As a consequence, X-STRs have proven particularly powerful in solving complex cases of disputed blood relatedness. However, valid quantification of the evidence provided by X-STR genotypes in the form of likelihood ratios requires that the recombination rates between markers are exactly known. In a collaborative family study, we used X-STR genotype data from 401 two- and three-generation families to derive valid estimates of the recombination rates between 12 forensic markers widely used in forensic testing, namely DXS10148, DXS10135, DXS8378 (together constituting linkage group I), DXS7132, DXS10079, DXS10074 (linkage group II), DXS10103, HPRTB, DXS10101 (linkage group III), DXS10146, DXS10134 and DXS7423 (linkage group IV). Our study is the first to simultaneously allow for mutation and recombination in the underlying likelihood calculations, thereby obviating the bias-prone practice of excluding ambiguous transmission events from further consideration. The statistical analysis confirms that linkage groups I and II are transmitted independently from one another whereas linkage groups II, III and IV are characterised by inter-group recombination fractions that are notably smaller than 50%. Evidence was also found for recombination within all four linkage groups, with recombination fraction estimates ranging as high as 2% in the case of DXS10146 and DXS10134.
Quednow BB, Brinkmeyer J, Mobascher A, Nothnagel M, Musso F, Gründer G, Savary N, Petrovsky N, Frommann I, Lennertz L, Spreckelmeyer KN, Wienker TF, Dahmen N, Thuerauf N, Clepce M, Kiefer F, Majic T, Mössner R, Maier W, Gallinat J, Diaz-Lacava A, Toliat MR, Thiele H, Nürnberg P, Wagner M, Winterer G.
Schizophrenia risk polymorphisms in the TCF4 gene interact with smoking in the modulation of auditory sensory gating.Proc Natl Acad Sci U S A,
(2012).
[abstract]
Abstract:
Several polymorphisms of the transcription factor 4 (TCF4) have been shown to increase the risk for schizophrenia, particularly TCF4 rs9960767. This polymorphism is associated with impaired sensorimotor gating measured by prepulse inhibition-an established endophenotype of schizophrenia. We therefore investigated whether TCF4 polymorphisms also affect another proposed endophenotype of schizophrenia, namely sensory gating assessed by P50 suppression of the auditory evoked potential. Although sensorimotor gating and sensory gating are not identical, recent data suggest that they share genetic fundamentals. In a multicenter study at six academic institutions throughout Germany, we applied an auditory P50 suppression paradigm to 1,821 subjects (1,023 never-smokers, 798 smokers) randomly selected from the general population. Samples were genotyped for 21 TCF4 polymorphisms. Given that smoking is highly prevalent in schizophrenia and affects sensory gating, we also assessed smoking behavior, cotinine plasma concentrations, exhaled carbon monoxide, and the Fagerström Test (FTND). P50 suppression was significantly decreased in carriers of schizophrenia risk alleles of the TCF4 polymorphisms rs9960767, rs10401120rs, rs17597926, and 17512836 (P < 0.0002-0.00005). These gene effects were modulated by smoking behavior as indicated by significant interactions of TCF4 genotype and smoking status; heavy smokers (FTND score ≥4) showed stronger gene effects on P50 suppression than light smokers and never-smokers. Our finding suggests that sensory gating is modulated by an interaction of TCF4 genotype with smoking, and both factors may play a role in early information processing deficits also in schizophrenia. Consequently, considering smoking behavior may facilitate the search for genetic risk factors for schizophrenia.
Helbig KL, Nothnagel M, Hampe J, Balschun T, Nikolaus S, Schreiber S, Franke A, Nothlings U.
A case-only study of gene-environment interaction between genetic susceptibility variants in NOD2 and cigarette smoking in Crohn's disease aetiology.BMC Med Genet,
13 (2012), 14.
[abstract]
Abstract:
ABSTRACT: BACKGROUND: Genetic variation in NOD2 and cigarette smoking are well-established risk factors for the development of Crohn's disease (CD). However, little is known about a potential interaction between these risk factors. We investigated gene-environment interactions between CD-associated NOD2 alleles and cigarette smoking in a large sample of patients with CD. METHODS: Three previously reported CD-associated variants in NOD2 (R702W, G908R, 1007fs) were genotyped in 1636 patients with CD continuously recruited between 1995 and 2010 based on physician referral. Data on history of smoking behaviour was obtained for all participants through a written questionnaire. Using a case-only design, we performed logistic regression analyses to investigate statistical interactions between NOD2 risk alleles and smoking status. RESULTS: We detected a significant negative interaction between carriership of at least one of the NOD2 risk alleles and history of ever having smoked (OR = 0.71; p = 0.005) as well as smoking at the time of CD diagnosis (OR = 0.68; p = 0.005). Subsequent separate analyses of the three variants revealed a significant negative interaction between the 1007fs variant and history of ever having smoked (OR = 0.64; p = 9 x 104) and smoking at the time of CD diagnosis (OR = 0.53; p = 7 x 105). CONCLUSIONS: The observed significant negative gene-environment interaction suggests that the risk increase for CD conferred simultaneously by cigarette smoking and the 1007fs NOD2 polymorphism is smaller than expected and may point to a biological interaction. Our findings warrant further investigation in epidemiological and functional studies to elucidate pathophysiology as well as to aid in the development of recommendations for disease prevention.
Brosch M, von Schönfels W, Ahrens M, Nothnagel M, Krawczak M, Laudes M, Sipos B, Becker T, Schreiber S, Röcken C, Schafmayer C, Hampe J.
SFRS10-A Splicing Factor Gene Reduced in Human Obesity?.Cell Metab,
15 (2012), 265-6.
Richter GM, Graetz C, Pohler P, Nothnagel M, Dommisch H, Laine ML, Folwaczny M, Noack B, Eickholz P, Groessner-Schreiber B, Jepsen S, Loos BG, Schreiber S, Schaefer AS.
Common genetic risk variants of TLR2 are not associated with periodontitis in large European case-control populations.J Clin Periodontol,
39 (2012), 315-22.
[abstract]
Abstract:
Common LD regions of TLR2 do not show genetic associations with periodontitis in the North West European population. Resequencing of exon 3 could not identify disease-associated rare variants in TLR2.
Schaefer AS, Richter GM, Dommisch H, Reinartz M, Nothnagel M, Noack B, Laine ML, Folwaczny M, Groessner-Schreiber B, Loos BG, Jepsen S, Schreiber S.
CDKN2BAS is associated with periodontitis in different European populations and is activated by bacterial infection.J Med Genet,
48 (2011), 38-47.
[abstract]
Abstract:
Epidemiological studies have indicated a relationship between coronary heart disease (CHD) and periodontitis. Recently, CDKN2BAS was reported as a shared genetic risk factor of CHD and aggressive periodontitis (AgP), but the causative variant has remained unknown. To identify and validate risk variants in different European populations, we first explored 150 kb of the genetic region of CDKN2BAS including the adjacent genes CDKN2A and CDKN2B, covering 51 tagging single nucleotide polymorphisms (tagSNPs) in AgP and chronic periodontitis (CP) in individuals of Dutch origin (n=313). In a second step, we tested the significant SNP associations in an independent AgP and CP population of German origin (n=1264). For the tagSNPs rs1360590, rs3217992, and rs518394, we could validate the associations with AgP before and after adjustment for the covariates smoking, gender and diabetes, with SNP rs3217992 being the most significant (OR 1.48, 95% CI 1.19 to 1.85; p=0.0004). We further showed in vivo gene expression of CDKN2BAS, CDKN2A, CDKN2B, and CDK4 in healthy and inflamed gingival epithelium (GE) and connective tissue (CT), and detected a significantly higher expression of CDKN2BAS in healthy CT compared to GE (p=0.004). After 24 h of stimulation with Porphyromonas gingivalis in Streptococcus gordonii pre-treated gingival fibroblast (HGF) and cultured gingival epithelial cells (GECs), we observed a 25-fold and fourfold increase of CDKN2BAS gene expression in HGFs (p=0.003) and GECs (p=0.004), respectively. Considering the global importance of CDKN2BAS in the disease risk of CHD, this observation supports the theory of inflammatory components in the disease physiology of CHD.
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.
Herrmann A, Haake A, Ammerpohl O, Martin-Guerrero I, Szafranski K, Stemshorn K, Nothnagel M, Kotsopoulos SK, Richter J, Warner J, Olson J, Link DR, Schreiber S, Krawczak M, Platzer M, Nürnberg P, Siebert R, Hampe J.
Pipeline for Large-Scale Microdroplet Bisulfite PCR-Based Sequencing Allows the Tracking of Hepitype Evolution in Tumors.PLoS One,
6 (2011), e21332.
[abstract]
Abstract:
Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into "hepitypes" and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer.
Thier S, Kuhlenbäumer G, Lorenz D, Nothnagel M, Nebel A, Christensen K, Schreiber S, Deuschl G, Klebe S.
GABA(A) receptor- and GABA transporter polymorphisms and risk for essential tremor.Eur J Neurol,
18 (2011), 1098-100.
[abstract]
Abstract:
Background: Clinical features and animal models of essential tremor (ET) suggest gamma-aminobutyric acid A receptor (GABA(A) R) subunits and GABA transporters as putative candidate genes. Methods: A total of 503 ET cases and 818 controls were investigated for an association between polymorphisms in 15 GABA(A) R and four GABA transporter genes and ET. Results: Nine nominally significant tagging SNPs (P values from 4.9 × 10(-2) to 5.2 × 10(-4) ) were found in the hypothesis generation stage. Five SNPs were followed up in a second verification stage but failed to reach significance. (P values from 0.30 to 0.77). Discussion: In our samples, no evidence of association between GABA(A) R and GABA transporter genes with ET was detected. Further studies are necessary to clarify the role of these genes in ET.
Dolmans GH, Werker PM, Hennies HC, Furniss D, Festen EA, Franke L, Becker K, van der Vlies P, Wolffenbuttel BH, Tinschert S, Toliat MR, Nothnagel M, Franke A, Klopp N, Wichmann HE, Nürnberg P, Giele H, Ophoff RA, Wijmenga C, .
Wnt Signaling and Dupuytren's Disease.N Engl J Med,
(2011).
[abstract]
Abstract:
Background Dupuytren's disease is a benign fibromatosis of the hands and fingers that leads to flexion contractures. We hypothesized that multiple genetic and environmental factors influence susceptibility to this disease and sought to identify susceptibility genes to better understand its pathogenesis. Methods We conducted a genomewide association study of 960 Dutch persons with Dupuytren's disease and 3117 controls (the discovery set) to test for association between the disease and genetic markers. We tested the 35 single-nucleotide polymorphisms (SNPs) most strongly associated with Dupuytren's disease (P<1×10(-4)) in the discovery set in three additional, independent case series comprising a total of 1365 affected persons and 8445 controls from Germany, the United Kingdom, and the Netherlands. Results Initially, we observed a significant genomewide association between Dupuytren's disease and 8 SNPs at three loci. Tests of replication and joint analysis of all data from 2325 patients with Dupuytren's disease and 11,562 controls yielded an association with 11 SNPs from nine different loci (P<5.0×10(-8)). Six of these loci contain genes known to be involved in the Wnt-signaling pathway: WNT4 (rs7524102) (P=2.8×10(-9); odds ratio, 1.28), SFRP4 (rs16879765) (P=5.6×10(-39); odds ratio, 1.98), WNT2 (rs4730775) (P=3.0×10(-8); odds ratio, 0.83), RSPO2 (rs611744) (P=7.9×10(-15); odds ratio, 0.75), SULF1 (rs2912522) (P=2.0×10(-13); odds ratio, 0.72), and WNT7B (rs6519955) (P=3.2×10(-33); odds ratio, 1.54). Conclusions This study implicates nine different loci involved in genetic susceptibility to Dupuytren's disease. The fact that six of these nine loci harbor genes encoding proteins in the Wnt-signaling pathway suggests that aberrations in this pathway are key to the process of fibromatosis in Dupuytren's disease.
Hofmann S, Fischer A, Till A, Müller-Quernheim J, Häsler R, Franke A, Gäde KI, Schaarschmidt H, , Rosenstiel P, Nebel A, Schürmann M, Nothnagel M, Schreiber S.
A genome-wide association study reveals evidence of association with sarcoidosis at 6p12.1.Eur Respir J,
(2011).
[abstract]
Abstract:
Sarcoidosis is a complex systemic inflammatory disease of unknown aetiology that is influenced by a variety of genetic and environmental factors. To identify further susceptibility loci for sarcoidosis, a genome-wide association study was conducted in 381 patients and 392 control individuals based on Affymetrix 100k GeneChip data. The top 25 SNPs were selected for validation in an independent study panel (1,582 patients vs. 1,783 controls). Variant rs10484410 on chromosome 6p12.1 was significantly associated, with a Bonferroni-corrected p value of 2.90×10(-2) in the validation sample and a nominal p value of 2.64×10(-4) in the GWAS. Extensive fine mapping of the novel locus narrowed down the signal to a region comprising the genes BAG2, C6orf65, KIAA1586, ZNF451 and RAB23. Verification of the sarcoidosis associated non-synonymous SNP rs1040461 in a further independent case-control sample and quantitative mRNA expression studies point to the RAB23 gene as the most likely risk factor. RAB23 is proposed to be involved in antibacterial defence processes and regulation of the sonic hedgehog signalling pathway. The identified association of the 6p12.1 locus with sarcoidosis implicates this locus as a further susceptibility factor, and RAB23 as a potential signalling component that may open up new perspectives in the pathophysiology of sarcoidosis.
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,
132 (2011), 324-30.
[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.
Thier S, Lorenz D, Nothnagel M, Stevanin G, Dürr A, Nebel A, Schreiber S, Kuhlenbäumer G, Deuschl G, Klebe S.
LINGO1 polymorphisms are associated with essential tremor in Europeans.Mov Disord,
25 (2010), 709-15.
[abstract]
Abstract:
Essential tremor (ET) is one of the most common movement disorders. Former association studies focussing on candidate genes in ET found a number of risk variants but most of them were not replicated. Recently, a genome-wide association study revealed two intronic sequence variants in the LINGO1 gene associated with ET. Here, we have confirmed association between sequence variants in the LINGO1 gene and the ET phenotype in independent German and French ET samples. The odds ratios for the identified intronic markers rs8030859 (P = 1.0x10(-4)), rs9652490 (P = 9.1x10(-4)), and rs11856808 (P = 3.6x10(-2)) were 1.72 (CI 1.31-2.26), 1.61 (CI 1.21-2.14), and 1.30 (CI 1.02-1.66), respectively, in our German sample. LINGO1 is an interesting candidate gene because it plays a key role in central nervous system biology, is selectively expressed in the nervous system, and is an inhibitor of oligodendrocyte differentiation and neuronal myelination. Our study gives further evidence that LINGO1 acts as a susceptibility gene for ET.
Fischer A, Nothnagel M, Schürmann M, Müller-Quernheim J, Schreiber S, Hofmann S.
A genome-wide linkage analysis in 181 German sarcoidosis families using clustered bi-allelic markers.Chest,
(2010).
[abstract]
Abstract:
Abstract BACKGROUND: Sarcoidosis (SA) is a systemic granulomatous inflammatory disorder with complex etiology and strong clustering in families. Genome-wide association studies have been successful in the identification of common risk variants for the disease. To reveal susceptibility variants with low frequencies but strong effects, we performed a genome-wide linkage scan in a large sample of SA families. METHODS: We genotyped 528 members of 181 German SA families for 3882 single nucleotide polymorphism (SNP) assays from the SNPlex System Human Linkage Mapping Set 4K (Applied Biosystems). RESULTS: Non-parametric linkage analysis revealed one region of suggestive linkage on chromosome 12p13.31 at 20 cM (LOD = 2.53; local P value (p(L)) = 0.0003) and another linkage peak of nearly suggestive linkage on 9q33.1 at 134 cM (LOD = 2.12; p(L) = 0.0009). The latter has been reported to show suggestive evidence for linkage in a sample of 229 African-American SA families before. Analysis of acute and chronically affected families revealed a subphenotype-specific linkage pattern and an additional, nearly suggestive linkage peak on chromosome 16p13.11 at 38 cM (LOD = 2.09; p(L) = 0.001), which was confined to acute SA. CONCLUSIONS: Our results propose that the respective regions might harbor r yet unidentified, possibly subphenotype-specific risk factors for the disease, e.g. with immune-related functions like the tumor necrosis factor receptor 1. They should be proved to be important for SA pathogenesis and investigated in detail with an emphasis on rare variants. Subphenotype-specific risk factors might serve for prognosis of the clinical course of the disease.
Schaefer AS, Richter GM, Nothnagel M, Laine ML, Noack B, Glas J, Schrezenmeir J, Groessner-Schreiber B, Jepsen S, Loos BG, Schreiber S.
COX-2 is Associated with Periodontitis in Europeans.J Dent Res,
(2010).
[abstract]
Abstract:
COX-2 plays an important role in periodontitis by mediating inflammatory reactions in periodontal tissues, and the COX-2 polymorphisms rs20417 and rs689466 have been reported to be associated with periodontitis in populations of Taiwanese and Chinese ethnicity. To test whether these variants were associated with periodontitis in populations of European ethnicity, we genotyped the single-nucleotide polymorphisms (SNPs) rs689466 and rs6681231, the latter a haplotype tagging SNP (htSNP) for rs20417 (r(2)>0.95), in our large-analysis population of individuals with aggressive (n = 532) and chronic periodontitis (n = 1052), and 2873 healthy control individuals. The rare G allele of htSNP rs6681231 was associated with aggressive periodontitis prior to and after adjustment for the covariates smoking, diabetes, and gender, with an odds ratio of 1.57 (95% confidence interval 1.18-2.08; p = 0.002). The validation of the association of rs20417 by the htSNP rs6681231 provides evidence for a general genetic risk of COX-2 variants in the pathogenesis of periodontitis.
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.
Schaefer AS, Richter GM, Nothnagel M, Manke T, Dommisch H, Jacobs G, Arlt A, Rosenstiel P, Noack B, Groessner-Schreiber B, Jepsen S, Loos BG, Schreiber S.
A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis.Hum Mol Genet,
19 (2010), 553-62.
[abstract]
Abstract:
Periodontitis is a widespread, complex inflammatory disease of the mouth, which results in a loss of gingival tissue and alveolar bone, with aggressive periodontitis (AgP) as its most severe form. To identify genetic risk factors for periodontitis, we conducted a genome-wide association study in German AgP patients. We found AgP to be strongly associated with the intronic SNP rs1537415, which is located in the glycosyltransferase gene GLT6D1. We replicated the association in a panel of Dutch generalized and localized AgP patients. In the combined analysis including 1758 subjects, rs1537415 reached a genome-wide significance level of P= 5.51 x 10(-9), OR = 1.59 (95% CI 1.36-1.86). The associated rare G allele of rs1537415 showed an enrichment of 10% in periodontitis cases (48.4% in comparison with 38.8% in controls). Fine-mapping and a haplotype analysis indicated that rs1537415 showed the strongest association signal. Sequencing identified no further associated variant. Tissue-specific expression analysis of GLT6D1 indicated high transcript levels in the leukocytes, the gingiva and testis. Analysis of potential transcription factor binding sites at this locus predicted a significant reduction of GATA-3 binding affinity, and an electrophoretic mobility assay indicated a T cell specific reduction of protein binding for the G allele. Overexpression of GATA-3 in HEK293 cells resulted in allele-specific binding of GATA-3, indicating the identity of GATA-3 as the binding protein. The identified association of GLT6D1 with AgP implicates this locus as an important susceptibility factor, and GATA-3 as a potential signaling component in the pathophysiology of periodontitis.
Rubin D, Helwig U, Nothnagel M, Fölsch U, Schreiber S, Schrezenmeir J.
Association of postprandial and fasting triglycerides with traits of the metabolic syndrome in the Metabolic Intervention Cohort Kiel (MICK).Eur J Endocrinol,
(2010).
[abstract]
Abstract:
Objective Postprandial (pp) lipid metabolism is associated with insulin resistance and diabetes type 2. In young men, pp triglycerides (TG) were stronger associated with parameters of the metabolic syndrome (MS) than fasting TG. We established a cohort of middle-aged men who were characterised for traits of the metabolic syndrome and pp lipid metabolism to determine if fasting or pp TG are most related to the MS. Research Design and Methods 1558 men were characterised for the MS. 755 underwent an oral metabolic tolerance test (OMTT) as a standardized high fat meal and an oral glucose tolerance test (OGTT). Blood samples were drawn in the fasting state and hourly until 9 hours for determination of TG and free fatty acids (FFA). Glucose and insulin were analysed until 5 hours pp. Results In the overall cohort 329 subjects (21.1%) had a complete MS referred to ATP III criteria and 650 (41.7%) subjects to IDF criteria. The association of pp TG with parameters of the MS was not stronger than association with fasting TG. Pp TG were independently associated with ss-cell function. Conclusions Pp TG did not show a higher correlation with features of the MS than fasting values. This finding is probably due to the high incidence of overweight in this middle-aged population.
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.
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.
Klebe S, Thier S, Lorenz D, Nothnagel M, Schreiber S, Klein C, Hagenah J, Kasten M, Berg D, Srulijes K, Gasser T, Deuschl G, Kuhlenbäumer G.
LINGO1 is not associated with Parkinson's disease in German patients.Am J Med Genet B Neuropsychiatr Genet,
(2010).
[abstract]
Abstract:
Essential tremor (ET) and Parkinson's disease (PD) are the most common movement disorders and show clinical, genetic, and pathophysiological overlap. Single-nucleotide polymorphisms (SNPs) in the leucine-rich repeat (LRR) and immunoglobulin (Ig) domain-containing, Nogo receptor-interacting protein gene (LINGO1) are associated with ET. LINGO1 is overexpressed in the substantia nigra (SN) of PD patients and inhibition of LINGO1 confers neuroprotection in a rodent model of PD. In this study we test the hypothesis whether SNPs in the LINGO1 gene that are associated with ET are also associated with PD. Three large German case-control samples from Kiel, Lübeck, and Tübingen (total: 1,798 cases and 1,482 controls) were genotyped for the three LINGO1 SNPs associated with ET. Association was assessed using allele- and genotype-based tests in each of the three samples separately, in the combined sample, and in subsets of patients with early-onset PD (<50 years) and of patients with a positive family history of PD. Neither of the three samples alone nor the combined sample showed evidence for association between LINGO1 SNPs and PD. The allele-based test showed a trend toward nominal association for all three SNPs in the Kiel sample. The subsets with early-onset PD or a positive family history did also not reveal evidence for association. SNPs in the LINGO1 gene associated with ET could not be shown to be associated with PD in our study population, despite a postulated overlap between both diseases. (c) 2010 Wiley-Liss, Inc.
Buch S, Schafmayer C, Völzke H, Seeger M, Miquel JF, Sookoian SC, Egberts JH, Arlt A, Pirola CJ, Lerch MM, John U, Franke A, von Kampen O, Brosch M, Nothnagel M, Kratzer W, Boehm BO, Bröring CD, Schreiber S, Krawczak M, Hampe J.
Loci from a genome-wide analysis of bilirubin levels are associated with gallstone risk and composition.Gastroenterology,
(2010).
[abstract]
Abstract:
BACKGROUND & AIMS:: Genome-wide association studies have mapped loci that are associated with serum levels of bilirubin. Bilirubin is a major component of gallstones, so we investigated whether these variants predict gallstone bilirubin content and overall risk for gallstones. METHODS:: Loci that were identified in a meta-analysis to meet a genome-wide significance level of P<1.0×10(-7) (UGT1A1, SLCO1B1, LST-3TM12, SLCO1A2) were analyzed in 1018 individuals with known gallstone composition. Gallstone risk was analyzed in 2606 German individuals that received operations for gallstone disease and 1121 controls and replicated in 210 cases and 496 controls from South America. RESULTS:: Using the presence of bilirubin as a phenotype, variants rs6742078 (UGT1A1, P=0.003), rs4149056 (SLCO1B1, P=0.003), and rs4149000 (SLCO1A2, P=0.015) were associated with gallstone composition. In regression analyses, only UGT1A1 and SLCO1B1 were independently retained in the model (r(2)(rs4149056_rs4149000)=0.66). UGT1A1 (rs6742078, P=0.018) was associated with overall gallstone risk. In a sex-stratified, post-hoc analysis, only male carriers of rs6742078 had an increased risk for gallstone disease (P=2.1×10(-7); OR(recessive)=2.34; P(women)=0.47). The sex-specific association of rs6742078 was confirmed in samples from South America (P(men)=0.046; OR(rec)=2.19, P(women)=0.96). CONCLUSION:: The UGT1A1 Gilbert syndrome variant rs6742078 is associated with gallstone disease in men; further studies are required into the sex-specific physiology of bilirubin and bile acid metabolism. Most gallstones associated with UGT1A1 variants are cholesterol gallstones, indicating the role of pigment particles in the pathogenesis of gallstone disease-possibly as nucleation factors. Variants of ABCG8 and UGT1A1 are the 2 major risk factors for overall gallstone disease-they contribute a population attributable fraction of 21.2% among men.
Fischer A, Nothnagel M, Franke A, Jacobs G, Saadati HR, Gaede KI, Rosenstiel P, Schürmann M, Müller-Quernheim J, Schreiber S, Hofmann S.
Association of IBD Risk Loci with Sarcoidosis and its Acute and Chronic Subphenotypes.Eur Respir J,
(2010).
[abstract]
Abstract:
Sarcoidosis is a complex granulomatous inflammatory disorder that shares several clinical and pathogenetic features with inflammatory bowel disease (IBD). Postulating a common genetic basis of inflammatory diseases, we tested 106 SNPs that are known or have been suggested to be associated with IBD for a potential association with sarcoidosis and its acute and chronic subphenotypes. We genotyped 1,996 German sarcoidosis patients, comprising 648 acute and 1,161 chronically affected individuals and 2,622 control subjects and 342 German trios with affected offspring using SNPlex technology. The non-synonymous SNP rs11209026 (Arg381Gln) in the interleukin-23 receptor (IL23R) gene was associated with chronic sarcoidosis (p=5.58x10(-5); OR=0.63), what was supported by the result of a TDT analysis in the independent family sample (pTDT=0.031; OR=0.50). Marker rs12035082 located at chromosome 1q24.3 was found to be associated with the acute subphenotype (p=6.80x10(-7); OR=1.36) and rs916977 (HERC2 locus; p=4.49x10(-5); OR=1.30) was associated with sarcoidosis. Our results highlight the potential importance of the IL23 signaling pathway for the development of chronic sarcoidosis. The finding links sarcoidosis pathogenesis to other inflammatory conditions and may contribute to new hypotheses on disease mechanisms.
Flachsbart F, Caliebe A, Nothnagel M, Kleindorp R, Nikolaus S, Schreiber S, Nebel A.
Depletion of potential A2M risk haplotype for Alzheimer's disease in long-lived individuals.Eur J Hum Genet,
18 (2010), 59-61.
[abstract]
Abstract:
Risk alleles for age-related diseases are expected to decrease in frequency in the population strata of increasing age. Consistent with this hypothesis, earlier studies showed a depletion of the Alzheimer's disease risk factor APOE*epsilon4 in long-lived individuals (LLIs). To evaluate whether this observation also holds for a previously suggested Alzheimer's disease risk haplotype in the A2M gene, we analyzed this particular haplotype in 1042 German LLIs (aged 95-100 years) and 1040 younger individuals (aged 60-75 years). Our results show a significant depletion of this haplotype in LLIs, thus confirming it as a mortality factor in the elderly. Consequently, our data support an involvement of the suggested A2M risk haplotype in the pathogenesis of Alzheimer's disease and adds new evidence to the risk-allele depletion hypothesis.
Schaefer AS, Richter GM, Groessner-Schreiber B, Noack B, Nothnagel M, El Mokhtari NE, Loos BG, Jepsen S, Schreiber S.
Identification of a shared genetic susceptibility locus for coronary heart disease and periodontitis.PLoS Genet,
5 (2009), e1000378.
[abstract]
Abstract:
Recent studies indicate a mutual epidemiological relationship between coronary heart disease (CHD) and periodontitis. Both diseases are associated with similar risk factors and are characterized by a chronic inflammatory process. In a candidate-gene association study, we identify an association of a genetic susceptibility locus shared by both diseases. We confirm the known association of two neighboring linkage disequilibrium regions on human chromosome 9p21.3 with CHD and show the additional strong association of these loci with the risk of aggressive periodontitis. For the lead SNP of the main associated linkage disequilibrium region, rs1333048, the odds ratio of the autosomal-recessive mode of inheritance is 1.99 (95% confidence interval 1.33-2.94; P = 6.9 x 10(-4)) for generalized aggressive periodontitis, and 1.72 (1.06-2.76; P = 2.6 x 10(-2)) for localized aggressive periodontitis. The two associated linkage disequilibrium regions map to the sequence of the large antisense noncoding RNA ANRIL, which partly overlaps regulatory and coding sequences of CDKN2A/CDKN2B. A closely located diabetes-associated variant was independent of the CHD and periodontitis risk haplotypes. Our study demonstrates that CHD and periodontitis are genetically related by at least one susceptibility locus, which is possibly involved in ANRIL activity and independent of diabetes associated risk variants within this region. Elucidation of the interplay of ANRIL transcript variants and their involvement in increased susceptibility to the interactive diseases CHD and periodontitis promises new insight into the underlying shared pathogenic mechanisms of these complex common diseases.
Helbig I, Mefford HC, Sharp AJ, Guipponi M, Fichera M, Franke A, Muhle H, de Kovel C, Baker C, von Spiczak S, Kron KL, Steinich I, Kleefuss-Lie AA, Leu C, Gaus V, Schmitz B, Klein KM, Reif PS, Rosenow F, Weber Y, Lerche H, Zimprich F, Urak L, Fuchs K, Feucht M, Genton P, Thomas P, Visscher F, de Haan GJ, Møller RS, Hjalgrim H, Luciano D, Wittig M, Nothnagel M, Elger CE, Nürnberg P, Romano C, Malafosse A, Koeleman BP, Lindhout D, Stephani U, Schreiber S, Eichler EE, Sander T.
15q13.3 microdeletions increase risk of idiopathic generalized epilepsy.Nat Genet,
41 (2009), 160-2.
[abstract]
Abstract:
We identified 15q13.3 microdeletions encompassing the CHRNA7 gene in 12 of 1,223 individuals with idiopathic generalized epilepsy (IGE), which were not detected in 3,699 controls (joint P = 5.32 x 10(-8)). Most deletion carriers showed common IGE syndromes without other features previously associated with 15q13.3 microdeletions, such as intellectual disability, autism or schizophrenia. Our results indicate that 15q13.3 microdeletions constitute the most prevalent risk factor for common epilepsies identified to date.
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.
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.
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.
Karlsen TH, Franke A, Melum E, Kaser A, Hov JR, Balschun T, Lie BA, Bergquist A, Schramm C, Weismüller TJ, Gotthardt D, Rust C, Philipp EE, Fritz T, Henckaerts L, Weersma R, Stokkers P, Ponsioen CY, Wijmenga C, Sterneck M, Nothnagel M, Hampe J, Teufel A, Runz H, Rosenstiel P, Stiehl A, Vermeire S, Beuers U, Manns M, Schrumpf E, Boberg KM, Schreiber S.
Genome-wide association analysis in primary sclerosing cholangitis.Gastroenterology,
(2009).
[abstract]
Abstract:
BACKGROUND & AIMS:: We aimed to characterize the genetic susceptibility to primary sclerosing cholangitis (PSC) by means of genome-wide association analysis of single nucleotide polymorphism (SNP) markers. METHODS:: A total of 443,816 SNPs on the Affymetrix SNP Array 5.0 were genotyped in 285 Norwegian PSC patients and 298 healthy controls. Associations detected in this discovery panel were re-examined in independent case-control panels from Scandinavia (137 PSC cases and 368 controls), Belgium/the Netherlands (229 PSC cases and 735 controls), and Germany (400 cases and 1832 controls). RESULTS:: The strongest associations were detected near HLA-B at chromosome 6p21 (rs3099844 odds ratio [OR] = 4.8; 95% confidence interval [CI] [3.6, 6.5]; P = 2.6x10-26 and rs2844559 OR = 4.7; 95% CI [3.5, 6.4]; P = 4.2x10-26 in the discovery panel). Outside the HLA complex, rs9524260 at chromosome 13q31 showed significant associations in 3 of 4 study panels. Lentiviral silencing of glypican 6 (GPC6), encoded at this locus, led to the upregulation of pro-inflammatory markers in a chlangiocyte cell-line. Of 15 established ulcerative colitis susceptibility loci, significant replication was obtained at chromosomes 2q35 and 3p21 (rs12612347 OR =1.26; 95% CI [1.06, 1.50] and rs3197999 OR=1.22; 95% CI [1.02, 1.47], respectively), with circumstantial evidence supporting the G protein-coupled bile acid receptor 1 ( GPBAR1) and macrophage-stimulating 1 ( MST1), respectively, as the likely disease genes. CONCLUSIONS:: Strong HLA associations and a subset of genes involved in bile homeostasis and other inflammatory conditions constitute key components of the genetic architecture of PSC.
Schaefer AS, Richter GM, Nothnagel M, Laine ML, Rühling A, Schäfer C, Cordes N, Noack B, Folwaczny M, Glas J, Dörfer C, Dommisch H, Groessner-Schreiber B, Jepsen S, Loos BG, Schreiber S.
A 3' UTR transition within DEFB1 is associated with chronic and aggressive periodontitis.Genes Immun,
(2009).
[abstract]
Abstract:
Periodontal diseases are complex inflammatory diseases and affect up to 20% of the worldwide population. An unbalanced reaction of the immune system toward microbial pathogens is considered as the key factor in the development of periodontitis. Defensins have a strong antimicrobial function and are important contributors of the immune system toward maintaining health. Here, we present the first systematic association study of DEFB1. Using a haplotype-tagging single nucleotide polymorphism (SNP) approach, including described promoter SNPs of DEFB1, we investigated the associations of the selected variants in a large population (N=1337 cases and 2887 ethnically matched controls). The 3' untranslated region SNP, rs1047031, showed the most significant association signal for homozygous carriers of the rare A allele (P=0.002) with an increased genetic risk of 1.3 (95% confidence interval: 1.11-1.57). The association was consistent with the specific periodontitis forms: chronic periodontitis (odds ratio=2.2 (95% confidence interval: 1.16-4.35), P=0.02), and aggressive periodontitis (odds ratio=1.3 (95% confidence interval 1.04-1.68), P=0.02). Sequencing of regulatory and exonic regions of DEFB1 identified no other associated variant, pointing toward rs1047031 as likely being the causative variant. Prediction of microRNA targets identified a potential microRNA-binding site at the position of rs1047031.Genes and Immunity advance online publication, 15 October 2009; doi:10.1038/gene.2009.75.
Ellinghaus D, Schreiber S, Franke A, Nothnagel M.
Current software for genotype imputation.Hum Genomics,
3 (2009), 371-80.
[abstract]
Abstract:
Genotype imputation for single nucleotide polymorphisms (SNPs) has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different software programs are available. In our experience, user-friendliness is often the deciding factor in the choice of software to solve a particular task. We therefore evaluated the usability of three publicly available imputation programs: BEAGLE, IMPUTE and MACH. We found all three programs to perform well with HapMap reference data, with little effort needed for data preparation and subsequent association analysis. Each of them has different strengths and weaknesses, however, and none is optimal for all situations.
Stemmler S, Nothnagel M, Parwez Q, Petrasch-Parwez E, Epplen JT, Hoffjan S.
Variation in genes of the epidermal differentiation complex in German atopic dermatitis patients.Int J Immunogenet,
36 (2009), 217-22.
[abstract]
Abstract:
The filaggrin (FLG) gene is one of the most widely replicated susceptibility genes for atopic dermatitis (AD) so far. Yet, FLG mutations cannot fully account for the original linkage peak on chromosome 1q21, a region comprising the so-called epidermal differentiation complex (EDC). Since the EDC contains numerous genes relevant for epidermal differentiation, we sought to evaluate variation in other genes located in this region in a German AD case-control cohort. Thirty-two single nucleotide polymorphisms (SNPs) in 21 genes across the EDC were genotyped in 402 unrelated AD patients and 325 non-atopic controls by means of restriction enzyme digestion or TaqMan assays. Allele and genotype frequencies were tested for differences between patients and controls by logistic regression. Haplotype frequencies were evaluated using the famhap software. Except for the already known association with FLG, we did not identify any additional significant associations of EDC genes with AD. Thus, in this German cohort, there is no evidence that additional genes in the EDC region apart from FLG contribute substantially to AD pathogenesis.
Loos BG, Fiebig A, Nothnagel M, Jepsen S, Groessner-Schreiber B, Franke A, Jervøe-Storm PM, Schenck K, van der Velden U, Schreiber S.
NOD1 gene polymorphisms in relation to aggressive periodontitis.Innate Immun,
15 (2009), 225-32.
[abstract]
Abstract:
BACKGROUND: NOD proteins are part of innate immunity mechanisms. They play a role in epithelial barrier functions and inflammatory responses to bacteria. Single nucleotide polymorphisms (SNPs) in the NOD1 gene have proven to be associated with inflammatory bowel disease (IBD) and asthma.OBJECTIVE: To investigate SNPs in the NOD1 gene in relation to aggressive periodontitis (AgP), a multifactorial, inflammatory disease of the supporting tissues of the teeth.MATERIALS AND METHODS: Five SNPs in the NOD1 gene (4 intronic and 1 exonic) were tested for association in a total of 415 AgP patients and 874 controls both of Northern European ancestry.RESULTS: The frequencies of the rare SNP alleles ranged between 21% and 26% among cases, and 20-27% among controls, and were not statistically different between cases and controls. Two SNPs were in strong linkage disequilibrium (r(2) = 0.97 in cases and 0.94 in controls). The overall haplotype distributions did not differ between cases and controls. We observed 8 haplotypes with a frequency of >or=1% among cases and/or controls, but none of these haplotype frequencies differed significantly among cases and controls. Logistic regression analyses with adjustment for gender and smoking status did not reveal significant associations with AgP for any of the 5 SNPs. This study had a power of >or=95% to detect associations with variants carrying relative risks of >or=1.5 for heterozygote carriers and >or=2.25 for homozygote carriers.CONCLUSIONS: Although SNPs in the NOD1 gene have been strongly associated with cases of IBD, the current study failed to show an association of NOD1 SNPs with AgP.
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,
40 (2008), 1103-6.
[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.
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.
Rubin D, Claas S, Pfeuffer M, Nothnagel M, Foelsch UR, Schrezenmeir J.
s-ICAM-1 and s-VCAM-1 in healthy men are strongly associated with traits of the metabolic syndrome, becoming evident in the postprandial response to a lipid-rich meal.Lipids Health Dis,
7 (2008), 32.
[abstract]
Abstract:
BACKGROUND: The importance of the postprandial state for the early stages of atherogenesis is increasingly acknowledged. We conducted assessment of association between postprandial triglycerides, insulin and glucose after ingestion of a standardized lipid-rich test meal, and soluble cellular adhesion molecules (sCAM) in young healthy subjects. METHODS: Metabolic parameters and sICAM-1, sVCAM-1 and E-selectin were measured before and hourly until 6 hours after ingestion of a lipid-rich meal in 30 healthy young men with fasting triglycerides <150 mg/dl and normal fasting glucose levels. Subjects were classified as either normal responders (NR) (postprandial triglyceride maxima < 260 mg/dl) or high responders (HR) (postprandial triglyceride maxima > 260 mg/dl). Levels of CAM were compared in HR and NR, and correlation with postprandial triglyceride, insulin and glucose response was assessed. RESULTS: Fasting sICAM-1 and sVCAM-1 levels were significantly higher in HR as compared to NR (p = 0.046, p = 0.03). For sE-selectin there was such a trend (p = 0.05). There was a strong positive and independent correlation between sICAM-1 and postprandial insulin maxima (r = 0.70, p < 0.001). sVCAM-1 showed significant correlation with postprandial triglycerides (AUC) (r = 0.37, p = 0.047). We found no correlation between sCAMs and fasting insulin or triglyceride concentrations. CONCLUSION: This independent association of postprandial triglycerides with sICAM-1 may indicate a particular impact of postprandial lipid metabolism on endothelial reaction.
Fiebig A, Jepsen S, Loos BG, Scholz C, Schäfer C, Rühling A, Nothnagel M, Eickholz P, van der Velden U, Schenck K, Schreiber S, Grössner-Schreiber B.
Polymorphisms in the interleukin-1 (IL1) gene cluster are not associated with aggressive periodontitis in a large Caucasian population.Genomics,
92 (2008), 309-15.
[abstract]
Abstract:
Polymorphisms in the interleukin-1 (IL1) gene have been suggested to influence transcription of IL1A (interleukin-1alpha) and IL1B (interleukin-1beta) and thereby the pathophysiology of periodontitis. This case-control association study on 415 northern European Caucasian patients with aggressive periodontitis (AgP) and 874 healthy controls was conducted to examine 10 single-nucleotide polymorphisms (SNPs) in the genes of the IL1 cluster for association with IL1A, IL1B, CKAP2L (cytoskeleton-associated protein 2-like), and IL1RN (IL-1 receptor antagonist). The results do not support an association between variants in the IL1 gene cluster and AgP. This case-control study had at least 95% power to detect genuine associations with variants carrying relative risks of at least 1.5 for heterozygous carriers and 2.25 for homozygous carriers. Previous reports of an association between IL1 promoter SNPs and periodontitis might reflect subpopulation effects and have to be interpreted with care.
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.
Fischer A, Valentonyte R, Nebel A, Nothnagel M, Müller-Quernheim J, Schürmann M, Schreiber S.
Female-specific association of C-C chemokine receptor 5 gene polymorphisms with Löfgren's syndrome.J Mol Med,
86 (2008), 553-61.
[abstract]
Abstract:
C-C chemokine receptors have been suggested to play an important role in sarcoidosis pathogenesis. Previous investigation of the C-C chemokine receptor 5 (CCR5) gene revealed the association of the HHC haplotype with "persistent lung involvement" in two European sarcoidosis populations. Based on this finding, we investigated a possible association of the HHC haplotype and its marker alleles in an extended German sarcoidosis sample that comprised 995 German sarcoidosis families including individuals with the chronic and acute form of the disease, further refined to patients with and without Löfgren's syndrome. We genotyped this sample and 538 healthy control subjects for 8 single nucleotide polymorphisms (SNPs) that define the HHC haplotype in the CCR5 genomic region. Analysis of 3 sarcoidosis phenotypes (chronic, acute and Löfgren's syndrome) revealed that the HHC haplotype was not associated with chronic sarcoidosis although a substantial overlap can be assumed between the chronic form examined in our study and "persistent parenchymal lung involvement", the phenotype for which an association was previously established. However, 2 marker alleles in the putative CCR5 promoter, which are part of the HHC haplotype, are associated with Löfgren's syndrome. Strikingly, the association is restricted to females. This finding is consistent with recently described sex-specific manifestations of Löfgren's syndrome and with previous functional studies suggesting an estrogen-dependent CCR5 expression. The female-specific association of SNPs in the putative CCR5 promoter region with Löfgren's syndrome raises the possibility that the dysregulated, sex-specific modification of CCR5 expression could contribute to the increased risk of women to develop the disease.
Nebel A, Flachsbart F, Schäfer A, Nothnagel M, Nikolaus S, Mokhtari NE, Schreiber S.
Role of the toll-like receptor 4 polymorphism Asp299Gly in longevity and myocardial infarction in German men.Mech Ageing Dev,
128 (2007 May-Jun), 409-11.
[abstract]
Abstract:
In a previous study on Sicilian men, an association of the functional polymorphism Asp299Gly in the TLR4 gene was reported with longevity and a reduced risk of myocardial infarction (MI). Here, we sought to confirm the findings in our extensive collection of 273 long-lived men (95-107 years), 606 male early-onset MI patients and 594 appropriate controls from Germany. Despite sufficient statistical power to replicate the findings observed in the South Italians, our results rule out a noteworthy influence of the TLR4 polymorphism upon human longevity or MI in German men. Therefore, the previously described associations in Sicilians might reflect either population-specific or potentially false-positive results.
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.
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.
El Mokhtari NE, Ott SJ, Nebel A, Schaefer A, Rosenstiel P, Foerster M, Nothnagel M, Simon R, Schreiber S.
Role of NOD2/CARD15 in coronary heart disease.BMC Genet,
8 (2007), 76.
[abstract]
Abstract:
ABSTRACT: BACKGROUND: Bacterial DNA has been repeatedly detected in atheromatous lesions of coronary heart disease (CHD) patients. Phylogenetic signatures in the atheroma lesions that are similar to those of bacterial biofilms on human barrier organs, including the respiratory or gastrointestinal tract, raise the question of a defective barrier function in CHD. NOD2 plays a major role in defense against bacterial invasion. Genetic variation in the CARD15 gene, which encodes NOD2, was previously shown to result in a barrier defect that causes chronic inflammatory disorders (e.g. Crohn disease). In the present study, we investigated the possible involvement of NOD2/CARD15 in the pathology of CHD by i) analyzing the local expression of NOD2 in atherectomy versus healthy tissue (n=5 each) using histochemical immunofluorescence and ii) by testing the three major functional CARD15 variants (R702W, G908R and 1007fs) for association with early-onset CHD in 900 German patients and 632 healthy controls. RESULTS: In atherectomy tissue of CHD patients, NOD2 was detected in inflammatory cells at the luminal sides of the lesions. However, the allele and genotype frequencies of the three major CARD15 polymorphisms did not differ between CHD patients and controls. CONCLUSION: In conclusion, the NOD2 up-regulation in atheroma lesions indicates an involvement of this protein in the pathology of CHD. Although NOD2 could be important in local immune response mechanisms, none of the analyzed CARD15 variants seem to play a significant role in the etiology of CHD.
Heckmann M, Holle JU, Arning L, Knaup S, Hellmich B, Nothnagel M, Jagiello P, Gross WL, Epplen JT, Wieczorek S.
The Wegener's Granulomatosis quantitative trait locus on chromosome 6p21.3 as characterized by tagSNP genotyping.Ann Rheum Dis,
(2007).
[abstract]
Abstract:
OBJECTIVE: A genomic region on chromosome 6p21.3, including HLA-DPB1, has been linked to Wegener's granulomatosis (WG). The basis of this association is difficult to be evaluated because of the complex haplotype block architecture of this region. We have designed a detailed HapMap based fine-mapping approach to identify the causative molecular genetic variation(s). METHODS: 282 WG patients and 380 healthy controls were genotyped for HLA-DPB1 as well as for 35 informative SNPs within the respective region. 25 of these SNPs have been selected as tagging SNPs for another 219 associated SNPs. Allele and genotype frequencies were analyzed separately, by means of contingency tables and logistic regression. Finally, the coding region of RING1 was directly sequenced in individuals who carried haplotypes that were correlated with contrasting WG risks. RESULTS: The previously reported strong association of WG with the HLA-DPB1*0401 allele was confirmed in an independent WG sample (n=108, pc=6.4E-08). Considering the complete cohort (n=282) the association remained highly significant in ANCA-positive (pc=1.26E-22), but not in ANCA-negative patients. A SNP 3' of HLA-DPB1 yielded the smallest p value and was associated with WG partly independently from the HLA-DPB1 alleles. Another informative SNP in the vicinity of RING1 revealed significant WG association that was also partly independent of HLA-DPB1. RING1 sequencing, however, did not reveal any variation potentially predisposing to WG. CONCLUSIONS: The HLA-DPB1/RING1 region is strongly associated with WG in ANCA-positive individuals. Further analyses of potential cis regulatory sequences of candidate genes HLA-DPB1, RING1 and RXRB appear warranted.
Rubin D, Helwig U, Nothnagel M, Lemke N, Schreiber S, Fölsch UR, Döring F, Schrezenmeir J.
Postprandial plasma adiponectin decreases after glucose and high fat meal and is independently associated with postprandial triacylglycerols but not with - 11388 promoter polymorphism.Br J Nutr,
(2007), 1-7.
[abstract]
Abstract:
Adiponectin is discussed to regulate energy balance and insulin sensitivity. Several studies indicated an association of fasting adiponectin with parameters of the metabolic syndrome. We investigated postprandial adiponectin release and its relation to traits of the metabolic syndrome. Serum adiponectin concentration after an oral glucose tolerance test and after ingestion of a standardised mixed, fat-containing meal in 110 male non-diabetic subjects was assessed. Fasting and postprandial adiponectin and the decrease of adiponectin were correlated with anthropometric and metabolic parameters. Subjects were genotyped for adiponectin - 11 388 G/A promoter single nucleotide polymorphism. Adiponectin slightly decreased after both test meals. A significant decrease was attained 5 and 6 h after the lipid load and 2 h after the glucose load. Particularly, the mixed meal postprandial adiponectin showed stronger correlations with most traits of the metabolic syndrome than fasting adiponectin: postprandial adiponectin with HDL (r 0.30) v. fasting adiponectin with HDL (r 0.23); with postprandial insulin (area under the curve): r - 0.20 v. r - 0.16; with fasting insulin: r 0.10 v. r 0.14; with BMI: r - 0.23 v. r - 0.20; with waist: r - 0.18 v. - 0.16; with systolic blood pressure: r - 0.14 v. r - 0.12; with diastolic blood pressure: r - 0.18 v. r - 0.15. In multivariate analysis, postprandial TAG were the only independent predictor of adiponectin. There was no significant association of adiponectin, NEFA and TAG with - 11 388 G/A adiponectin promoter polymorphism. Our findings favour the interpretation that postprandial adiponectin has the strongest and independent associations to postprandial TAG metabolism.
Macaluso F, Nothnagel M, Parwez Q, Petrasch-Parwez E, Bechara FG, Epplen JT, Hoffjan S.
Polymorphisms in NACHT-LRR (NLR) genes in atopic dermatitis.Exp Dermatol,
16 (2007), 692-8.
[abstract]
Abstract:
Atopic dermatitis (AD) is a chronic skin disease affecting up to 15% of children in industrialized countries. AD belongs to the group of atopic disorders characterized by excessive immune reactions to ubiquitous antigens. Complex interactions between genetic and environmental factors have been suggested for atopic disorders. Dysregulation of the innate immune system appears crucial for the pathogenesis of AD. The NACHT-LRRs (NLRs) represent a group of innate immune receptors with special relevance for inflammatory processes. In order to investigate the role of variation in NLR genes for AD, we genotyped 23 single nucleotide polymorphisms (SNPs) in seven selected NLR genes (CARD4, CARD15, CARD12, NALP1, NALP3, NALP12, MHC2TA) in 392 AD patients and 297 controls by restriction enzyme digestion or TaqMan assays. Single-SNP analysis demonstrated significant associations of the CARD15_R702W variation and the NALP12_In9 T-allele with AD (P = 0.008 and P = 0.03, resp.; insignificant after Bonferroni correction). In the CARD4 gene, a rare haplotype was more frequent in AD patients than in controls. Interactions between all pairs of SNPs in the seven genes were analysed by logistic regression. Significant interactions comprised SNPs in the CARD4 gene (CARD4_In1 and CARD4_Ex6, P = 6.56 x 10(-7); CARD4_Prom und CARD4_Ex6, P = 2.45 x 10(-4)) and promoter polymorphisms in the CARD12 and NALP1 genes (P = 4.31 x 10(-4)). In conclusion, variation in individual genes from the NLR family as well as interactions within this group of innate immune receptor genes could play a role in AD pathogenesis. Investigations in other populations and functional studies are warranted to clarify contributions of NLR variation for this frequent skin disease.
Helwig U, Rubin D, Klapper M, Li Y, Nothnagel M, Fölsch UR, Döring F, Schreiber S, Schrezenmeir J.
The association of fatty acid-binding protein 2 A54T polymorphism with postprandial lipemia depends on promoter variability.Metabolism,
56 (2007), 723-31.
[abstract]
Abstract:
Studies on the association of fatty acid-binding protein 2 (FABP2) A54T and promoter polymorphism, and type 2 diabetes mellitus, insulin, and triglyceride levels are controversial. The aim of this study was to investigate the interfering effect of FABP2 A54T and promoter polymorphism on the postprandial response to a mixed meal and an oral glucose load. Seven hundred men from the Metabolic Intervention Cohort Kiel underwent a standard glucose tolerance test and a standardized mixed meal test and were genotyped by use of the Taqman method. When calculated independently from promoter variability, postprandial triglyceride levels were significantly higher and postprandial insulin sensitivity (homeostasis model assessment index) was lower in homozygous carriers of FABP2 T54T compared with carriers of the FABP2 exon wild-type allele (FABP2 A54A and A54T). This confirms previous findings. The effect of the exon T54T genotype on triglyceride levels and insulin sensitivity, however, was dependent on promoter variability. We found a significant increase in postprandial triglyceride levels and a decrease in insulin sensitivity due to T54T only in the presence of the homozygous B genotype at the promoter polymorphism. Similar results were obtained after oral glucose tolerance test. Reporter gene assays indicated a higher responsiveness to peroxisome proliferator-activating receptor-gamma (PPAR-gamma)/retinoid X receptor (RXR) of FABP2 promoter B vs promoter A. Synergism between a higher inducibility of FABP2 expression and a higher activity of T54 variant may explain higher postprandial triglycerides in case of combined genotype (promoter B + T54). This interference and different linkage disequilibrium between FABP2 exon and promoter polymorphisms may explain the different results obtained in different cohorts.
Helwig U, Rubin D, Kiosz J, Schreiber S, Fölsch UR, Nothnagel M, Döring F, Schrezenmeir J.
The minor allele of the PPARgamma2 pro12Ala polymorphism is associated with lower postprandial TAG and insulin levels in non-obese healthy men.Br J Nutr,
97 (2007), 847-54.
[abstract]
Abstract:
The PPARgamma Pro12Ala polymorphism has been associated in several studies with a decreased risk of obesity, type 2 diabetes and insulin resistance. Weak hints are available about the influence of PPARgamma Pro12Ala on postprandial metabolism. In 708 men, aged 45 to 65 years the PPARgamma2 Pro12Ala genotypes were determined and postprandial TAG, insulin, glucose and NEFA after a standardized mixed fat meal and insulin and glucose after a glucose load (oral glucose tolerance test; OGTT) were assessed. Using the total sample, we did not find a significant impact of the genotype on the postprandial metabolism. In the subgroup with BMI <30 kg/m2, fasting and postprandial TAG and insulin levels as well as homeostasis model assessment of insulin resistance (HOMA) were significantly lower in the Ala12Ala group than in the Pro12Pro group after the mixed meal. In contrast, the groups did not differ in insulin levels and HOMA after the OGTT. To investigate if differences between a fat-containing meal and OGTT are caused by adiponectin, we examined a BMI- and age-matched subgroup. No differences were found between the genotypic groups. The effects of the PPARgamma2 polymorphism on insulin sensitivity are mediated by affluent dietary fat. We did not find evidence that adiponectin as a fatty-acid-dependent adipocyte factor is a causative factor for this phenomenon.
Schimming TT, Parwez Q, Petrasch-Parwez E, Nothnagel M, Epplen JT, Hoffjan S.
Association of toll-interacting protein gene polymorphisms with atopic dermatitis.BMC Dermatol,
7 (2007), 3.
[abstract]
Abstract:
BACKGROUND: Atopic dermatitis (AD) is a common inflammatory skin disorder, affecting up to 15% of children in industrialized countries. Toll-interacting protein (TOLLIP) is an inhibitory adaptor protein within the toll-like receptor (TLR) pathway, a part of the innate immune system that recognizes structurally conserved molecular patterns of microbial pathogens, leading to an inflammatory immune response. METHODS: In order to detect a possible role of TOLLIP variation in the pathogenesis of AD, we screened the entire coding sequence of the TOLLIP gene by SSCP in 50 AD patients. We identified an amino acid exchange in exon 6 (Ala222Ser) and a synonymous variation in exon 4 (Pro139Pro). Subsequently, these two variations and four additional non-coding polymorphisms (-526 C/G, two polymorphisms in intron 1 and one in the 3'UTR) were genotyped in 317 AD patients and 224 healthy controls. RESULTS: The -526G allele showed borderline association with AD in our cohort (p = 0.012; significance level after correction for multiple testing 0.0102). Haplotype analysis did not yield additional information. Evaluation of mRNA expression by quantitative real-time polymerase chain reaction in six probands with the CC and six with the GG genotype at the -526 C/G locus did not reveal significant differences between genotypes. CONCLUSION: Variation in the TOLLIP gene may play a role in the pathogenesis of AD. Yet, replication studies in other cohorts and populations are warranted to confirm these association results.
Hoffjan S, Parwez Q, Petrasch-Parwez E, Falkenstein D, Nothnagel M, Epplen JT.
Association screen for atopic dermatitis candidate gene regions using microsatellite markers in pooled DNA samples.Int J Immunogenet,
33 (2006), 401-9.
[abstract]
Abstract:
Atopic dermatitis (AD) is a chronic inflammatory skin disease affecting up to 16% of children in developed countries. A complex genetic background for AD has been suggested, with genetic as well as environmental factors influencing disease susceptibility. Among other factors, dysregulation in both the innate and the adaptive immune system has been proposed to play a role in AD pathophysiology. We present here an extended association screen for AD using microsatellite markers in 154 genes related to innate and adaptive immunity in pooled DNA samples from 150 German children with AD and 100 controls. After Bonferroni correction, no marker revealed a significant association with AD. Yet, markers representing the nuclear factor kappa B (NFKB)1 and chemokine receptor (CCR)4 genes showed differences in allelic distributions between cases and controls for both pooled DNA analysis and individual genotyping and were thus further investigated. Evaluation of additional single nucleotide polymorphisms (SNP) in the NFKB1 and CCR4 genes revealed no association of individual SNPs with AD. In contrast, haplotype analyses showed a significantly different haplotype distribution between patients and controls for CCR4 (P < 0.001). Furthermore, when SNP-SNP interaction effects were analysed for these two genes, we found significant evidence for epistatic interactions between SNPs within each of the two genes but no evidence for a gene-gene interaction, suggesting that variation in or near both the CCR4 and the NFKB1 genes might individually contribute to AD pathogenesis.
Nothnagel M, Rohde K.
The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates.Am J Hum Genet,
77 (2005), 988-98.
[abstract]
Abstract:
The definition of haplotype blocks of single-nucleotide polymorphisms (SNPs) has been proposed so that the haplotypes can be used as markers in association studies and to efficiently describe human genetic variation. The International Haplotype Map (HapMap) project to construct a comprehensive catalog of haplotypic variation in humans is underway. However, a number of factors have already been shown to influence the definition of blocks, including the population studied and the sample SNP density. Here, we examine the effect that marker selection has on the definition of blocks and the pattern of haplotypes by using comparable but complementary SNP sets and a number of block definition methods in various genomic regions and populations that were provided by the Encyclopedia of DNA Elements (ENCODE) project. We find that the chosen SNP set has a profound effect on the block-covered sequence and block borders, even at high marker densities. Our results question the very concept of discrete haplotype blocks and the possibility of generalizing block findings from the HapMap project. We comparatively apply the block-free tagging-SNP approach and discuss both the haplotype approach and the tagging-SNP approach as means to efficiently catalog genetic variation.
Nothnagel M, Fürst R, Rohde K.
Entropy as a measure for linkage disequilibrium over multilocus haplotype blocks.Hum Hered,
54 (2002), 186-98.
[abstract]
Abstract:
OBJECTIVE: The presence of linkage disequilibrium (LD) forms the basis for a range of uses, including the fine-mapping of diseases and studies on human genealogy. Recent findings indicate that single nucleotide polymorphisms (SNP) can occur in blocks of limited haplotypic diversity with high degrees of LD. Commonly used measures for LD, such as r(2) and D', consider only two loci and might miss information to appropriately describe LD in larger haplotypic structures. METHODS: We introduce the Normalized Entropy Difference, epsilon, as a new multilocus measure for LD. A related quantity, deltaS, provides an approximate chi(2) test for the significance of LD. The ability of the measure to detect haplotype blocks is investigated using simulated data sets as well as a real data set previously analyzed by Daly et al. (2001). RESULTS: epsilon allows for arbitrary numbers of loci, describes LD with regard to the loci sequence, and can be interpreted as a multilocus extension of r(2). The application of epsilon to the data sets demonstrated the measure's ability to appropriately describe simultaneous multilocus LD and to detect haplotype blocks. CONCLUSIONS: epsilon is a reasonable multilocus LD measure and might be of potential use in the construction of the human haplotype map.
Gordon D, Finch SJ, Nothnagel M, Ott J.
Power and sample size calculations for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms.Hum Hered,
54 (2002), 22-33.
[abstract]
Abstract:
The purpose of this work is to quantify the effects that errors in genotyping have on power and the sample size necessary to maintain constant asymptotic Type I and Type II error rates (SSN) for case-control genetic association studies between a disease phenotype and a di-allelic marker locus, for example a single nucleotide polymorphism (SNP) locus. We consider the effects of three published models of genotyping errors on the chi-square test for independence in the 2 x 3 table. After specifying genotype frequencies for the marker locus conditional on disease status and error model in both a genetic model-based and a genetic model-free framework, we compute the asymptotic power to detect association through specification of the test's non-centrality parameter. This parameter determines the functional dependence of SSN on the genotyping error rates. Additionally, we study the dependence of SSN on linkage disequilibrium (LD), marker allele frequencies, and genotyping error rates for a dominant disease model. Increased genotyping error rate requires a larger SSN. Every 1% increase in sum of genotyping error rates requires that both case and control SSN be increased by 2-8%, with the extent of increase dependent upon the error model. For the dominant disease model, SSN is a nonlinear function of LD and genotyping error rate, with greater SSN for lower LD and higher genotyping error rate. The combination of lower LD and higher genotyping error rates requires a larger SSN than the sum of the SSN for the lower LD and for the higher genotyping error rate.
Nothnagel M, Ott J.
Statistical gene mapping of traits in humans--hypertension as a complex trait: is it amenable to genetic analysis?.Semin Nephrol,
22 (2002), 105-14.
[abstract]
Abstract:
Gene mapping refers to the localization of disease genes on the human gene map. The currently used mathematical methods for gene mapping are outlined and compared. The example of Gilles de la Tourette syndrome is discussed in detail.
Schuster H, Lamprecht A, Junghans C, Dietz B, Baron H, Nothnagel M, Müller-Myhsok B, Luft FC.
Approaches to the genetics of cardiovascular disease through genetic field work.Kidney Int,
53 (1998), 1449-54.
[abstract]
Abstract:
Successful molecular genetic studies of complex disease require exact, careful phenotypization, which is more difficult than that performed for monogenic diseases. We have developed a family-oriented field working approach, which relies on index patients, their primary care physicians, and a minimum number of field working staff. The patients are responsible for recruiting their family members. Packets containing an explanatory pamphlet, an informed consent statement, a questionnaire, and blood cuvettes are provided. Data are transferred from questionnaire and from the laboratory into a computer program that facilitates construction of the family tree. We have applied this genetic field working approach primarily to patients with lipid disorders. Coupling results from genetic field working with modern DNA diagnostic tests such as the oligonucleotide ligation assay, has enabled us to effectively identify patients with familial hypercholesterolemia in the German population. We are now extending genetic field working to hypertension. Hypertension is much more difficult to study, because the phenotype is more difficult to discern and document. Both complex diseases have the disadvantage that the parents of the index patients are likely to already be dead. Nevertheless, we concentrate on the recruitment of large pedigrees, sibling pairs with parents whenever possible, and trios consisting of index patient and both parents or index patient, parent and sibling. With these constellations we can conduct association studies, linkage analysis, and novel combinations of both approaches.
