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Lucy J Davison,
Chris Wallace,
Jason D Cooper,
Nathan F Cope,
Nicola K Wilson,
Deborah J Smyth,
Joanna M M Howson,
Nada Saleh,
Abdullah Al-Jeffery,
Karen L Angus, [......],
Angela Rankin,
Hendrik Sager,
Nilesh J Samani,
Jennifer Sambrook,
Gerd Schmitz,
Michael Scholz,
Laura Schroeder,
Heribert Schunkert,
Ann-Christine Syvannen,
Stefanie Tennstedt
[show abstract]
[hide abstract]
ABSTRACT: The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes.
Human Molecular Genetics 01/2012; 21(2):322-33. · 7.64 Impact Factor
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David Adams,
Lucia Altucci,
Stylianos E Antonarakis,
Juan Ballesteros,
Stephan Beck,
Adrian Bird,
Christoph Bock,
Bernhard Boehm,
Elias Campo,
Andrea Caricasole, [......],
Salvatore Spicuglia,
Michael Stratton,
Hendrik G Stunnenberg,
Amos Tanay,
David Torrents,
Alfonso Valencia,
Edo Vellenga,
Martin Vingron,
Jörn Walter,
Spike Willcocks
Nature Biotechnology 01/2012; 30(3):224-6. · 29.50 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: It has been suggested that pathway analysis can complement single-SNP analysis in exploring genomewide association data. Pathway analysis incorporates the available biological knowledge of genes and SNPs and is expected to improve the chances of revealing the underlying genetic architecture of complex traits. Methods for pathway analysis can be classified as competitive (enrichment) or self-contained (association) according to the hypothesis tested. Although association tests are statistically more powerful than enrichment tests they can be difficult to calibrate because biases in analysis accumulate across multiple SNPs or genes. Furthermore, enrichment tests can be more scientifically relevant than association tests, as they detect pathways with relatively more evidence for association than the remaining genes. Here we show how some well known association tests can be simply adapted to test for enrichment, and compare their performance to some established enrichment tests. We propose versions of the Adaptive Rank Truncated Product (ARTP), Tail Strength Measure and Fisher's combination of p-values for testing the enrichment null hypothesis. We compare the behaviour of these proposed methods with the established Hypergeometric Test and Gene-Set Enrichment Analysis (GSEA). The results of the simulation study show that the modified version of the ARTP method has generally the best performance across the situations considered. The methods were also applied for finding enriched pathways for body mass index (BMI) and platelet function phenotypes. The pathway analysis of BMI identified the Vasoactive Intestinal Peptide pathway as significantly associated with BMI. This pathway has been previously reported as associated with BMI and the risk of obesity. The ARTP method was the method that identified the largest number of enriched pathways across all tested pathway databases and phenotypes. The simulation and data application results are in agreement with previous work on association tests and suggests that the ARTP should be preferred for both enrichment and association testing.
PLoS ONE 01/2012; 7(7):e41018. · 4.09 Impact Factor
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Nicolas Greliche,
Tanja Zeller,
Philipp S Wild,
Maxime Rotival,
Arne Schillert,
Andreas Ziegler,
Panos Deloukas,
Jeanette Erdmann,
Christian Hengstenberg, Willem H Ouwehand,
Nilesh J Samani,
Heribert Schunkert,
Thomas Munzel,
Karl J Lackner,
François Cambien,
Alison H Goodall,
Laurence Tiret,
Stefan Blankenberg,
David-Alexandre Trégouët
[show abstract]
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ABSTRACT: We aimed to assess whether pri-miRNA SNPs (miSNPs) could influence monocyte gene expression, either through marginal association or by interacting with polymorphisms located in 3'UTR regions (3utrSNPs). We then conducted a genome-wide search for marginal miSNPs effects and pairwise miSNPs × 3utrSNPs interactions in a sample of 1,467 individuals for which genome-wide monocyte expression and genotype data were available. Statistical associations that survived multiple testing correction were tested for replication in an independent sample of 758 individuals with both monocyte gene expression and genotype data. In both studies, the hsa-mir-1279 rs1463335 was found to modulate in cis the expression of LYZ and in trans the expression of CNTN6, CTRC, COPZ2, KRT9, LRRFIP1, NOD1, PCDHA6, ST5 and TRAF3IP2 genes, supporting the role of hsa-mir-1279 as a regulator of several genes in monocytes. In addition, we identified two robust miSNPs × 3utrSNPs interactions, one involving HLA-DPB1 rs1042448 and hsa-mir-219-1 rs107822, the second the H1F0 rs1894644 and hsa-mir-659 rs5750504, modulating the expression of the associated genes.As some of the aforementioned genes have previously been reported to reside at disease-associated loci, our findings provide novel arguments supporting the hypothesis that the genetic variability of miRNAs could also contribute to the susceptibility to human diseases.
PLoS ONE 01/2012; 7(9):e45863. · 4.09 Impact Factor
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Suthesh Sivapalaratnam,
Hanneke Basart,
Nicholas A Watkins,
Stepanie Maiwald,
Augusto Rendon,
Unni Krishnan,
Brigitte M Sondermeijer,
Esther E Creemers,
Sara J Pinto-Sietsma,
Kees Hovingh, Willem H Ouwehand,
John J P Kastelein,
Alison H Goodall,
Mieke D Trip
[show abstract]
[hide abstract]
ABSTRACT: The burden of cardiovascular disease (CVD) cannot be fully addressed by therapy targeting known pathophysiological pathways. Even with stringent control of all risk factors CVD events are only diminished by half. A number of additional pathways probably play a role in the development of CVD and might serve as novel therapeutic targets. Genome wide expression studies represent a powerful tool to identify such novel pathways. We compared the expression profiles in monocytes from twenty two young male patients with premature familial CAD with those from controls matched for age, sex and smoking status, without a family history of CVD. Since all patients were on statins and aspirin treatment, potentially affecting the expression of genes in monocytes, twelve controls were subsequently treated with simvastatin and aspirin for 6 and 2 weeks, respectively. By whole genome expression arrays six genes were identified to have differential expression in the monocytes of patients versus controls; ABCA1, ABCG1 and RGS1 were downregulated in patients, whereas ADRB2, FOLR3 and GSTM1 were upregulated. Differential expression of all genes, apart from GSTM1, was confirmed by qPCR. Aspirin and statins altered gene expression of ABCG1 and ADBR2. All finding were validated in a second group of twenty four patients and controls. Differential expression of ABCA1, RSG1 and ADBR2 was replicated. In conclusion, we identified these 3 genes to be expressed differently in CAD cases which might play a role in the pathogenesis of atherosclerotic vascular disease.
PLoS ONE 01/2012; 7(2):e32166. · 4.09 Impact Factor
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Jonas Carlsson Almlöf,
Per Lundmark,
Anders Lundmark,
Bing Ge,
Seraya Maouche,
Harald H H Göring,
Ulrika Liljedahl,
Camilla Enström,
Jessy Brocheton,
Carole Proust, [......],
Christian Hengstenberg,
Nilesh J Samani,
Jeanette Erdmann,
Heribert Schunkert,
Tomi Pastinen,
Panos Deloukas,
Alison H Goodall, Willem H Ouwehand,
François Cambien,
Ann-Christine Syvänen
[show abstract]
[hide abstract]
ABSTRACT: A large number of genome-wide association studies have been performed during the past five years to identify associations between SNPs and human complex diseases and traits. The assignment of a functional role for the identified disease-associated SNP is not straight-forward. Genome-wide expression quantitative trait locus (eQTL) analysis is frequently used as the initial step to define a function while allele-specific gene expression (ASE) analysis has not yet gained a wide-spread use in disease mapping studies. We compared the power to identify cis-acting regulatory SNPs (cis-rSNPs) by genome-wide allele-specific gene expression (ASE) analysis with that of traditional expression quantitative trait locus (eQTL) mapping. Our study included 395 healthy blood donors for whom global gene expression profiles in circulating monocytes were determined by Illumina BeadArrays. ASE was assessed in a subset of these monocytes from 188 donors by quantitative genotyping of mRNA using a genome-wide panel of SNP markers. The performance of the two methods for detecting cis-rSNPs was evaluated by comparing associations between SNP genotypes and gene expression levels in sample sets of varying size. We found that up to 8-fold more samples are required for eQTL mapping to reach the same statistical power as that obtained by ASE analysis for the same rSNPs. The performance of ASE is insensitive to SNPs with low minor allele frequencies and detects a larger number of significantly associated rSNPs using the same sample size as eQTL mapping. An unequivocal conclusion from our comparison is that ASE analysis is more sensitive for detecting cis-rSNPs than standard eQTL mapping. Our study shows the potential of ASE mapping in tissue samples and primary cells which are difficult to obtain in large numbers.
PLoS ONE 01/2012; 7(12):e52260. · 4.09 Impact Factor
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Maxime Rotival,
Tanja Zeller,
Philipp S Wild,
Seraya Maouche,
Silke Szymczak,
Arne Schillert,
Raphaele Castagné,
Arne Deiseroth,
Carole Proust,
Jessy Brocheton, [......],
Gilles Montalescot, Willem H Ouwehand,
Nilesh J Samani,
Heribert Schunkert,
David-Alexandre Tregouet,
Andreas Ziegler,
Alison H Goodall,
François Cambien,
Laurence Tiret,
Stefan Blankenberg
[show abstract]
[hide abstract]
ABSTRACT: One major expectation from the transcriptome in humans is to characterize the biological basis of associations identified by genome-wide association studies. So far, few cis expression quantitative trait loci (eQTLs) have been reliably related to disease susceptibility. Trans-regulating mechanisms may play a more prominent role in disease susceptibility. We analyzed 12,808 genes detected in at least 5% of circulating monocyte samples from a population-based sample of 1,490 European unrelated subjects. We applied a method of extraction of expression patterns-independent component analysis-to identify sets of co-regulated genes. These patterns were then related to 675,350 SNPs to identify major trans-acting regulators. We detected three genomic regions significantly associated with co-regulated gene modules. Association of these loci with multiple expression traits was replicated in Cardiogenics, an independent study in which expression profiles of monocytes were available in 758 subjects. The locus 12q13 (lead SNP rs11171739), previously identified as a type 1 diabetes locus, was associated with a pattern including two cis eQTLs, RPS26 and SUOX, and 5 trans eQTLs, one of which (MADCAM1) is a potential candidate for mediating T1D susceptibility. The locus 12q24 (lead SNP rs653178), which has demonstrated extensive disease pleiotropy, including type 1 diabetes, hypertension, and celiac disease, was associated to a pattern strongly correlating to blood pressure level. The strongest trans eQTL in this pattern was CRIP1, a known marker of cellular proliferation in cancer. The locus 12q15 (lead SNP rs11177644) was associated with a pattern driven by two cis eQTLs, LYZ and YEATS4, and including 34 trans eQTLs, several of them tumor-related genes. This study shows that a method exploiting the structure of co-expressions among genes can help identify genomic regions involved in trans regulation of sets of genes and can provide clues for understanding the mechanisms linking genome-wide association loci to disease.
PLoS Genetics 12/2011; 7(12):e1002367. · 8.69 Impact Factor
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Toby Johnson,
Tom R Gaunt,
Stephen J Newhouse,
Sandosh Padmanabhan,
Maciej Tomaszewski,
Meena Kumari,
Richard W Morris,
Ioanna Tzoulaki,
Eoin T O'Brien,
Neil R Poulter, [......],
Robert Roberts,
Christopher Newton-Cheh,
Lude Franke,
Alice V Stanton,
Anna F Dominiczak,
Martin Farrall,
Aroon D Hingorani,
Nilesh J Samani,
Mark J Caulfield,
Patricia B Munroe
[show abstract]
[hide abstract]
ABSTRACT: Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies.
The American Journal of Human Genetics 11/2011; 89(6):688-700. · 10.60 Impact Factor
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Sonia Shah,
Christopher P Nelson,
Tom R Gaunt,
Pim van der Harst,
Timothy Barnes,
Peter S Braund,
Debbie A Lawlor,
Juan-Pablo Casas,
Sandosh Padmanabhan,
Fotios Drenos, [......],
Rudolf A de Boer,
Gerjan Navis,
Wiek H van Gilst,
Bongani M Mayosi,
John R Thompson,
Meena Kumari,
Peter W MacFarlane,
Ian N M Day,
Aroon D Hingorani,
Nilesh J Samani
[show abstract]
[hide abstract]
ABSTRACT: Presence of left ventricular hypertrophy on an ECG (ECG-LVH) is widely assessed clinically and provides prognostic information in some settings. There is evidence for significant heritability of ECG-LVH. We conducted a large-scale gene-centric association analysis of 4 commonly measured indices of ECG-LVH.
We calculated the Sokolow-Lyon index, Cornell product, 12-lead QRS voltage sum, and 12-lead QRS voltage product in 10 256 individuals from 3 population-based cohorts and typed their DNA using a customized gene array (the Illumina HumanCVD BeadChip 50K array), containing 49 094 genetic variants in ≈2100 genes of cardiovascular relevance. We followed-up promising associations in 11 777 additional individuals. We identified and replicated 4 loci associated with ECG-LVH indices: 3p22.2 (SCN5A, rs6797133, P=1.22 × 10(-7)) with Cornell product and 12q13.3 (PTGES3, rs2290893, P=3.74 × 10(-8)), 15q25.2 (NMB, rs2292462, P=3.23 × 10(-9)), and 15q26.3 (IGF1R, rs4966014, P=1.26 × 10(-7)) with the 12-lead QRS voltage sum. The odds ratio of being in the top decile for the 12-lead QRS voltage sum for those carrying 6 trait-raising alleles at the 12q13.3, 15q25.2, and 15q26.3 loci versus those carrying 0 to 1 alleles was 1.60 (95% CI: 1.20 to 2.29). Lead single-nucleotide polymorphisms at the 12q13.3 and 15q25.2 loci showed significant expression quantitative trait loci effects in monocytes.
These findings provide novel insights into the genetic determination of ECG-LVH. The findings could help to improve our understanding of the mechanisms determining this prognostically important trait.
Circulation Cardiovascular Genetics 09/2011; 4(6):626-35. · 6.11 Impact Factor
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Adam S Butterworth,
Peter S Braund,
Martin Farrall,
Robert J Hardwick,
Danish Saleheen,
John F Peden,
Nicole Soranzo,
John C Chambers,
Suthesh Sivapalaratnam,
Marcus E Kleber, [......],
Anders Hamsten,
Alistair S Hall,
Jaspal S Kooner,
Simon G Thompson,
John R Thompson,
Panos Deloukas, Willem H Ouwehand,
Hugh Watkins,
John Danesh,
Nilesh J Samani
[show abstract]
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ABSTRACT: Coronary artery disease (CAD) has a significant genetic contribution that is incompletely characterized. To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants. We examined 49,094 genetic variants in ∼2,100 genes of cardiovascular relevance, using a customised gene array in 15,596 CAD cases and 34,992 controls (11,202 cases and 30,733 controls of European descent; 4,394 cases and 4,259 controls of South Asian origin). We attempted to replicate putative novel associations in an additional 17,121 CAD cases and 40,473 controls. Potential mechanisms through which the novel variants could affect CAD risk were explored through association tests with vascular risk factors and gene expression. We confirmed associations of several previously known CAD susceptibility loci (eg, 9p21.3:p<10(-33); LPA:p<10(-19); 1p13.3:p<10(-17)) as well as three recently discovered loci (COL4A1/COL4A2, ZC3HC1, CYP17A1:p<5×10(-7)). However, we found essentially null results for most previously suggested CAD candidate genes. In our replication study of 24 promising common variants, we identified novel associations of variants in or near LIPA, IL5, TRIB1, and ABCG5/ABCG8, with per-allele odds ratios for CAD risk with each of the novel variants ranging from 1.06-1.09. Associations with variants at LIPA, TRIB1, and ABCG5/ABCG8 were supported by gene expression data or effects on lipid levels. Apart from the previously reported variants in LPA, none of the other ∼4,500 low frequency and functional variants showed a strong effect. Associations in South Asians did not differ appreciably from those in Europeans, except for 9p21.3 (per-allele odds ratio: 1.14 versus 1.27 respectively; P for heterogeneity = 0.003). This large-scale gene-centric analysis has identified several novel genes for CAD that relate to diverse biochemical and cellular functions and clarified the literature with regard to many previously suggested genes.
PLoS Genetics 09/2011; 7(9):e1002260. · 8.69 Impact Factor
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Suthesh Sivapalaratnam,
Rosienne Farrugia,
Max Nieuwdorp,
Cordelia F Langford,
Rachel T van Beem,
Stephanie Maiwald,
Jaap Jan Zwaginga,
Arief Gusnanto,
Nicholas A Watkins,
Mieke D Trip, Willem H Ouwehand
[show abstract]
[hide abstract]
ABSTRACT: It is widely accepted that atherosclerosis and inflammation are intimately linked. Monocytes play a key role in both of these processes and we hypothesized that activation of inflammatory pathways in monocytes would lead to, among others, proatherogenic changes in the monocyte transcriptome. Such differentially expressed genes in circulating monocytes would be strong candidates for further investigation in disease association studies.
Endotoxin, lipopolysaccharide (LPS), or saline control was infused in healthy volunteers. Monocyte RNA was isolated, processed and hybridized to Hver 2.1.1 spotted cDNA microarrays. Differential expression of key genes was confirmed by RT-PCR and results were compared to in vitro data obtained by our group to identify candidate genes.
All subjects who received LPS experienced the anticipated clinical response indicating successful stimulation. One hour after LPS infusion, 11 genes were identified as being differentially expressed; 1 down regulated and 10 up regulated. Four hours after LPS infusion, 28 genes were identified as being differentially expressed; 3 being down regulated and 25 up regulated. No genes were significantly differentially expressed following saline infusion. Comparison with results obtained in in vitro experiments lead to the identification of 6 strong candidate genes (BATF, BID, C3aR1, IL1RN, SEC61B and SLC43A3)
In vivo endotoxin exposure of healthy individuals resulted in the identification of several candidate genes through which systemic inflammation links to atherosclerosis.
BMC Medical Genomics 08/2011; 4:64. · 3.69 Impact Factor
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Dirk S Paul,
James P Nisbet,
Tsun-Po Yang,
Stuart Meacham,
Augusto Rendon,
Katta Hautaviita,
Jonna Tallila,
Jacqui White,
Marloes R Tijssen,
Suthesh Sivapalaratnam,
Hanneke Basart,
Mieke D Trip,
Berthold Göttgens,
Nicole Soranzo, Willem H Ouwehand,
Panos Deloukas
PLoS Genetics 07/2011; 7(7). · 8.69 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: Genomewide association meta-analysis studies have identified > 100 independent genetic loci associated with blood cell indices, including volume and count of platelets and erythrocytes. Although several of these loci encode known regulators of hematopoiesis, the mechanism by which most sequence variants exert their effect on blood cell formation remains elusive. An example is the Rho guanine nucleotide exchange factor, ARHGEF3, which was previously implicated by genomewide association meta-analysis studies in bone cell biology. Here, we report on the unexpected role of ARHGEF3 in regulation of iron uptake and erythroid cell maturation. Although early erythroid differentiation progressed normally, silencing of arhgef3 in Danio rerio resulted in microcytic and hypochromic anemia. This was rescued by intracellular supplementation of iron, showing that arhgef3-depleted erythroid cells are fully capable of hemoglobinization. Disruption of the arhgef3 target, RhoA, also produced severe anemia, which was, again, corrected by iron injection. Moreover, silencing of ARHGEF3 in erythromyeloblastoid cells K562 showed that the uptake of transferrin was severely impaired. Taken together, this is the first study to provide evidence for ARHGEF3 being a regulator of transferrin uptake in erythroid cells, through activation of RHOA.
Blood 06/2011; 118(18):4967-76. · 9.90 Impact Factor
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Dirk S Paul,
James P Nisbet,
Tsun-Po Yang,
Stuart Meacham,
Augusto Rendon,
Katta Hautaviita,
Jonna Tallila,
Jacqui White,
Marloes R Tijssen,
Suthesh Sivapalaratnam,
Hanneke Basart,
Mieke D Trip,
Berthold Göttgens,
Nicole Soranzo, Willem H Ouwehand,
Panos Deloukas
[show abstract]
[hide abstract]
ABSTRACT: Turning genetic discoveries identified in genome-wide association (GWA) studies into biological mechanisms is an important challenge in human genetics. Many GWA signals map outside exons, suggesting that the associated variants may lie within regulatory regions. We applied the formaldehyde-assisted isolation of regulatory elements (FAIRE) method in a megakaryocytic and an erythroblastoid cell line to map active regulatory elements at known loci associated with hematological quantitative traits, coronary artery disease, and myocardial infarction. We showed that the two cell types exhibit distinct patterns of open chromatin and that cell-specific open chromatin can guide the finding of functional variants. We identified an open chromatin region at chromosome 7q22.3 in megakaryocytes but not erythroblasts, which harbors the common non-coding sequence variant rs342293 known to be associated with platelet volume and function. Resequencing of this open chromatin region in 643 individuals provided strong evidence that rs342293 is the only putative causative variant in this region. We demonstrated that the C- and G-alleles differentially bind the transcription factor EVI1 affecting PIK3CG gene expression in platelets and macrophages. A protein-protein interaction network including up- and down-regulated genes in Pik3cg knockout mice indicated that PIK3CG is associated with gene pathways with an established role in platelet membrane biogenesis and thrombus formation. Thus, rs342293 is the functional common variant at this locus; to the best of our knowledge this is the first such variant to be elucidated among the known platelet quantitative trait loci (QTLs). Our data suggested a molecular mechanism by which a non-coding GWA index SNP modulates platelet phenotype.
PLoS Genetics 06/2011; 7(6):e1002139. · 8.69 Impact Factor
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Michael A Nalls,
David J Couper,
Toshiko Tanaka,
Frank J A van Rooij,
Ming-Huei Chen,
Albert V Smith,
Daniela Toniolo,
Neil A Zakai,
Qiong Yang,
Andreas Greinacher, [......],
Andrew B Singleton,
Dena G Hernandez,
Dan L Longo,
Nicole Soranzo,
Jacqueline C M Witteman,
Bruce M Psaty,
Luigi Ferrucci,
Tamara B Harris,
Christopher J O'Donnell,
Santhi K Ganesh
[show abstract]
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ABSTRACT: White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count-6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count-17q21; basophil count- 3p21 near RPN1 and C3orf27; lymphocyte count-6p21, 19p13 at EPS15L1; monocyte count-2q31 at ITGA4, 3q21, 8q24 an intergenic region, 9q31 near EDG2), including three previously reported associations and seven novel associations. To investigate functional relationships among variants contributing to variability in the six WBC traits, we utilized gene expression- and pathways-based analyses. We implemented gene-clustering algorithms to evaluate functional connectivity among implicated loci and showed functional relationships across cell types. Gene expression data from whole blood was utilized to show that significant biological consequences can be extracted from our genome-wide analyses, with effect estimates for significant loci from the meta-analyses being highly corellated with the proximal gene expression. In addition, collaborative efforts between the groups contributing to this study and related studies conducted by the COGENT and RIKEN groups allowed for the examination of effect homogeneity for genome-wide significant associations across populations of diverse ancestral backgrounds.
PLoS Genetics 06/2011; 7(6):e1002113. · 8.69 Impact Factor
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Marloes R Tijssen,
Ana Cvejic,
Anagha Joshi,
Rebecca L Hannah,
Rita Ferreira,
Ariel Forrai,
Dana C Bellissimo,
S Helen Oram,
Peter A Smethurst,
Nicola K Wilson,
Xiaonan Wang,
Katrin Ottersbach,
Derek L Stemple,
Anthony R Green, Willem H Ouwehand,
Berthold Göttgens
[show abstract]
[hide abstract]
ABSTRACT: Hematopoietic differentiation critically depends on combinations of transcriptional regulators controlling the development of individual lineages. Here, we report the genome-wide binding sites for the five key hematopoietic transcription factors--GATA1, GATA2, RUNX1, FLI1, and TAL1/SCL--in primary human megakaryocytes. Statistical analysis of the 17,263 regions bound by at least one factor demonstrated that simultaneous binding by all five factors was the most enriched pattern and often occurred near known hematopoietic regulators. Eight genes not previously appreciated to function in hematopoiesis that were bound by all five factors were shown to be essential for thrombocyte and/or erythroid development in zebrafish. Moreover, one of these genes encoding the PDZK1IP1 protein shared transcriptional enhancer elements with the blood stem cell regulator TAL1/SCL. Multifactor ChIP-Seq analysis in primary human cells coupled with a high-throughput in vivo perturbation screen therefore offers a powerful strategy to identify essential regulators of complex mammalian differentiation processes.
Developmental cell 05/2011; 20(5):597-609. · 13.36 Impact Factor
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Jason D Cooper,
Deborah J Smyth,
Neil M Walker,
Helen Stevens,
Oliver S Burren,
Chris Wallace,
Christopher Greissl,
Elizabeth Ramos-Lopez,
Elina Hyppönen,
David B Dunger,
Timothy D Spector, Willem H Ouwehand,
Thomas J Wang,
Klaus Badenhoop,
John A Todd
[show abstract]
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ABSTRACT: Vitamin D deficiency (25-hydroxyvitamin D [25(OH)D] <50 nmol/L) is commonly reported in both children and adults worldwide, and growing evidence indicates that vitamin D deficiency is associated with many extraskeletal chronic disorders, including the autoimmune diseases type 1 diabetes and multiple sclerosis.
We measured 25(OH)D concentrations in 720 case and 2,610 control plasma samples and genotyped single nucleotide polymorphisms from seven vitamin D metabolism genes in 8,517 case, 10,438 control, and 1,933 family samples. We tested genetic variants influencing 25(OH)D metabolism for an association with both circulating 25(OH)D concentrations and disease status.
Type 1 diabetic patients have lower circulating levels of 25(OH)D than similarly aged subjects from the British population. Only 4.3 and 18.6% of type 1 diabetic patients reached optimal levels (≥75 nmol/L) of 25(OH)D for bone health in the winter and summer, respectively. We replicated the associations of four vitamin D metabolism genes (GC, DHCR7, CYP2R1, and CYP24A1) with 25(OH)D in control subjects. In addition to the previously reported association between type 1 diabetes and CYP27B1 (P = 1.4 × 10(-4)), we obtained consistent evidence of type 1 diabetes being associated with DHCR7 (P = 1.2 × 10(-3)) and CYP2R1 (P = 3.0 × 10(-3)).
Circulating levels of 25(OH)D in children and adolescents with type 1 diabetes vary seasonally and are under the same genetic control as in the general population but are much lower. Three key 25(OH)D metabolism genes show consistent evidence of association with type 1 diabetes risk, indicating a genetic etiological role for vitamin D deficiency in type 1 diabetes.
Diabetes 03/2011; 60(5):1624-31. · 8.29 Impact Factor
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Heribert Schunkert,
Inke R König,
Sekar Kathiresan,
Muredach P Reilly,
Themistocles L Assimes,
Hilma Holm,
Michael Preuss,
Alexandre F R Stewart,
Maja Barbalic,
Christian Gieger, [......],
Alistair S Hall,
Panos Deloukas,
John R Thompson,
Kari Stefansson,
Robert Roberts,
Unnur Thorsteinsdottir,
Christopher J O'Donnell,
Ruth McPherson,
Jeanette Erdmann,
Nilesh J Samani
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ABSTRACT: We performed a meta-analysis of 14 genome-wide association studies of coronary artery disease (CAD) comprising 22,233 individuals with CAD (cases) and 64,762 controls of European descent followed by genotyping of top association signals in 56,682 additional individuals. This analysis identified 13 loci newly associated with CAD at P < 5 × 10⁻⁸ and confirmed the association of 10 of 12 previously reported CAD loci. The 13 new loci showed risk allele frequencies ranging from 0.13 to 0.91 and were associated with a 6% to 17% increase in the risk of CAD per allele. Notably, only three of the new loci showed significant association with traditional CAD risk factors and the majority lie in gene regions not previously implicated in the pathogenesis of CAD. Finally, five of the new CAD risk loci appear to have pleiotropic effects, showing strong association with various other human diseases or traits.
Nature Genetics 03/2011; 43(4):333-8. · 35.53 Impact Factor
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Cornelis A Albers,
Ana Cvejic,
Rémi Favier,
Evelien E Bouwmans,
Marie-Christine Alessi,
Paul Bertone,
Gregory Jordan,
Ross N W Kettleborough,
Graham Kiddle,
Myrto Kostadima,
Randy J Read,
Botond Sipos,
Suthesh Sivapalaratnam,
Peter A Smethurst,
Jonathan Stephens,
Katrin Voss,
Alan Nurden,
Augusto Rendon,
Paquita Nurden, Willem H Ouwehand
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ABSTRACT: Gray platelet syndrome (GPS) is a predominantly recessive platelet disorder that is characterized by mild thrombocytopenia with large platelets and a paucity of α-granules; these abnormalities cause mostly moderate but in rare cases severe bleeding. We sequenced the exomes of four unrelated individuals and identified NBEAL2 as the causative gene; it has no previously known function but is a member of a gene family that is involved in granule development. Silencing of nbeal2 in zebrafish abrogated thrombocyte formation.
Nature Genetics 01/2011; 43(8):735-7. · 35.53 Impact Factor
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Christian Gieger,
Aparna Radhakrishnan,
Ana Cvejic,
Weihong Tang,
Eleonora Porcu,
Giorgio Pistis,
Jovana Serbanovic-Canic,
Ulrich Elling,
Alison H Goodall,
Yann Labrune, [......],
Inga Prokopenko,
Derek Stemple,
Daniela Toniolo,
Lorenz Wernisch,
Serena Sanna,
Andrew A Hicks,
Augusto Rendon,
Manuel A Ferreira, Willem H Ouwehand,
Nicole Soranzo
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ABSTRACT: Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function.
Nature 01/2011; 480(7376):201-8. · 36.28 Impact Factor
