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Garnier S, Truong V, Brocheton J, Zeller T, Rovital M, Wild PS, Ziegler A, Munzel T, Tiret L, Blankenberg S, Deloukas P, Erdmann J, Hengstenberg C, Samani NJ, Schunkert H, Ouwehand WH, Goodall AH, Cambien F, Trégouët DA. Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. PLoS Genet 2013; 9:e1003240. [PMID: 23382694 PMCID: PMC3561129 DOI: 10.1371/journal.pgen.1003240] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 11/27/2012] [Indexed: 11/19/2022] Open
Abstract
In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL) was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ~2,1 × 10(9) haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >10(4)-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested for 412 probes for which SNPs (or proxies) that defined the detected haplotypes were available in the Gutenberg Health Study composed of 1,374 individuals. At the Bonferroni correction level of 1.2 × 10(-4) (~0.05/412), 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci.
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Affiliation(s)
- Sophie Garnier
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Vinh Truong
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Jessy Brocheton
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Maxime Rovital
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Philipp S. Wild
- Department of Medicine II, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Ziegler
- Institut für Medizinische Biometrie und Statistik, Universität Lübeck, Lübeck, Germany
| | | | - Thomas Munzel
- Department of Medicine II, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Laurence Tiret
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Stefan Blankenberg
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Panos Deloukas
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Christian Hengstenberg
- Klinik und Poliklinik für Innere Medizin II, Universität Regensburg, Regensburg, Germany
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom
| | | | - Willem H. Ouwehand
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Alison H. Goodall
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom
| | - François Cambien
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - David-Alexandre Trégouët
- INSERM, UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- * E-mail:
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