Genome-Wide Haplotype Analysis of Cis Expression Quantitative Trait Loci in Monocytes

PLoS Genetics

Volumn 9, Issue 1, 2013, Pages

  Garnier, Sophie ^a,b   Truong, Vinh ^a,b   Brocheton, Jessy ^a   Zeller, Tanja ^c   Rovital, Maxime ^a   Wild, Philipp S ^d   Ziegler, Andreas ^e   Munzel, Thomas ^d   Tiret, Laurence ^a,b   Blankenberg, Stefan ^c   Deloukas, Panos ^f   Erdmann, Jeannette ^e   Hengstenberg, Christian ^g   Samani, Nilesh J ^h,i   Schunkert, Heribert ^e   Ouwehand, Willem H ^f,j   Goodall, Alison H ^h,i   Cambien, François ^a,b   Trégouët, David Alexandre ^a,b  

^a INSERM   (France)

^b SORBONNE UNIVERSITÉ   (France)

^c UNIVERSITY HEART CENTER HAMBURG   (Germany)

^d JOHANNES GUTENBERG UNIVERSITY   (Germany)

^e UNIVERSITY OF LÜBECK   (Germany)

^f WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^g UNIVERSITY HOSPITAL REGENSBURG   (Germany)

^h UNIVERSITY OF LEICESTER   (United Kingdom)

ⁱ GLENFIELD HOSPITAL   (United Kingdom)

^j UNIVERSITY OF CAMBRIDGE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HAPLOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; MONOCYTE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HUMANS; MONOCYTES; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 84873517235     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003240     Document Type: Article

References (43)

1. Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M, (2009) Mapping complex disease traits with global gene expression. Nat Rev Genet 10: 184-194.
2. Li J, Burmeister M, (2005) Genetical genomics: combining genetics with gene expression analysis. Hum Mol Genet 14 Spec No. 2: R163-169.
3. Montgomery SB, Dermitzakis ET, (2009) The resolution of the genetics of gene expression. Hum Mol Genet 18: R211-215.
4. Goring HH, Curran JE, Johnson MP, Dyer TD, Charlesworth J, et al. (2007) Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 39: 1208-1216.
5. Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, et al. (2007) A genome-wide association study of global gene expression. Nat Genet 39: 1202-1207.
6. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224.
7. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, et al. (2008) Genetics of gene expression and its effect on disease. Nature 452: 423-428.
8. Schadt EE, Molony C, Chudin E, Hao K, Yang X, et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6: e107 doi:10.1371/journal.pbio.0060107.
9. Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, et al. (2010) Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS ONE 5: e10693 doi:10.1371/journal.pone.0010693.
10. Jansen RC, Nap JP, (2001) Genetical genomics: the added value from segregation. Trends Genet 17: 388-391.
11. Murphy A, Chu JH, Xu M, Carey VJ, Lazarus R, et al. (2010) Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes. Hum Mol Genet 19: 4745-4757.
12. Nica AC, Dermitzakis ET, (2008) Using gene expression to investigate the genetic basis of complex disorders. Hum Mol Genet 17: R129-134.
13. Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, et al. (2007) Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448: 470-473.
14. Heinig M, Petretto E, Wallace C, Bottolo L, Rotival M, et al. (2010) A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature 467: 460-464.
15. Buil A, Tregouet DA, Souto JC, Saut N, Germain M, et al. (2010) C4BPB/C4BPA is a new susceptibility locus for venous thrombosis with unknown protein S-independent mechanism: results from genome-wide association and gene expression analyses followed by case-control studies. Blood 115: 4644-4650.
16. Frere C, Tregouet DA, Morange PE, Saut N, Kouassi D, et al. (2006) Fine mapping of quantitative trait nucleotides underlying thrombin-activatable fibrinolysis inhibitor antigen levels by a transethnic study. Blood 108: 1562-1568.
17. Bodin L, Verstuyft C, Tregouet DA, Robert A, Dubert L, et al. (2005) Cytochrome P450 2C9 (CYP2C9) and vitamin K epoxide reductase (VKORC1) genotypes as determinants of acenocoumarol sensitivity. Blood 106: 135-140.
18. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, et al. (2008) SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24: 2938-2939.
19. Tregouet DA, Konig IR, Erdmann J, Munteanu A, Braund PS, et al. (2009) Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat Genet 41: 283-285.
20. Gagliardi F, Jones B, Grey F, Begin ME, Heikkurinen M, (2005) Building an infrastructure for scientific Grid computing: status and goals of the EGEE project. Philos Transact A Math Phys Eng Sci 363: 1729-1742.
21. Tregouet DA, Garelle V, (2007) A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies. Bioinformatics 23: 1038-1039.
22. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR, (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34: 816-834.
23. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
24. Kamatani Y, Matsuda K, Okada Y, Kubo M, Hosono N, et al. (2010) Genome-wide association study of hematological and biochemical traits in a Japanese population. Nat Genet 42: 210-215.
25. Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, et al. (2010) Variants in FAM13A are associated with chronic obstructive pulmonary disease. Nat Genet 42: 200-202.
26. Albagha OM, Wani SE, Visconti MR, Alonso N, Goodman K, et al. (2011) Genome-wide association identifies three new susceptibility loci for Paget's disease of bone. Nat Genet 43: 685-689.
27. Tao S, Wang Z, Feng J, Hsu FC, Jin G, et al. (2012) A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. Carcinogenesis 33: 598-603.
28. Kooner JS, Saleheen D, Sim X, Sehmi J, Zhang W, et al. (2011) Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. Nat Genet 43: 984-989.
29. Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, et al. (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 6: e1000895 doi:10.1371/journal.pgen.1000895.
30. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888 doi:10.1371/journal.pgen.1000888.
31. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753.
32. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, et al. (2011) Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11: 446-450.
33. Shah S, Nelson CP, Gaunt TR, van der Harst P, Barnes T, et al. (2011) Four Genetic Loci Influencing Electrocardiographic Indices of Left Ventricular Hypertrophy. Circ Cardiovasc Genet.
34. Rotival M, Zeller T, Wild PS, Maouche S, Szymczak S, et al. (2011) Integrating genome-wide genetic variations and monocyte expression data reveals trans-regulated gene modules in humans. PLoS Genet 7: e1002367 doi:10.1371/journal.pgen.1002367.
35. Castagne R, Rotival M, Zeller T, Wild PS, Truong V, et al. (2011) The choice of the filtering method in microarrays affects the inference regarding dosage compensation of the active X-chromosome. PLoS ONE 6: e23956 doi:10.1371/journal.pone.0023956.
36. Castagne R, Zeller T, Rotival M, Szymczak S, Truong V, et al. (2011) Influence of sex and genetic variability on expression of X-linked genes in human monocytes. Genomics 98: 320-326.
37. Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JF, Ritchie ME, et al. (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res 38: e17.
38. Du P, Kibbe WA, Lin SM, (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics 24: 1547-1548.
39. Lambert JC, Grenier-Boley B, Harold D, Zelenika D, Chouraki V, et al. (2012) Genome-wide haplotype association study identifies the FRMD4A gene as a risk locus for Alzheimer's disease. Mol Psychiatry [Epub ahead of print].
40. Tregouet DA, Ricard S, Nicaud V, Arnould I, Soubigou S, et al. (2004) In-depth haplotype analysis of ABCA1 gene polymorphisms in relation to plasma ApoA1 levels and myocardial infarction. Arterioscler Thromb Vasc Biol 24: 775-781.
41. Tregouet DA, Escolano S, Tiret L, Mallet A, Golmard JL, (2004) A new algorithm for haplotype-based association analysis: the Stochastic-EM algorithm. Ann Hum Genet 68: 165-177.
42. Morange PE, Saut N, Alessi MC, Yudkin JS, Margaglione M, et al. (2007) Association of plasminogen activator inhibitor (PAI)-1 (SERPINE1) SNPs with myocardial infarction, plasma PAI-1, and metabolic parameters: the HIFMECH study. Arterioscler Thromb Vasc Biol 27: 2250-2257.
43. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.