A systematic eQTL study of cis-trans epistasis in 210 HapMap individuals

European Journal of Human Genetics

Volumn 20, Issue 1, 2012, Pages 97-101

  Becker, Jessica ^a   Wendland, Jens R ^b   Haenisch, Britta ^a   Nöthen, Markus M ^a   Schumacher, Johannes ^a  

^a UNIVERSITY OF BONN   (Germany)

^b F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

cis regulation; epistasis; eQTLs; interaction; trans regulation

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CHROMOSOME NOR; CIS TRANS ISOMERISM; CONTROLLED STUDY; FOLLOW UP; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC EPISTASIS; GENETIC TRANSCRIPTION; GENOTYPE; HAPLOTYPE MAP; HUMAN; MAJOR CLINICAL STUDY; MARKER GENE; PRIORITY JOURNAL; QUALITY CONTROL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

DATABASES, NUCLEIC ACID; EPISTASIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC MARKERS; GENETIC TESTING; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HAPMAP PROJECT; HUMANS; LINKAGE DISEQUILIBRIUM; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; TRANSCRIPTOME;

EID: 83255187278     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2011.156     Document Type: Article

References (54)

1. Dimas AS, Deutsch S, Stranger BE et al: Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 2009; 325: 1246-1250.
2. Dixon AL, Liang L, Moffatt MF et al: A genome-wide association study of global gene expression. Nat Genet 2007; 39: 1202-1207. (Pubitemid 47482680)
3. Dombroski BA, Nayak RR, Ewens KG, Ankener W, Cheung VG, Spielman RS: Gene expression and genetic variation in response to endoplasmic reticulum stress in human cells. Am J Hum Genet 2010; 86: 719-729.
4. Goring HH, Curran JE, Johnson MP et al: Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 2007; 39: 1208-1216. (Pubitemid 47482685)
5. Idaghdour Y, Czika W, Shianna KV et al: Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nat Genet 2010; 42: 62-67.
6. Morley M, Molony CM, Weber TM et al: Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430: 743-747. (Pubitemid 39071339)
7. Myers AJ, Gibbs JR, Webster JA et al: A survey of genetic human cortical gene expression. Nat Genet 2007; 39: 1494-1499. (Pubitemid 350191339)
8. Stranger BE, Forrest MS, Dunning M et al: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007; 315: 848-853.
9. Stranger BE, Nica AC, Forrest MS et al: Population genomics of human gene expression. Nat Genet 2007; 39: 1217-1224. (Pubitemid 47482691)
10. Veyrieras JB, Kudaravalli S, Kim SY et al: High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 2008; 4: e1000214.
11. Cheung VG, Nayak RR, Wang IX et al: Polymorphic cis-and trans-regulation of human gene expression. PLoS Bio 2010; 8.
12. Cheung VG, Spielman RS: Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat rev 2009; 10: 595-604.
13. Fraser P, Bickmore W: Nuclear organization of the genome and the potential for gene regulation. Nature 2007; 447: 413-417. (Pubitemid 46816747)
14. Gondor A, Ohlsson R: Chromosome crosstalk in three dimensions. Nature 2009; 461: 212-217.
15. Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA: Interchromosomal associations between alternatively expressed loci. Nature 2005; 435: 637-645. (Pubitemid 40825504)
16. Williams A, Spilianakis CG, Flavell RA: Interchromosomal association and gene regulation in trans. Trends Genet 2010; 26: 188-197.
17. Herold C, Steffens M, Brockschmidt FF, Baur MP, Becker T: INTERSNP: genome-wide interaction analysis guided by a priori information. Bioinformatics 2009; 25: 3275-3281.
18. Steffens M, Becker T, Sander T et al: Feasible and successful: genome-wide interaction analysis involving all 1.9f10(11) pair-wise interaction tests. Hum Hered 2010; 69: 268-284.
19. Wan X, Yang C, Yang Q et al: BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies. Am J Hum Genet 2010; 87: 325-340.
20. Barbosa-Morais NL, Dunning MJ, Samarajiwa SA et al: A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res 2010; 38: e17.
21. Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575. (Pubitemid 47330214)
22. Graham RR, Cotsapas C, Davies L et al: Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet 2008; 40: 1059-1061.
23. Gregersen PK, Amos CI, Lee AT et al: REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat Genet 2009; 41: 820-823.
24. Han JW, Zheng HF, Cui Y et al: Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet 2009; 41: 1234-1237.
25. Hom G, Graham RR, Modrek B et al: Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med 2008; 358: 900-909. (Pubitemid 351397089)
26. Marroni F, Pfeufer A, Aulchenko YS et al: A genome-wide association scan of RR and QT interval duration in 3 European genetically isolated populations: the EUROSPAN project. Circ Cardiovasc Genet 2009; 2: 322-328.
27. Nair RP, Duffin KC, Helms C et al: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Nat Genet 2009; 41: 199-204.
28. Zhernakova A, van Diemen CC, Wijmenga C: Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev 2009; 10: 43-55.
29. Cordell HJ: Detecting gene-gene interactions that underlie human diseases. Nat Rev 2009; 10: 392-404.
30. Cirulli ET, Kasperaviciute D, Attix DK et al: Common genetic variation and performance on standardized cognitive tests. Eur J Hum Genet 2010; 18: 815-820.
31. Schymick JC, Scholz SW, Fung HC et al: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2007; 6: 322-328. (Pubitemid 46367937)
32. Need AC, Attix DK, McEvoy JM et al: A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. Hum Mol Genet 2009; 18: 4650-4661.
33. Stefansson H, Ophoff RA, Steinberg S et al: Common variants conferring risk of schizophrenia. Nature 2009; 460: 744-747.
34. Levy D, Larson MG, Benjamin EJ et al: Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. BMC Med Genet 2007; 8(Suppl 1): S3.
35. Soranzo N, Rivadeneira F, Chinappen-Horsley U et al: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. PLoS Genet 2009; 5: e1000445.
36. Weedon MN, Lango H, Lindgren CM et al: Genome-wide association analysis identifies 20. loci that influence adult height. Nat Genet 2008; 40: 575-583. (Pubitemid 351601210)
37. Asano K, Matsushita T, Umeno J et al: A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. Nat Genet 2009; 41: 1325-1329.
38. Barrett JC, Hansoul S, Nicolae DL et al: Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 2008; 40: 955-962.
39. McArdle PF, Parsa A, Chang YP et al: Association of a common nonsynonymous variant in GLUT9 with serum uric acid levels in old order amish. Arthritis Rheum 2008; 58: 2874-2881.
40. Wallace C, Newhouse SJ, Braund P et al: Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. Am J Hum Genet 2008; 82: 139-149. (Pubitemid 351735954)
41. Crowther-Swanepoel D, Broderick P, Di Bernardo MC et al: Common variants at 2q37.3, 8q24.21, 15q21.3 and 16q24.1 influence chronic lymphocytic leukemia risk. Nat Genet 2010; 42: 132-136.
42. Shrestha S, Irvin MR, Taylor KD et al: A genome-wide association study of carotid atherosclerosis in HIV-infected men. Aids 2010; 24: 583-592.
43. Daly AK, Donaldson PT, Bhatnagar P et al: HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat Genet 2009; 41: 816-819.
44. Gudbjartsson DF, Walters GB, Thorleifsson G et al: Many sequence variants affecting diversity of adult human height. Nat Genet 2008; 40: 609-615. (Pubitemid 351601211)
45. Kim JJ, Lee HI, Park T et al: Identification of 15 loci influencing height in a Korean population. J Hum Genet 2010; 55: 27-31.
46. Gudbjartsson DF, Bjornsdottir US, Halapi E et al: Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. Nat Genet 2009; 41: 342-347.
47. Ganesh SK, Zakai NA, van Rooij FJ et al: Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Nat Genet 2009; 41: 1191-1198.
48. Vasan RS, Glazer NL, Felix JF et al: Genetic variants associated with cardiac structure and function: a meta-analysis and replication of genome-wide association data. JAMA 2009; 302: 168-178.
49. MS-consortium: Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20. Nat Genet 2009; 41: 824-828.
50. Easton DF, Pooley KA, Dunning AM et al: Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007; 447: 1087-1093. (Pubitemid 47014426)
51. Kathiresan S, Voight BF, Purcell S et al: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet 2009; 41: 334-341.
52. Kathiresan S, Melander O, Guiducci C et al: Six new loci associated with blood lowdensity lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 2008; 40: 189-197. (Pubitemid 351171402)
53. Sabatti C, Service SK, Hartikainen AL et al: Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet 2009; 41: 35-46.
54. Willer CJ, Sanna S, Jackson AU et al: Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 2008; 40: 161-169. (Pubitemid 351171403)