Expression quantitative trait loci analysis identifies associations between genotype and gene expression in human intestine

Gastroenterology

Volumn 144, Issue 7, 2013, Pages

  Kabakchiev, Boyko ^a   Silverberg, Mark S ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

IBD; SNPdb; Systems Biology; Transcriptomics

Indexed keywords

ANTIGEN PRESENTATION; ARTICLE; CELL DIVISION; CROHN DISEASE; ENTERITIS; FIBROBLAST; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENOTYPE; HUMAN; ILEUM; LIVER; LYMPHOBLASTOID CELL LINE; MONOCYTE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; T LYMPHOCYTE;

EID: 84878289023     PISSN: 00165085     EISSN: 15280012     Source Type: Journal    
DOI: 10.1053/j.gastro.2013.03.001     Document Type: Article

References (46)

1. R.J. Klein, C. Zeiss, E.Y. Chew Complement factor H polymorphism in age-related macular degeneration Science 308 2005 385 389
2. M.F. Moffatt, M. Kabesch, L. Liang Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma Nature 448 2007 470 473
3. K. Wang, H. Zhang, D. Ma Common genetic variants on 5p14.1 associate with autism spectrum disorders Nature 459 2009 528 533
4. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
5. J.B. Meigs, A.K. Manning, C.S. Fox Genome-wide association with diabetes-related traits in the Framingham Heart Study BMC Med Genet 8 Suppl 1 2007 S16
6. A. Meguro, H. Inoko, M. Ota Genome-wide association study of normal tension glaucoma: common variants in SRBD1 and ELOVL5 contribute to disease susceptibility Ophthalmology 117 2010 1331 e5 1338 e5
7. D.M. Maraganore, M. de Andrade, T.G. Lesnick High-resolution whole-genome association study of Parkinson disease Am J Hum Genet 77 2005 685 693
8. G. Thorleifsson, G.B. Walters, D.F. Gudbjartsson Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity Nat Genet 41 2009 18 24
9. C.M. O'Seaghdha, Q. Yang, N.L. Glazer Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels Hum Mol Genet 19 2010 4296 4303
10. A. Hazra, P. Kraft, J. Selhub Common variants of FUT2 are associated with plasma vitamin B12 levels Nat Genet 40 2008 1160 1162
11. D. Levy, M.G. Larson, E.J. Benjamin Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness BMC Med Genet 8 Suppl 1 2007 S3
12. W. Qiu, M.H. Cho, J.H. Riley Genetics of sputum gene expression in chronic obstructive pulmonary disease PLoS One 6 2011 e24395
13. A. Murphy, J.H. Chu, M. Xu Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes Hum Mol Genet 19 2010 4745 4757
14. T. Zeller, P. Wild, S. Szymczak Genetics and beyond - the transcriptome of human monocytes and disease susceptibility PLoS One 5 2010 e10693
15. S. Deutsch, R. Lyle, E.T. Dermitzakis Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes Hum Mol Genet 14 2005 3741 3749
16. E.E. Schadt, C. Molony, E. Chudin Mapping the genetic architecture of gene expression in human liver PLoS Biol 6 2008 e107
17. J.R. Gibbs, M.P. van der Brug, D.G. Hernandez Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain PLoS Genet 6 2010 e1000952
18. J.K. Pickrell, J.C. Marioni, A.A. Pai Understanding mechanisms underlying human gene expression variation with RNA sequencing Nature 464 2010 768 772
19. T. Babak, P. Garrett-Engele, C.D. Armour Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation BMC Genomics 11 2010 473
20. J. Majewski, T. Pastinen The study of eQTL variations by RNA-seq: from SNPs to phenotypes Trends Genet 27 2011 72 79
21. E. Lalonde, K.C. Ha, Z. Wang RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression Genome Res 21 2011 545 554
22. A.C. Nica, L. Parts, D. Glass The architecture of gene regulatory variation across multiple human tissues: the MuTHER study PLoS Genet 7 2011 e1002003
23. J. Fu, M.G. Wolfs, P. Deelen Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression PLoS Genet 8 2012 e1002431
24. D.L. Nicolae, E. Gamazon, W. Zhang Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS PLoS Genet 6 2010 e1000888
25. R.L. Moskowitz, N.A. Shepherd, R.J. Nicholls An assessment of inflammation in the reservoir after restorative proctocolectomy with ileoanal ileal reservoir Int J Colorectal Dis 1 1986 167 174
26. W.J. Sandborn, W.J. Tremaine, K.P. Batts Pouchitis after ileal pouch-anal anastomosis: a Pouchitis Disease Activity Index Mayo Clin Proc 69 1994 409 415
27. A. Schroeder, O. Mueller, S. Stocker The RIN: an RNA integrity number for assigning integrity values to RNA measurements BMC Mol Biol 7 2006 3
28. R.A. Irizarry, B. Hobbs, F. Collin Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 4 2003 249 264
29. W.E. Johnson, C. Li, A. Rabinovic Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 8 2007 118 127
30. W.H. Kruskal, W.A. Wallis Use of ranks in one-criterion variance analysis J Am Stat Assoc 47 1952 583 621
31. Y. Benjamini, Y. Hochberg Controlling the false discovery rate: a practical and powerful approach to multiple testing J R Stat Soc Series B (Methodological) 57 1995 289 300
32. B.E. Stranger, A.C. Nica, M.S. Forrest Population genomics of human gene expression Nat Genet 39 2007 1217 1224
33. A.S. Dimas, S. Deutsch, B.E. Stranger Common regulatory variation impacts gene expression in a cell type-dependent manner Science 325 2009 1246 1250
34. L. Jostins, S. Ripke, R.K. Weersma Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease Nature 491 2012 119 124
35. T. Tanioka, A. Hattori, S. Masuda Human leukocyte-derived arginine aminopeptidase The third member of the oxytocinase subfamily of aminopeptidases J Biol Chem 278 2003 32275 32283
36. F.M. Mesak, N. Osada, K. Hashimoto Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2-XRR and macaque testis BMC Genomics 4 2003 32
37. D.P. McGovern, M.R. Jones, K.D. Taylor Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease Hum Mol Genet 19 2010 3468 3476
38. A. Franke, D.P. McGovern, J.C. Barrett Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci Nat Genet 42 2010 1118 1125
39. C.A. Anderson, G. Boucher, C.W. Lees Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47 Nat Genet 43 2011 246 252
40. K. Fransen, M.C. Visschedijk, S. van Sommeren Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease Hum Mol Genet 19 2010 3482 3488
41. V.D. Peltekova, R.F. Wintle, L.A. Rubin Functional variants of OCTN cation transporter genes are associated with Crohn disease Nat Genet 36 2004 471 475
42. C.L. Noble, E.R. Nimmo, H. Drummond The contribution of OCTN1/2 variants within the IBD5 locus to disease susceptibility and severity in Crohn's disease Gastroenterology 129 2005 1854 1864
43. S. Vermeire, M. Pierik, T. Hlavaty Association of organic cation transporter risk haplotype with perianal penetrating Crohn's disease but not with susceptibility to IBD Gastroenterology 129 2005 1845 1853
44. M.S. Silverberg, J.H. Cho, J.D. Rioux Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study Nat Genet 41 2009 216 220
45. T. Raman, T.P. O'Connor, N.R. Hackett Quality control in microarray assessment of gene expression in human airway epithelium BMC Genomics 10 2009 493
46. K.S. Viljoen, J.M. Blackburn Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity BMC Genomics 14 2013 14