Population‐specific genome‐wide mapping of expression quantitative trait loci in the colon of Han Chinese

Journal of Digestive Diseases

Volumn 17, Issue 9, 2016, Pages 600-609

  Guo, Chang Cun ^a   Wei, Ni ^a   Liang, Shu Hui ^a   Wang, Biao Luo ^a   Sha, Su Mei ^a   Wu, Kai Chun ^a  

^a FOURTH MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Chinese Han population; Expression quantitative trait locus; Inflammatory bowel diseases; Single nucleotide polymorphisms; Ulcerative colitis

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BLOOD SAMPLING; CLINICAL ARTICLE; COLON BIOPSY; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOME; GENOTYPE; HAN CHINESE; HISTONE MODIFICATION; HUMAN; HUMAN TISSUE; MALE; PRIORITY JOURNAL; PROTEIN BINDING; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION INITIATION SITE; ULCERATIVE COLITIS; CASE CONTROL STUDY; COLON; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE ONTOLOGY; GENETIC PREDISPOSITION; GENETIC TRANSCRIPTION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HISTONE CODE; METABOLISM; PROCEDURES;

CASE-CONTROL STUDIES; COLITIS, ULCERATIVE; COLON; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE ONTOLOGY; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HISTONE CODE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; TRANSCRIPTION, GENETIC;

EID: 85017487720     PISSN: 17512972     EISSN: 17512980     Source Type: Journal    
DOI: 10.1111/1751-2980.12399     Document Type: Article

References (34)

1. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait‐associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010; 6: e1000888.
2. Jostins L, Ripke S, Weersma RK et al. Host‐microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491: 119–24.
3. Liu JZ, van Sommeren S, Huang H et al.; International Multiple Sclerosis Genetics Consortium; International IBD Genetics Consortium. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet 2015; 47: 979–86.
4. McGovern DP, Kugathasan S, Cho JH. Genetics of inflammatory bowel diseases. Gastroenterology 2015; 149: 1163–76.e2.
5. Mokry M, Middendorp S, Wiegerinck CL et al. Many inflammatory bowel disease risk loci include regions that regulate gene expression in immune cells and the intestinal epithelium. Gastroenterology 2014; 146: 1040–7.
6. Stranger BE, Forrest MS, Clark AG et al. Genome‐wide associations of gene expression variation in humans. PLoS Genet 2005; 1: e78.
7. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG. Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 2007; 39: 226–31.
8. Schadt EE, Molony C, Chudin E et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008; 6: e107.
9. Ding J, Gudjonsson JE, Liang L et al. Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis‐eQTL signals. Am J Hum Genet 2010; 87: 779–89.
10. Grundberg E, Small KS, Hedman ÅK et al.; Multiple Tissue Human Expression Resource (MuTHER) Consortium. Mapping cis‐ and trans‐regulatory effects across multiple tissues in twins. Nat Genet 2012; 44: 1084–9.
11. Gibbs JR, van der Brug MP, Hernandez DG et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 2010; 6: e1000952.
12. Montgomery SB, Sammeth M, Gutierrez-Arcelus M et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 2010; 464: 773–7.
13. Stranger BE, Nica AC, Forrest MS et al. Population genomics of human gene expression. Nat Genet 2007; 39: 1217–24.
14. Petretto E, Mangion J, Dickens NJ et al. Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet 2006; 2: e172.
15. Kabakchiev B, Silverberg MS. Expression quantitative trait loci analysis identifies associations between genotype and gene expression in human intestine. Gastroenterology 2013; 144: 1488–96.e3.
16. Hulur I, Gamazon ER, Skol AD et al. Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci. BMC Genomics 2015; 16: 138.
17. Singh T, Levine AP, Smith PJ, Smith AM, Segal AW, Barrett JC. Characterization of expression quantitative trait loci in the human colon. Inflamm Bowel Dis 2015; 21: 251–6.
18. Ng SC. Emerging leadership lecture: Inflammatory bowel disease in Asia: emergence of a “Western” disease. J Gastroenterol Hepatol 2015; 30: 440–5.
19. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome‐wide association studies. PLoS Genet 2009; 5: e1000529.
20. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome‐wide association studies through pre‐phasing. Nat Genet 2012; 44: 955–9.
21. Shabalin AA. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 2012; 28: 1353–8.
22. Zhu LJ, Gazin C, Lawson ND et al. ChIPpeakAnno: a bioconductor package to annotate ChIP‐seq and ChIP‐chip data. BMC Bioinformatics 2010; 11: 237.
23. Zheng Q, Wang XJ. GOEAST: a web‐based software toolkit for gene ontology enrichment analysis. Nucleic Acids Res 2008; 36: W358–63.
24. Solé X, Guinó E, Valls J, Iniesta R, Moreno V. SNPStats: a web tool for the analysis of association studies. Bioinformatics 2006; 22: 1928–9.
25. Anderson CA, Boucher G, Lees CW et al. Meta‐analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 2011; 43: 246–52.
26. de Souza HS, Fiocchi C. Immunopathogenesis of IBD: current state of the art. Nat Rev Gastroenterol Hepatol 2016; 13: 13–27.
27. Muro M, López-Hernández R, Mrowiec A. Immunogenetic biomarkers in inflammatory bowel diseases: role of the IBD3 region. World J Gastroenterol 2014; 20: 15037–48.
28. Hosomi S, Kaser A, Blumberg RS. Role of endoplasmic reticulum stress and autophagy as interlinking pathways in the pathogenesis of inflammatory bowel disease. Curr Opin Gastroenterol 2015; 31: 81–8.
29. Liang L, Morar N, Dixon AL et al. A cross‐platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines. Genome Res 2013; 23: 716–26.
30. Dimas AS, Deutsch S, Stranger BE et al. Common regulatory variation impacts gene expression in a cell type‐dependent manner. Science 2009; 325: 1246–50.
31. Wen X, Luca F, Pique-Regi R. Cross‐population joint analysis of eQTLs: fine mapping and functional annotation. PLoS Genet 2015; 11: e1005176.
32. Narahara M, Higasa K, Nakamura S et al. Large‐scale East‐ Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants. PLoS One 2014; 9: e100924.
33. Peters JE, Lyons PA, Lee JC et al. Insight into genotypephenotype associations through eQTL mapping in multiple cell types in health and immune‐mediated disease. PLoS Genet 2016; 12: e1005908.
34. Guo C, Wu K. Risk genes of inflammatory bowel disease in Asia: what are the most important pathways affected? Dig Dis 2016; 34: 5–11.