Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility loci for type 2 diabetes mellitus

American Journal of Epidemiology

Volumn 176, Issue 5, 2012, Pages 423-430

  Greenawalt, Danielle M ^a   Sieberts, Solveig K ^b   Cornelis, Marilyn C ^c   Girman, Cynthia J ^a   Zhong, Hua ^b   Yang, Xia ^b   Guinney, Justin ^b   Qi, Lu ^c   Hu, Frank B ^c  

^a MERCK RESEARCH LABORATORIES   (United States)

^b SAGE BIONETWORKS   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

expression single nucleotide polymorphism; gene set enrichment analysis; genome wide association study; integrative genomic analysis; single nucleotide polymorphism; type 2 diabetes

Indexed keywords

ANTIGEN; LYMPHOCYTE ANTIGEN 75; PEPTIDASE; PHOSPHATIDYLINOSITOL TRANSFER PROTEIN; PROTEIN; TRANSCRIPTION FACTOR 7 LIKE 2; UBIQUITIN SPECIFIC PEPTIDASE 36; UNCLASSIFIED DRUG;

ANTIGEN; COHORT ANALYSIS; DIABETES; DISEASE CONTROL; DISEASE TREATMENT; ETIOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; POLYMORPHISM;

ADIPOCYTE; ARTICLE; CASE CONTROL STUDY; CELL DIFFERENTIATION; COHORT ANALYSIS; CONTROLLED STUDY; FEMALE; FOLLOW UP; GENE EXPRESSION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETICS; HUMAN; MAJOR CLINICAL STUDY; MALE; NON INSULIN DEPENDENT DIABETES MELLITUS; PROSPECTIVE STUDY; PROTEIN EXPRESSION; SINGLE NUCLEOTIDE POLYMORPHISM;

ADAM PROTEINS; ANTIGENS, CD; CASE-CONTROL STUDIES; COHORT STUDIES; DIABETES MELLITUS, TYPE 2; FEMALE; GENE EXPRESSION REGULATION; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LECTINS, C-TYPE; MALE; MEMBRANE TRANSPORT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSPECTIVE STUDIES; RECEPTORS, CELL SURFACE; TRANSCRIPTION FACTOR 7-LIKE 2 PROTEIN; UBIQUITIN THIOLESTERASE;

UNITED STATES;

EID: 84865801091     PISSN: 00029262     EISSN: 14766256     Source Type: Journal    
DOI: 10.1093/aje/kws123     Document Type: Article

References (36)

1. The Diabetes Atlas. 4th ed. Brussels, Belgium: International Diabetes Federation; 2009.
2. Narayan KM, Boyle JP, Geiss LS, et al. Impact of recent increase in incidence on future diabetes burden: U.S., 2005-2050. Diabetes Care. 2006;29(9):2114-2116.
3. Hindorff LA, Sethupathy P, Junkins HA, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA. 2009;106(23):9362-9367.
4. Zeggini E, Scott LJ, Saxena R, et al. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 2008;40(5):638-645.
5. Tong Y, Lin Y, Zhang Y, et al. Association between TCF7L2 gene polymorphisms and susceptibility to type 2 diabetes mellitus: a large Human Genome Epidemiology (HuGE) review and meta-analysis. BMC Med Genet. 2009;10(1):15. (doi:10.1186/1471-2350-10-15).
6. Cauchi S, El Achhab Y, Choquet H, et al. TCF7L2 is reproducibly associated with type 2 diabetes in various ethnic groups: a global meta-analysis. J Mol Med (Berl). 2007;85(7): 777-782.
7. Yan Y, North KE, Heiss G, et al. Transcription factor 7-like 2 (TCF7L2) polymorphism and context-specific risk of impaired fasting glucose in African American and Caucasian adults: the Atherosclerosis Risk in Communities (ARIC) Study. Diabetes Metab Res Rev. 2010;26(5):371-377.
8. Wu MC, Kraft P, Epstein MP, et al. Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet. 2010;86(6):929-942.
9. Zhong H, Yang X, Kaplan LM, et al. Integrating pathway analysis and genetics of gene expression for genome-wide association studies. Am J Hum Genet. 2010;86(4):581-591.
10. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545-15550.
11. Raychaudhuri S, Plenge RM, Rossin EJ, et al. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. International Schizophrenia Consortium. PLoS Genet. 2009; 5(6):e1000534. (doi:10.1371/journal.pgen.1000534).
12. Qi L, Cornelis MC, Kraft P, et al. Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes. Meta-Analysis of Glucose and Insulin-related traits Consortium (MAGIC); Diabetes Genetics Replication and Meta-analysis (DIAGRAM) Consortium. Hum Mol Genet. 2010;19(13): 2706-2715.
13. Rimm EB, Giovannucci EL, Willett WC, et al. Prospective study of alcohol consumption and risk of coronary disease in men. Lancet. 1991;338(8765):464-468.
14. Colditz GA, Hankinson SE. The Nurses' Health Study: lifestyle and health among women. Nat Rev Cancer. 2005; 5(5):388-396.
15. Hughes TR, Mao M, Jones AR, et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol. 2001;19(4):342-347.
16. Li Y, Willer C, Sanna S, et al. Genotype imputation. Annu Rev Genomics Hum Genet. 2009;10(1):387-406.
17. 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(3):559-575.
18. Aulchenko YS, Struchalin MV, van Duijn CM. ProbABEL package for genome-wide association analysis of imputed data. BMC Bioinformatics. 2010;11(1):134. (doi:10.1186/1471-2105-11-134).
19. Price AL, Patterson NJ, Plenge RM, et al. Principal components analysis corrects for stratification in genomewide association studies. Nat Genet. 2006;38(8):904-909.
20. Emilsson V, Thorleifsson G, Zhang B, et al. Genetics of gene expression and its effect on disease. Nature. 2008;452(7186): 423-428.
21. Greenawalt DM, Dobrin R, Chudin E, et al. A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res. 2011;21(7):1008-1016.
22. Schadt EE, Molony C, Chudin E, et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 2008;6(5):e107. (doi:10.1371/ journal.pbio.0060107).
23. Zhong H, Beaulaurier J, Lum PY, et al. Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet. 2010;6(5):e1000932. (doi:10.1371/journal.pgen.1000932).
24. Ogata H, Goto S, Sato K, et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999;27(1):29-34.
25. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57(1):289-300.
26. Dina C, Meyre D, Gallina S, et al. Variation in FTO contributes to childhood obesity and severe adult obesity. Nat Genet. 2007;39(6):724-726.
27. Salonen JT, Uimari P, Aalto JM, et al. Type 2 diabetes wholegenome association study in four populations: the DiaGen Consortium. Am J Hum Genet. 2007;81(2):338-345.
28. Grant SF, Thorleifsson G, Reynisdottir I, et al. Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes. Nat Genet. 2006;38(3):320-323.
29. Chen Y, Zhu J, Lum PY, et al. Variations in DNA elucidate molecular networks that cause disease. Nature. 2008; 452(7186):429-435.
30. Furukawa S, Fujita T, Shimabukuro M, et al. Increased oxidative stress in obesity and its impact on metabolic syndrome. J Clin Invest. 2004;114(12):1752-1761.
31. Cornelis MC, Tchetgen Tchetgen EJ, Liang L, et al. Geneenvironment interactions in genome-wide association studies: a comparative study of tests applied to empirical studies of type 2 diabetes. Am J Epidemiol. 2012;175(3):191-202.
32. Bhattacharya S, Dey D, Roy SS. Molecular mechanism of insulin resistance. J Biosci. 2007;32(2):405-413.
33. Odom DT, Zizlsperger N, Gordon DB, et al. Control of pancreas and liver gene expression by HNF transcription factors. Science. 2004;303(5662):1378-1381.
34. Wang S, Yehya N, Schadt EE, et al. Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet. 2006;2(2):e15. (doi:10.1371/journal.pgen.0020015).
35. Guest CB, Park MJ, Johnson DR, et al. The implication of proinflammatory cytokines in type 2 diabetes. Front Biosci. 2008;13(1):5187-5194.
36. Perry JR, McCarthy MI, Hattersley AT, et al. Interrogating type 2 diabetes genome-wide association data using a biological pathway-based approach. Wellcome Trust Case Control Consortium. Diabetes. 2009;58(6):1463-1467.