Pathway-based genome-wide association analysis of coronary heart disease identifies biologically important gene sets

European Journal of Human Genetics

Volumn 20, Issue 11, 2012, Pages 1168-1173

  De Las Fuentes, Lisa ^a   Yang, Wei ^a   Dávila Román, Victor G ^a   Gu, C Charles ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

gene set enrichment; genome wide association; pathway based analysis; SNP

Indexed keywords

GLYCEROLIPID; RAC1 PROTEIN; SULFUR AMINO ACID;

ADULT; AMINO ACID METABOLISM; ANALYTIC METHOD; ANGIOGENESIS; ARTICLE; CELL MOTILITY; CONTROLLED STUDY; FATTY ACID METABOLISM; FATTY ACID SYNTHESIS; FEMALE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; ISCHEMIC HEART DISEASE; LIPID METABOLISM; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; VARIABLE SET ENRICHMENT ANALYSIS;

CASE-CONTROL STUDIES; CORONARY DISEASE; GENETIC LOCI; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; METABOLIC NETWORKS AND PATHWAYS; POLYMORPHISM, SINGLE NUCLEOTIDE; RAC1 GTP-BINDING PROTEIN;

EID: 84867742795     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2012.66     Document Type: Article

References (54)

1. Maher B: Personal genomes: the case of the missing heritability. Nature 2008; 456: 18-21.
2. Manolio TA, Collins FS, Cox NJ et al: Finding the missing heritability of complex diseases. Nature 2009; 461: 747-753.
3. Zhang K, Weder AB, Eskin E, O'Connor DT: Genome-wide case/control studies in hypertension: only the 'tip of the iceberg'. J Hypertens 2010; 28: 1115-1123.
4. Torkamani A, Topol EJ, Schork NJ: Pathway analysis of seven common diseases assessed by genome-wide association. Genomics 2008; 92: 265-272.
5. 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: 15545-15550.
6. Wang K, Li M, Bucan M: Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 2007; 81: 1278-1283.
7. Park JY, Li W, Zheng D et al: Comparative analysis of mRNA isoform expression in cardiac hypertrophy and development reveals multiple post-transcriptional regulatory modules. PLoS One 2011; 6: e22391.
8. Yang W, de las Fuentes L, Davila-Roman VG, Charles Gu C: Variable set enrichment analysis in genome-wide association studies. Eur J Hum Genet 2011; 19: 893-900.
9. Cupples LA, Arruda HT, Benjamin EJ et al: The Framingham Heart Study 100 K SNP genome-wide association study resource: overview of 17 phenotype working group reports. BMC Med Genet 2007; 8: Suppl 1 S1.
10. Kannel WB, Wolf PA, Garrison RJ: Monograph chapter 34: some risk factor related to the annual incidence of cardiovascular disease and death using pooled repeated biennial measurements: framingham heart study, 30-year follow-up. Springfield, MA: National Technical Information Service, 1987; pp 1-459.
11. 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.
12. Knight S, Abo RP, Wong J, Thomas A, Camp NJ: Pedigree association: assigning individual weights to pedigree members for genetic association analysis. BMC Proc 2009; 3: Suppl 7 S121.
13. McArdle PF, O'Connell JR, Pollin TI et al: Accounting for relatedness in family based genetic association studies. Hum Hered 2007; 64: 234-242.
14. Kleinbaum DG, Kupper LL: Applied regression analysis and other multivariable methods. North Scituate, MA: Duxbury Press, 1978.
15. Horwitz B: Simulating functional interactions in the brain: a model for examining correlations between regional cerebral metabolic rates. Int J Biomed Comput 1990; 26: 149-170.
16. Cordell HJ: Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 2009; 10: 392-404.
17. Zhao J, Jin L, Xiong M: Test for interaction between two unlinked loci. Am J Hum Genet 2006; 79: 831-845.
18. Howell WM, Ali S, Rose-Zerilli MJ, Ye S: VEGF polymorphisms and severity of atherosclerosis. J Med Genet 2005; 42: 485-490.
19. Petrovic D, Verhovec R, Globocnik Petrovic M, Osredkar J, Peterlin B: Association of vascular endothelial growth factor gene polymorphism with myocardial infarction in patients with type 2 diabetes. Cardiology 2007; 107: 291-295.
20. Heid IM, Jackson AU, Randall JC et al: Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet 2010; 42: 949-960.
21. Linsel-Nitschke P, Gotz A, Medack A et al: Genetic variation in the arachidonate 5-lipoxygenase-activating protein (ALOX5AP) is associated with myocardial infarction in the German population. Clin Sci (Lond) 2008; 115: 309-315.
22. Lee CR, North KE, Bray MS, Couper DJ, Heiss G, Zeldin DC: Cyclooxygenase polymorphisms and risk of cardiovascular events: the Atherosclerosis Risk in Communities (ARIC) study. Clin Pharmacol Ther 2008; 83: 52-60.
23. Rudock ME, Liu Y, Ziegler JT et al: Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid calcium in the Diabetes Heart Study. Atherosclerosis 2009; 203: 459-465.
24. van der Net JB, Versmissen J, Oosterveer DM et al: Arachidonate 5-lipoxygenase-activating protein (ALOX5AP) gene and coronary heart disease risk in familial hypercholesterolemia. Atherosclerosis 2009; 203: 472-478.
25. Burdon KP, Rudock ME, Lehtinen AB et al: Human lipoxygenase pathway gene variation and association with markers of subclinical atherosclerosis in the diabetes heart study. Mediators Inflamm 2010; 2010: 170153.
26. Hegener HH, Diehl KA, Kurth T, Gaziano JM, Ridker PM, Zee RY: Polymorphisms of prostaglandin-endoperoxide synthase 2 gene, and prostaglandin-E receptor 2 gene, C-reactive protein concentrations and risk of atherothrombosis: a nested case-control approach. J Thromb Haemost 2006; 4: 1718-1722.
27. Love-Gregory L, Sherva R, Schappe T et al: Common CD36 SNPs reduce protein expression and may contribute to a protective atherogenic profile. Hum Mol Genet 2011; 20: 193-201.
28. Knowles JW, Wang H, Itakura H et al: Association of polymorphisms in platelet and hemostasis system genes with acute myocardial infarction. Am Heart J 2007; 154: 1052-1058.
29. Oguri M, Kato K, Yokoi K et al: Association of genetic variants with myocardial infarction in Japanese individuals with metabolic syndrome. Atherosclerosis 2009; 206: 486-493.
30. Hegener HH, Lee IM, Cook NR, Ridker PM, Zee RY: Association of adiponectin gene variations with risk of incident myocardial infarction and ischemic stroke: a nested case-control study. Clin Chem 2006; 52: 2021-2027.
31. Anand SS, Xie C, Pare G et al: Genetic variants associated with myocardial infarction risk factors in over 8000 individuals from five ethnic groups: The INTERHEART Genetics Study. Circ Cardiovasc Genet 2009; 2: 16-25.
32. Koide S, Kugiyama K, Sugiyama S et al: Association of polymorphism in glutamate-cysteine ligase catalytic subunit gene with coronary vasomotor dysfunction and myocardial infarction. J Am Coll Cardiol 2003; 41: 539-545.
33. Zhao H, Sun J, Deschamps AM et al: Myristoylated methionine sulfoxide reductase a protects the heart from ischemia-reperfusion injury. Am J Physiol Heart Circ Physiol 2011; 301: H1513-H1518.
34. Prentice HM, Moench IA, Rickaway ZT, Dougherty CJ, Webster KA, Weissbach H: MSRA protects cardiac myocytes against hypoxia/reoxygenation induced cell death. Biochem Biophys Res Commun 2008; 366: 775-778.
35. Kobayashi T, Watanabe Y, Saito Y et al: Mice lacking the glutamate-cysteine ligase modifier subunit are susceptible to myocardial ischaemia-reperfusion injury. Cardio-vasc Res 2010; 85: 785-795.
36. Rallidis LS, Gialeraki A, Komporozos C et al: Role of methylenetetrahydrofolate reductase 677C-4T polymorphism in the development of premature myocardial infarction. Atherosclerosis 2008; 200: 115-120.
37. Ilhan N, Kucuksu M, Kaman D, Ozbay Y: The 677 C/T MTHFR polymorphism is associated with essential hypertension, coronary artery disease, and higher homo-cysteine levels. Arch Med Res 2008; 39: 125-130.
38. Ma J, Stampfer MJ, Hennekens CH et al: Methylenetetrahydrofolate reductase polymorphism, plasma folate, homocysteine, and risk of myocardial infarction in US physicians. Circulation 1996; 94: 2410-2416.
39. Lewis SJ, Ebrahim S, Davey Smith G: Meta-analysis of MTHFR 677C-4T polymorphism and coronary heart disease: does totality of evidence support causal role for homocysteine and preventive potential of folate? BMJ 2005; 331: 1053.
40. Weisberg IS, Park E, Ballman KV et al: Investigations of a common genetic variant in betaine-homocysteine methyltransferase (BHMT) in coronary artery disease. Atherosclerosis 2003; 167: 205-214.
41. Klerk M, Lievers KJ, Kluijtmans LA et al: The 2756A4G variant in the gene encoding methionine synthase: its relation with plasma homocysteine levels and risk of coronary heart disease in a Dutch case-control study. Thromb Res 2003; 110: 87-91.
42. de Vogel S, Wouters KA, Gottschalk RW et al: Genetic variants of methyl metabolizing enzymes and epigenetic regulators: associations with promoter CpG island hyper-methylation in colorectal cancer. Cancer Epidemiol Biomarkers Prev 2009; 18: 3086-3096.
43. Williams KT, Schalinske KL: Tissue-specific alterations of methyl group metabolism and DNA hypermethylation in the Zucker (type 2) diabetic fatty rat. Diabetes Metab Res Rev 2011; 28: 123-131.
44. Shan L, Li J, Wei M et al: Disruption of Rac1 signaling reduces ischemia-reperfusion injury in the diabetic heart by inhibiting calpain. Free Radic Biol Med 2010; 49: 1804-1814.
45. Doerries C, Grote K, Hilfiker-Kleiner D et al: Critical role of the NAD(P)H oxidase subunit p47phox for left ventricular remodeling/dysfunction and survival after myocardial infarction. Circ Res 2007; 100: 894-903.
46. Looi YH, Grieve DJ, Siva A et al: Involvement of Nox2 NADPH oxidase in adverse cardiac remodeling after myocardial infarction. Hypertension 2008; 51: 319-325.
47. Koren MJ, Devereux RB, Casale PN, Savage DD, Laragh JH: Relation of left ventricular mass and geometry to morbidity and mortality in uncomplicated essential hypertension. Ann Intern Med 1991; 114: 345-352.
48. Levy D, Garrison RJ, Savage DD, Kannel WB, Castelli WP: Prognostic implications of echocardiographically determined left ventricular mass in the Framingham Heart Study. N Engl J Med 1990; 322: 1561-1566.
49. Jee SH, Sull JW, Lee JE et al: Adiponectin concentrations: a genome-wide association study. Am J Hum Genet 2010; 87: 545-552.
50. Chung CM et al: Trait locus of adiponectin on CDH13 that predicts cardiometabolic outcomes. Diabetes 2011; 60: 2417-2423.
51. Org E, Eyheramendy S, Juhanson P et al: Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations. Hum Mol Genet 2009; 18: 2288-2296.
52. Segre AV, Diagram Consortium, MAGIC investigators et al: Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits. PLoS Genet 2010; 6.
53. Pers TH, Hansen NT, Lage K et al: Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes. Genet Epidemiol 2011; 35: 318-332.
54. Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB: Protein interaction-based genome-wide analysis of incident coronary heart disease. Circ Cardiovasc Genet 2011; 4: 549-556.