Genetic associations with expression for genes implicated in GWAS studies for atherosclerotic cardiovascular disease and blood phenotypes

Human Molecular Genetics

Volumn 23, Issue 3, 2014, Pages 795-782

  Zhang, Xiaoling ^a,b   Johnson, Andrew D ^a,b   Hendricks, Audrey E ^a,b   Hwang, Shih Jen ^a,b   Tanriverdi, Kahraman ^c   Ganesh, Santhi K ^d   Smith, Nicholas L ^e,f   Peyser, Patricia A ^g   Freedman, Jane E ^c   O'Donnell, Christopher J ^a,b,h  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b FRAMINGHAM HEART STUDY   (United States)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF MICHIGAN HEALTH SYSTEM   (United States)

^e UNIVERSITY OF WASHINGTON   (United States)

^f GROUP HEALTH RESEARCH INSTITUTE   (United States)

^g UNIVERSITY OF MICHIGAN   (United States)

^h MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGED; ARTICLE; ATHEROSCLEROTIC CARDIOVASCULAR DISEASE; BLOOD; FEMALE; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC MODEL; HUMAN; LEUKOCYTE; MAJOR CLINICAL STUDY; MALE; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; ATHEROSCLEROSIS; BIOLOGICAL MODEL; CARDIOVASCULAR DISEASE; COMPUTER SIMULATION; GENETIC PREDISPOSITION; GENETICS; PHYSIOLOGY; PSEUDOGENE; REPRODUCIBILITY; RISK FACTOR; UNITED STATES;

ACYL COENZYME A DESATURASE; FADS2 PROTEIN, HUMAN; LIPID; LIPOPROTEIN LIPASE; LPL PROTEIN, HUMAN;

ATHEROSCLEROSIS; CARDIOVASCULAR DISEASES; COMPUTER SIMULATION; FATTY ACID DESATURASES; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LEUKOCYTES; LIPIDS; LIPOPROTEIN LIPASE; MASSACHUSETTS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PSEUDOGENES; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; RISK FACTORS;

EID: 84892470422     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddt461     Document Type: Article

References (61)

1. Roger, V.L., Go, A.S., Lloyd-Jones, D.M., Benjamin, E.J., Berry, J.D., Borden, W.B., Bravata, D.M., Dai, S., Ford, E.S., Fox, C.S. et al. (2012) Executive summary: heart disease and stroke statistics - 2012 update: a report from the American heart association. Circulation, 125, 188-197.
2. Detrano, R., Guerci, A.D., Carr, J.J., Bild, D.E., Burke, G., Folsom, A.R., Liu, K., Shea, S., Szklo, M., Bluemke, D.A. et al. (2008) Coronary calcium as a predictor of coronary events in four racial or ethnic groups. N. Engl. J.Med., 358, 1336-1345.
3. Polak, J.F., Pencina, M.J., Pencina, K.M., O'Donnell, C.J., Wolf, P.A. and D'Agostino, R.B. Sr. (2011) Carotid-wall intima-media thickness and cardiovascular events. N. Engl. J. Med., 365, 213-221.
4. Danesh, J., Lewington, S., Thompson, S.G., Lowe, G.D., Collins, R., Kostis, J.B., Wilson, A.C., Folsom, A.R., Wu, K., Benderly, M. et al. (2005) Plasma fibrinogen level and the risk of major cardiovascular diseases and nonvascular mortality: an individual participant meta-analysis. JAMA, 294, 1799-1809.
5. Smith, A., Patterson, C., Yarnell, J., Rumley, A., Ben-Shlomo,Y. and Lowe, G. (2005) Which hemostatic markers add to the predictive value of conventional risk factors for coronary heart disease and ischemic stroke?The caerphilly study. Circulation, 112, 3080-3087.
6. Folsom, A.R., Cushman, M., Heckbert, S.R., Ohira, T., Rasmussen-Torvik, L. and Tsai, M.Y. (2007) Factor VII coagulant activity, factor VII -670A/C and -402G/A polymorphisms, and risk of venous thromboembolism. J. Thromb. Haemost., 5, 1674-1678.
7. Carpeggiani, C., Coceani, M., Landi, P., Michelassi, C. and L'Abbate, A. (2010)ABOBlood group alleles: a risk factor for coronary artery disease.An angiographic study. Atherosclerosis, 211, 461-466.
8. Zakai, N.A., Katz, R., Hirsch, C., Shlipak, M.G., Chaves, P.H., Newman, A.B. and Cushman, M. (2005) A prospective study of anemia status, hemoglobin concentration, and mortality in an elderly cohort: the cardiovascular health study. Arch. Intern. Med., 165, 2214-2220.
9. Ganesh, S.K., Zakai, N.A., van Rooij, F.J., Soranzo, N., Smith, A.V., Nalls, M.A., Chen, M.H., Kottgen, A., Glazer, N.L., Dehghan, A. et al. (2009) Multiple loci influence erythrocyte phenotypes in theCHARGEconsortium. Nat. Genet., 41, 1191-1198.
10. O'Donnell, C.J. and Nabel, E.G. (2011) Genomics of cardiovascular disease. N. Engl. J. Med., 365, 2098-2109.
11. Schunkert, H., Konig, I.R., Kathiresan, S., Reilly, M.P., Assimes, T.L., Holm, H., Preuss, M., Stewart, A.F., Barbalic, M., Gieger, C. et al. (2011) Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat. Genet., 43, 333-338.
12. Wang, F., Xu, C.Q., He, Q., Cai, J.P., Li, X.C., Wang, D., Xiong, X., Liao, Y.H., Zeng, Q.T., Yang, Y.Z. et al. (2011) Genome-wide association identifies a susceptibility locus for coronary artery disease in the Chinese Han population. Nat. Genet., 43, 345-349.
13. The Coronary Artery Disease (C4D) Genetics Consortium. (2011) A genome-wide association study in Europeans and south Asians identifies five new loci for coronary artery disease. Nat. Genet., 43, 339-344.
14. Reiner, A.P., Lettre, G., Nalls, M.A., Ganesh, S.K., Mathias, R., Austin, M.A., Dean, E., Arepalli, S., Britton, A., Chen, Z. et al. (2011)Genome-wide association study of white blood cell count in 16,388 African Americans: the continental origins and genetic epidemiology network (COGENT). PLoS Genet., 7, e1002108.
15. Johnson, A.D., Yanek, L.R., Chen, M.H., Faraday, N., Larson, M.G., Tofler, G., Lin, S.J., Kraja, A.T., Province, M.A., Yang, Q. et al. (2010) Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists. Nat. Genet., 42, 608-613.
16. Lovely, R.S., Yang, Q., Massaro, J.M., Wang, J., D'Agostino, R.B. Sr, O'Donnell, C.J., Shannon, J. and Farrell, D.H. (2011) Assessment of genetic determinants of the association of {gamma}' fibrinogen in relation to cardiovascular disease. Arterioscler Thromb. Vasc. Biol., 31, 2345-2352.
17. Dehghan, A., Yang, Q., Peters, A., Basu, S., Bis, J.C., Rudnicka, A.R., Kavousi, M., Chen, M.H., Baumert, J., Lowe, G.D. et al. (2009) Association of novel genetic loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts. Circ. Cardiovasc. Genet., 2, 125-133.
18. Smith, N.L., Chen, M.H.,Dehghan, A., Strachan, D.P., Basu, S., Soranzo, N., Hayward, C., Rudan, I., Sabater-Lleal, M., Bis, J.C. et al. (2010) Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von willebrand factor: the CHARGE (cohorts for heart and aging research in genome epidemiology) consortium. Circulation, 121, 1382-1392.
19. Bis, J.C., Kavousi, M., Franceschini, N., Isaacs, A., Abecasis, G.R., Schminke, U., Post, W.S., Smith, A.V., Cupples, L.A., Markus, H.S. et al. (2011) Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque. Nat. Genet., 43, 940-947.
20. O'Donnell, C.J., Kavousi, M., Smith, A.V., Kardia, S.L., Feitosa, M.F., Hwang, S.J., Sun, Y.V., Province, M.A., Aspelund, T., Dehghan, A. et al. (2011) Genome-wide association study for coronary artery calcification With follow-up in myocardial infarction. Circulation, 124, 2855-2864.
21. Sadee, W., Wang, D., Papp, A.C., Pinsonneault, J.K., Smith, R.M., Moyer, R.A. and Johnson, A.D. (2011) Pharmacogenomics of the RNA world: structuralRNApolymorphisms in drug therapy. Clin. Pharmacol. Ther., 89, 355-365.
22. Ioannidis, J.P., Thomas, G. and Daly, M.J. (2009) Validating, augmenting and refining genome-wide association signals. Nat. Rev. Genet., 10, 318-329.
23. Cheung, V.G. and Spielman, R.S. (2009) Genetics of human gene expression: mappingDNAvariants that influence gene expression. Nat. Rev. Genet., 10, 595-604.
24. Cookson, W., Liang, L., Abecasis, G., Moffatt, M. and Lathrop, M. (2009) Mapping complex disease traits with global gene expression. Nat. Rev. Genet., 10, 184-194.
25. Zeller, T., Wild, P., Szymczak, S., Rotival, M., Schillert, A., Castagne, R., Maouche, S., Germain, M., Lackner, K., Rossmann, H. et al. (2010) Genetics and beyond - the transcriptome of human monocytes and disease susceptibility. PLoS ONE, 5, e10693.
26. Fehrmann, R.S., Jansen, R.C., Veldink, J.H., Westra, H.J., Arends, D., Bonder, M.J., Fu, J., Deelen, P., Groen, H.J., Smolonska, A. et al. (2011) Trans-eQTLs reveal that independent genetic variants associated with a complexphenotype convergeon intermediate genes, with a major role for the HLA. PLoS Genet., 7, e1002197.
27. Teslovich, T.M., Musunuru, K., Smith, A.V., Edmondson, A.C., Stylianou, I.M., Koseki, M., Pirruccello, J.P., Ripatti, S., Chasman, D.I., Willer, C.J. et al. (2010) Biological, clinical and population relevance of 95 loci for blood lipids. Nature, 466, 707-713.
28. Freedman, J.E., Larson, M.G., Tanriverdi, K., O'Donnell, C.J., Morin, K., Hakanson, A.S., Vasan, R.S., Johnson, A.D., Iafrati, M.D. and Benjamin, E.J. (2010) Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framingham heart study. Circulation, 122, 119-129.
29. Li, J. and Ji, L. (2005) Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity (Edinburgh), 95, 221-227.
30. Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter, D.J., McCarthy, M.I., Ramos, E.M., Cardon, L.R., Chakravarti, A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
31. Huang, J., Johnson, A.D. and O'Donnell, C.J. (2011) PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies. Bioinformatics, 27, 1201-1206.
32. Dixon, A.L., Liang, L., Moffatt, M.F., Chen, W., Heath, S., Wong, K.C., Taylor, J., Burnett, E., Gut, I., Farrall, M. et al. (2007) A genome-wide association study of global gene expression. Nat. Genet., 39, 1202-1207.
33. Newton-Cheh, C., Johnson, T., Gateva, V., Tobin, M.D., Bochud, M., Coin, L., Najjar, S.S., Zhao, J.H., Heath, S.C., Eyheramendy, S. et al. (2009) Genome-wide association study identifies eight loci associated with blood pressure. Nat. Genet., 41, 666-676.
34. Wain, L.V., Verwoert, G.C., O'Reilly, P.F., Shi, G., Johnson, T., Johnson, A.D., Bochud, M., Rice, K.M., Henneman, P., Smith, A.V. et al. (2011) Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure. Nat. Genet., 43, 1005-1011.
35. Ehret, G.B., Munroe, P.B., Rice, K.M., Bochud, M., Johnson, A.D., Chasman, D.I., Smith, A.V., Tobin, M.D., Verwoert, G.C., Hwang, S.J. et al. (2011) Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature, 478, 103-109.
36. Kathiresan, S., Voight, B.F., Purcell, S., Musunuru, K., Ardissino, D., Mannucci, P.M., Anand, S., Engert, J.C., Samani, N.J., Schunkert, H. et al. (2009) Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat. Genet., 41, 334-341.
37. Murphy, A., Chu, J.H., Xu, M., Carey, V.J., Lazarus, R., Liu, A., Szefler, S.J., Strunk, R., Demuth, K., Castro, M. et al. (2010) Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes. Hum. Mol. Genet., 19, 4745-4757.
38. Goring, H.H., Curran, J.E., Johnson, M.P., Dyer, T.D., Charlesworth, J., Cole, S.A., Jowett, J.B., Abraham, L.J., Rainwater, D.L., Comuzzie, A.G. et al. (2007) Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat. Genet., 39, 1208-1216.
39. Heinzen, E.L., Ge, D., Cronin, K.D., Maia, J.M., Shianna, K.V., Gabriel, W.N., Welsh-Bohmer, K.A., Hulette, C.M., Denny, T.N. and Goldstein, D.B. (2008) Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol., 6, e1.
40. Idaghdour, Y., Czika, W., Shianna, K.V., Lee, S.H., Visscher, P.M., Martin, H.C., Miclaus, K., Jadallah, S.J., Goldstein, D.B., Wolfinger, R.D. et al. (2010) Geographical genomics of human leukocyte gene expression variation in southern morocco. Nat. Genet., 42, 62-67.
41. Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A.S., Zink, F., Zhu, J., Carlson, S., Helgason, A., Walters, G.B., Gunnarsdottir, S. et al. (2008) Genetics of gene expression and its effect on disease. Nature, 452, 423-428.
42. Soranzo, N., Spector, T.D., Mangino, M., Kuhnel, B., Rendon, A., Teumer, A., Willenborg, C., Wright, B., Chen, L., Li, M. et al. (2009)Agenome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the haemGen consortium. Nat. Genet., 41, 1182-1190.
43. Zhu, J., Zhang, B., Smith, E.N., Drees, B., Brem, R.B., Kruglyak, L., Bumgarner, R.E. and Schadt, E.E. (2008) Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat. Genet., 40, 854-861.
44. Yang, X., Deignan, J.L., Qi, H., Zhu, J., Qian, S., Zhong, J., Torosyan, G., Majid, S., Falkard, B., Kleinhanz, R.R. et al. (2009) Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat. Genet., 41, 415-423.
45. Chen, Y., Zhu, J., Lum, P.Y., Yang, X., Pinto, S., Macneil, D.J., Zhang, C., Lamb, J., Edwards, S., Sieberts, S.K. et al. (2008) Variations in DNA elucidate molecular networks that cause disease. Nature, 452, 429-435.
46. Heinig,M., Petretto, E., Wallace, C., Bottolo, L., Rotival,M., Lu, H., Li, Y., Sarwar, R., Langley, S.R., Bauerfeind, A. et al. (2010) A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature, 467, 460-464.
47. Nicolae, D.L., Gamazon, E., Zhang, W., Duan, S., Dolan, M.E. and Cox, N.J. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet., 6, e1000888.
48. Greenawalt, D.M., Dobrin, R., Chudin, E., Hatoum, I.J., Suver, C., Beaulaurier, J., Zhang, B., Castro, V., Zhu, J., Sieberts, S.K. et al. (2011) A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res., 21, 1008-1016.
49. Johnson, A.D., Zhang, Y., Papp, A.C., Pinsonneault, J.K., Lim, J.E., Saffen, D., Dai, Z., Wang, D. and Sadee, W. (2008) Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. Pharmacogenet. Genomics, 18, 781-791.
50. Harismendy, O., Notani, D., Song, X., Rahim, N.G., Tanasa, B., Heintzman, N., Ren, B., Fu, X.D., Topol, E.J., Rosenfeld, M.G. et al. (2011) 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response. Nature, 470, 264-268.
51. Musunuru, K., Strong, A., Frank-Kamenetsky, M., Lee, N.E., Ahfeldt, T., Sachs, K.V., Li, X., Li, H., Kuperwasser, N., Ruda, V.M. et al. (2010) From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature, 466, 714-719.
52. Folkersen, L., van't Hooft, F., Chernogubova, E., Agardh, H.E., Hansson, G.K., Hedin, U., Liska, J., Syvanen, A.C., Paulsson-Berne, G., Franco-Cereceda, A. et al. (2010) Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular disease. Circ. Cardiovasc. Genet., 3, 365-373.
53. Montgomery, S.B. and Dermitzakis, E.T. (2011) From expression QTLs to personalized transcriptomics. Nat. Rev. Genet., 12, 277-282.
54. Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
55. Dawber, T.R., Kannel, W.B. and Lyell, L.P. (1963) An approach to longitudinal studies in acommunity: the Framinghamstudy. Ann. N. Y. Acad. Sci., 107, 539-556.
56. Kannel, W.B., Feinleib, M., McNamara, P.M., Garrison, R.J. and Castelli, W.P. (1979) An investigation of coronary heart disease in families. The Framingham offspring study. Am. J. Epidemiol., 110, 281-290.
57. Feinleib, M., Kannel, W.B., Garrison, R.J., McNamara, P.M. and Castelli, W.P. (1975) The Framingham offspring study. Design and preliminary data. Prev. Med., 4, 518-525.
58. Splansky, G.L., Corey, D., Yang, Q., Atwood, L.D., Cupples, L.A., Benjamin, E.J., D'Agostino, R.B. Sr, Fox, C.S., Larson, M.G., Murabito, J.M. et al. (2007) The third generation cohort of the national heart, lung, and blood institute's Framingham heart study: design, recruitment, and initial examination. Am. J. Epidemiol., 165, 1328-1335.
59. Li, Y., Willer, C.J., Ding, J., Scheet, P. and Abecasis, G.R. (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol., 34, 816-834.
60. Dupuis, J., Siegmund, D.O. and Yakir, B. (2007) A unified framework for linkage and association analysis of quantitative traits. Proc. Natl. Acad. Sci. USA, 104, 20210-20215.
61. Myers, A.J., Gibbs, J.R., Webster, J.A., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., Leung, D., Bryden, L., Nath, P. et al. (2007)Asurvey of genetic human cortical gene expression. Nat. Genet., 39, 1494-1499.