Genome-wide significant loci: How important are they?: Systems genetics to understand heritability of coronary artery disease and other common complex disorders

Journal of the American College of Cardiology

Volumn 65, Issue 8, 2015, Pages 830-845

  Björkegren, Johan L M ^a,b,c   Kovacic, Jason C ^a   Dudley, Joel T ^a   Schadt, Eric E ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b KAROLINSKA INSTITUTE   (Sweden)

^c UNIVERSITY OF TARTU   (Estonia)

Author keywords

atherosclerosis; atherosclerotic plaque; genome wide association study; myocardial infarction; primary prevention; regulatory gene networks

Indexed keywords

ATHEROSCLEROSIS; CARDIOVASCULAR RISK; CEREBROVASCULAR ACCIDENT; CLINICAL FEATURE; CORONARY ARTERY DISEASE; DISEASE COURSE; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENE TARGETING; GENETIC ASSOCIATION; GENETIC REGULATION; GENETIC VARIABILITY; HEART INFARCTION; HERITABILITY; HUMAN; MOLECULAR GENETICS; MOLECULAR PATHOLOGY; MONOGENIC DISORDER; NONHUMAN; PRIORITY JOURNAL; RARE DISEASE; REVIEW; RISK FACTOR; SYSTEMS GENETICS; GENETIC PREDISPOSITION; GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

CORONARY ARTERY DISEASE; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS;

EID: 84923342405     PISSN: 07351097     EISSN: 15583597     Source Type: Journal    
DOI: 10.1016/j.jacc.2014.12.033     Document Type: Review

References (95)

1. V. Hughes Epigenetics: the sins of the father Nature 507 2014 22 24
2. S. Cortijo, R. Wardenaar, and M. Colome-Tatche Mapping the epigenetic basis of complex traits Science 343 2014 1145 1148
3. R. Holliday DNA methylation and epigenetic mechanisms Cell Biophys 15 1989 15 20
4. G. Felsenfeld A brief history of epigenetics Cold Spring Harb Perspect Biol 6 2014 a018200
5. S.H. Friend, and E.E. Schadt Translational genomics. Clues from the resilient Science 344 2014 970 972
6. C.S. Ku, N. Naidoo, and Y. Pawitan Revisiting Mendelian disorders through exome sequencing Hum Genet 129 2011 351 370
7. S. Hägg, J. Skogsberg, and J. Lundström Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study PLoS Genet 5 2009 e1000754
8. R. Roberts Genetics of coronary artery disease Circ Res 114 2014 1890 1903
9. N.J. Samani, J. Erdmann, A.S. Hall for the WTCCC and the Cardiogenics Consortium Genomewide association analysis of coronary artery disease N Engl J Med 357 2007 443 453
10. A. Helgadottir, G. Thorleifsson, and A. Manolescu A common variant on chromosome 9p21 affects the risk of myocardial infarction Science 316 2007 1491 1493
11. R. McPherson, A. Pertsemlidis, and N. Kavaslar A common allele on chromosome 9 associated with coronary heart disease Science 316 2007 1488 1491
12. P. Deloukas, S. Kanoni, C. Willenborg for the CARDIoGRAMplusC4D Consortium Large-scale association analysis identifies new risk loci for coronary artery disease Nat Genet 45 2013 25 33
13. Hindorff LA, MacArthur J, Morales J, et al. A catalog of published genome-wide association studies. Available at: http://www.genome.gov/gwastudies. Accessed December 21, 2014.
14. T.A. Manolio, F.S. Collins, and N.J. Cox Finding the missing heritability of complex diseases Nature 461 2009 747 753
15. M.E. Marenberg, N. Risch, and L.F. Berkman Genetic susceptibility to death from coronary heart disease in a study of twins N Engl J Med 330 1994 1041 1046
16. J. Yang, B. Benyamin, and B.P. McEvoy Common SNPs explain a large proportion of the heritability for human height Nat Genet 42 2010 565 569
17. E.E. Schadt, and J.L. Bjorkegren NEW: network-enabled wisdom in biology, medicine, and health care Sci Transl Med 4 2012 115rv1
18. M.J. Joyner, and F.G. Prendergast Chasing Mendel: five questions for personalized medicine J Physiol 592 2014 2381 2388
19. M. Allaby A Dictionary of Zoology 2nd edition 1999 Oxford University Press New York, NY vi, 597
20. J. Narula, and J.C. Kovacic Putting TCFA in clinical perspective J Am Coll Cardiol 64 2014 681 683
21. J. Skogsberg, J. Lundstrom, and A. Kovacs Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes PLoS Genet 4 2008 e1000036
22. J.L. Bjorkegren, S. Hagg, and H.A. Talukdar Plasma cholesterol-induced lesion networks activated before regression of early, mature, and advanced atherosclerosis PLoS Genet 10 2014 e1004201
23. S. Hagg, M. Salehpour, and P. Noori Carotid plaque age is a feature of plaque stability inversely related to levels of plasma insulin PloS One 6 2011 e18248
24. A.J. Lusis Atherosclerosis Nature 407 2000 233 241
25. T. Kubo, A. Maehara, and G.S. Mintz The dynamic nature of coronary artery lesion morphology assessed by serial virtual histology intravascular ultrasound tissue characterization J Am Coll Cardiol 55 2010 1590 1597
26. J.F. Bentzon, F. Otsuka, and R. Virmani Mechanisms of plaque formation and rupture Circ Res 114 2014 1852 1866
27. C.M. Lusk, G. Dyson, and A.G. Clark Validated context-dependent associations of coronary heart disease risk with genotype variation in the chromosome 9p21 region: the Atherosclerosis Risk in Communities study Hum Genet 133 2014 1105 1116
28. M.N. Peters, J.C. Moscona, and M.J. Katz Natural disasters and myocardial infarction: the six years after Hurricane Katrina Mayo Clin Proc 89 2014 472 477
29. C. Chan, J. Elliott, and R. Troughton Acute myocardial infarction and stress cardiomyopathy following the Christchurch earthquakes PloS One 8 2013 e68504
30. E.N. Smith, and L. Kruglyak Gene-environment interaction in yeast gene expression PLoS Biol 6 2008 e83
31. D.A. Smirnov, M. Morley, and E. Shin Genetic analysis of radiation-induced changes in human gene expression Nature 459 2009 587 591
32. C.E. Romanoski, S. Lee, and M.J. Kim Systems genetics analysis of gene-by-environment interactions in human cells Am J Hum Genet 86 2010 399 410
33. L.D. Orozco, B.J. Bennett, and C.R. Farber Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages Cell 151 2012 658 670
34. P.A. James, S. Oparil, and B.L. Carter 2014 evidence-based guideline for the management of high blood pressure in adults: report from the panel members appointed to the Eighth Joint National Committee (JNC 8) JAMA 311 2014 507 520
35. T. Ogihara, T. Saruta, H. Rakugi for the Valsartan in Elderly Isolated Systolic Hypertension Study Group Target blood pressure for treatment of isolated systolic hypertension in the elderly: valsartan in elderly isolated systolic hypertension study Hypertension 56 2010 196 202
36. JATOS Study Group Principal results of the Japanese trial to assess optimal systolic blood pressure in elderly hypertensive patients (JATOS) Hypertension Res 31 2008 2115 2127
37. M.P. Reilly, M. Li, and J. He Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies Lancet 377 2011 383 392
38. G.K. Hansson Inflammation, atherosclerosis, and coronary artery disease N Engl J Med 352 2005 1685 1695
39. P. Libby, P.M. Ridker, G.K. Hansson Leducq Transatlantic Network on Atherothrombosis Inflammation in atherosclerosis: from pathophysiology to practice J Am Coll Cardiol 54 2009 2129 2138
40. B.A. Kidd, L.A. Peters, and E.E. Schadt Unifying immunology with informatics and multiscale biology Nat Immunol 15 2014 118 127
41. A.J. Lusis, and J.N. Weiss Cardiovascular networks: systems-based approaches to cardiovascular disease Circulation 121 2010 157 170
42. M. Civelek, and A.J. Lusis Systems genetics approaches to understand complex traits Nat Rev Genet 15 2014 34 48
43. J.N. Weiss, A. Karma, and W.R. MacLellan "Good enough solutions" and the genetics of complex diseases Circ Res 111 2012 493 504
44. A.L. Barabasi, and Z.N. Oltvai Network biology: understanding the cell's functional organization Nat Rev Genet 5 2004 101 113
45. E.E. Schadt Molecular networks as sensors and drivers of common human diseases Nature 461 2009 218 223
46. A.L. Barabasi, N. Gulbahce, and J. Loscalzo Network medicine: a network-based approach to human disease Nat Rev Genet 12 2011 56 68
47. B. Zhang, and S. Horvath A general framework for weighted gene co-expression network analysis Stat Appl Genet Mol Biol 4 2005 Article17
48. Y. Chen, J. Zhu, and P.Y. Lum Variations in DNA elucidate molecular networks that cause disease Nature 452 2008 429 435
49. V. Emilsson, G. Thorleifsson, and B. Zhang Genetics of gene expression and its effect on disease Nature 452 2008 423 428
50. I.M. Wang, B. Zhang, and X. Yang Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers Mol Syst Biol 8 2012 594
51. J. Millstein, B. Zhang, and J. Zhu Disentangling molecular relationships with a causal inference test BMC Genet 10 2009 23
52. E.E. Schadt, J. Lamb, and X. Yang An integrative genomics approach to infer causal associations between gene expression and disease Nat Genet 37 2005 710 717
53. Y. Liu, N. Qiao, and S. Zhu A novel Bayesian network inference algorithm for integrative analysis of heterogeneous deep sequencing data Cell Res 23 2013 440 443
54. N. Hubner, C.A. Wallace, and H. Zimdahl Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease Nat Genet 37 2005 243 253
55. W. Cookson, L. Liang, and G. Abecasis Mapping complex disease traits with global gene expression Nat Rev Genet 10 2009 184 194
56. D.L. Nicolae, E. Gamazon, and W. Zhang Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS PLoS Genet 6 2010 e1000888
57. H.P. Kang, A.A. Morgan, and R. Chen Coanalysis of GWAS with eQTLs reveals disease-tissue associations AMIA Jt Summits Transl Sci Proc 2012 35 41
58. H.J. Westra, M.J. Peters, and T. Esko Systematic identification of trans eQTLs as putative drivers of known disease associations Nat Genet 45 2013 1238 1243
59. H. Foroughi Asl, A.H. Talukdar, and A.S. Kindt Expression quantitative trait loci acting across multiple tissues are enriched in inherited risk for coronary artery disease Circ Cardiovasc Genet 2015 Jan 11 [E-pub ahead of print]
60. S. Kathiresan, B.F. Voight, S. Purcell for the Myocardial Infarction Genetics Consortium Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants Nat Genet 41 2009 334 341
61. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
62. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
63. R. Dobrin, J. Zhu, and C. Molony Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease Genome Biol 10 2009 R55
64. J. Zhu, P.Y. Lum, and J. Lamb An integrative genomics approach to the reconstruction of gene networks in segregating populations Cytogenet Genome Res 105 2004 363 374
65. E.E. Schadt, C. Molony, and E. Chudin Mapping the genetic architecture of gene expression in human liver PLoS Biol 6 2008 e107
66. P. Langfelder, and S. Horvath Eigengene networks for studying the relationships between co-expression modules BMC Syst Biol 1 2007 54
67. J. Zhu, B. Zhang, and E.N. Smith Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks Nat Genet 40 2008 854 861
68. X. Yang, B. Zhang, and C. Molony Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver Genome Res 20 2010 1020 1036
69. GTEx Consortium The Genotype-Tissue Expression (GTEx) project Nat Genet 45 2013 580 585
70. B. Lin, J.T. White, and W. Lu Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease Cancer Res 65 2005 3081 3091
71. R.K. Nibbe, M. Koyuturk, and M.R. Chance An integrative -omics approach to identify functional sub-networks in human colorectal cancer PLoS Comput Biol 6 2010 e1000639
72. B. Zhang, C. Gaiteri, and L.G. Bodea Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease Cell 153 2013 707 720
73. S.Y. Shin, E.B. Fauman, and A.K. Petersen An atlas of genetic influences on human blood metabolites Nat Genet 46 2014 543 550
74. J. Kim, N. Ghasemzadeh, and D.J. Eapen Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death Genome Medicine 6 2014 40
75. J. Zhu, P. Sova, and Q. Xu Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation PLoS Biol 10 2012 e1001301
76. J. Qi, H.F. Asl, and J. Bjorkegren kruX: matrix-based non-parametric eQTL discovery BMC Bioinformatics 15 2014 11
77. J.L. Huynh, P. Garg, and T.H. Thin Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains Nat Neurosci 17 2014 121 130
78. G.J. Gu, M. Friedman, and C. Jost Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation New Biotechnol 30 2013 144 152
79. S. Pan, R. Aebersold, and R. Chen Mass spectrometry based targeted protein quantification: methods and applications J Proteome Res 8 2009 787 797
80. J.C. Chan, D.E. Piper, and Q. Cao A proprotein convertase subtilisin/kexin type 9 neutralizing antibody reduces serum cholesterol in mice and nonhuman primates Proc Natl Acad Sci U S A 106 2009 9820 9825
81. L.T. Clark, and F. El-Atat Metabolic syndrome in African Americans: implications for preventing coronary heart disease Clin Cardiol 30 2007 161 164
82. G. Lettre, C.D. Palmer, and T. Young Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project PLoS Genet 7 2011 e1001300
83. L. Qi, and H. Campos Genetic predictors for cardiovascular disease in Hispanics Trends Cardiovasc Med 21 2011 15 20
84. H. Zhong, J. Beaulaurier, and P.Y. Lum Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes PLoS Genet 6 2010 e1000932
85. H. Zhong, X. Yang, and L.M. Kaplan Integrating pathway analysis and genetics of gene expression for genome-wide association studies Am J Hum Genet 86 2010 581 591
86. Y.H. Hsu, M.C. Zillikens, and S.G. Wilson An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility loci for osteoporosis-related traits PLoS Genet 6 2010 e1000977
87. V.P. Makinen, M. Civelek, and Q. Meng Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease PLoS Genet 10 2014 e1004502
88. M.M. Shang, H.A. Talukdar, and J.J. Hofmann Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis Arterioscler Thromb Vasc Biol 34 2014 2068 2077
89. X. Yang, L. Peterson, and R. Thieringer Identification and validation of genes affecting aortic lesions in mice J Clinical Invest 120 2010 2414 2422
90. M.J. Keiser, V. Setola, and J.J. Irwin Predicting new molecular targets for known drugs Nature 462 2009 175 181
91. S. Rashid, D.E. Curtis, and R. Garuti Decreased plasma cholesterol and hypersensitivity to statins in mice lacking Pcsk9 Proc Natl Acad Sci U S A 102 2005 5374 5379
92. J. Lamb, E.D. Crawford, and D. Peck The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease Science 313 2006 1929 1935
93. C. Knox, V. Law, and T. Jewison DrugBank 3.0: a comprehensive resource for 'omics' research on drugs Nucleic Acids Res 39 2011 D1035 D1041
94. J.T. Dudley, M. Sirota, and M. Shenoy Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease Sci Transl Med 3 2011 96ra76
95. N.S. Jahchan, J.T. Dudley, and P.K. Mazur A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors Cancer Disc 3 2013 1364 1377