Expression Quantitative Trait Loci Acting Across Multiple Tissues Are Enriched in Inherited Risk for Coronary Artery Disease

Circulation: Cardiovascular Genetics

Volumn 8, Issue 2, 2015, Pages 305-315

  Foroughi Asl, Hassan ^a   Talukdar, Husain A ^a   Kindt, Alida S D ^b   Jain, Rajeev K ^d   Ermel, Raili ^d,e   Ruusalepp, Arno ^d,f   Nguyen, Khanh Dung H ^g   Dobrin, Radu ^h   Reilly, Dermot F ^g   Schunkert, Heribert ⁱ   Samani, Nilesh J ^j   Braenne, Ingrid ^k   Erdmann, Jeanette ^k   Melander, Olle ^l   Qi, Jianlong ^m   Ivert, Torbjörn ⁿ   Skogsberg, Josefin ^a   Schadt, Eric E ^h   Michoel, Tom ^c,m   Björkegren, Johan L M ^a,d,f,h  

^a Department of Medical Biophysics and Biochemistry   (Sweden)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

^d UNIVERSITY OF TARTU   (Estonia)

^e TARTU UNIVERSITY HOSPITAL   (Estonia)

^f Karolinska Science Park   (Sweden)

^g MERCK RESEARCH LABORATORIES   (United States)

^h MOUNT SINAI SCHOOL OF MEDICINE   (United States)

ⁱ TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^j UNIVERSITY OF LEICESTER   (United Kingdom)

^k UNIVERSITY OF LÜBECK   (Germany)

^l LUND UNIVERSITY HOSPITAL   (Sweden)

^m UNIVERSITY OF FREIBURG   (Germany)

ⁿ KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

more..

Author keywords

coronary artery disease; expression quantitative trait locus; genetics

Indexed keywords

CHOLESTEROL ESTER; DNA; MESSENGER RNA; RNA; SMALL INTERFERING RNA; MUSCLE PROTEIN;

ARTICLE; CELL LINE; CLINICAL ARTICLE; CONTROLLED STUDY; CORONARY ARTERY ATHEROSCLEROSIS; CORONARY ARTERY DISEASE; CORONARY RISK; DISEASE SEVERITY; EXPRESSION QUANTITATIVE TRAIT LOCI; FLYWCH1 GENE; FOAM CELL; G3BP1 GENE; GENE EXPRESSION; GENE SEGREGATION; GENE TARGETING; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; HIGH RISK PATIENT; HUMAN; HUMAN CELL; HUMAN TISSUE; INHERITANCE; MONOCYTE; PRIORITY JOURNAL; PSORS1C3 GENE; QUANTITATIVE TRAIT LOCUS; REGULATOR GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SNAPIN GENE; THP1 CELL LINE; TISSUE CHARACTERIZATION; TISSUE SPECIFICITY; ANTIBODY SPECIFICITY; BIOSYNTHESIS; CLINICAL TRIAL; FEMALE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; MALE; METABOLISM;

CORONARY ARTERY DISEASE; DATABASES, GENETIC; FEMALE; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MUSCLE PROTEINS; ORGAN SPECIFICITY; QUANTITATIVE TRAIT LOCI;

EID: 84923328349     PISSN: 1942325X     EISSN: 19423268     Source Type: Journal    
DOI: 10.1161/CIRCGENETICS.114.000640     Document Type: Article

References (29)

1. Schadt EE, Björkegren JL. NEW: network-enabled wisdom in biology, medicine, and health care. Sci Transl Med. 2012;4:115-1. doi: 10.1126/scitranslmed.3002132.
2. CARDIoGRAMplusC4D Consortium, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet. 2013;45:25-33.
3. Hindorff LA, MacArthur J, Morales J, Junkins HA, Hall PN, Klemm AK, et al. A catalog of published genome-wide association studies. Available at: http://Www.Genome.Gov/gwastudies. Accessed November 21, 2013.
4. Schunkert H, König IR, Kathiresan S, Reilly MP, Assimes TL, Holm H, et al; Cardiogenics; CARDIoGRAM Consortium. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet. 2011;43:333-338. doi: 10.1038/ng.784.
5. Peden JF, Farrall M. Thirty-five common variants for coronary artery disease: the fruits of much collaborative labour. Hum Mol Genet. 2011;20:R198-R205. doi: 10.1093/hmg/ddr384.
6. Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, et al. Variations in DNA elucidate molecular networks that cause disease. Nature. 2008;452:429-435. doi: 10.1038/nature06757.
7. Orozco LD, Bennett BJ, Farber CR, Ghazalpour A, Pan C, Che N, et al. Unraveling inflammatory responses using systems genetics and geneenvironment interactions in macrophages. Cell. 2012;151:658-670. doi: 10.1016/j.cell.2012.08.043.
8. Tegnér J, Skogsberg J, Björkegren J. Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits. J Lipid Res. 2007;48:267-277. doi: 10.1194/jlr.R600030-JLR200.
9. Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009;461:218-223. doi: 10.1038/nature08454.
10. Hägg S, Skogsberg J, Lundström J, Noori P, Nilsson R, Zhong H, et al. 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. 2009;5:e1000754. doi: 10.1371/journal. pgen.1000754.
11. Myocardial Infarction Genetics Consortium, Kathiresan S, Voight BF, Purcell S, Musunuru K, Ardissino D, et al. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet. 2009;41:334-341.
12. The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661-678.
13. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 2008;6:e107. doi: 10.1371/journal.pbio.0060107.
14. Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics. 2010;26:2336-2337. doi: 10.1093/bioinformatics/btq419.
15. The 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56-65.
16. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA. 2009;106:9362-9367. doi: 10.1073/pnas.0903103106.
17. Kindt AS, Navarro P, Semple CA, Haley CS. The genomic signature of trait-associated variants. BMC Genomics. 2013;14:108. doi: 10.1186/1471-2164-14-108.
18. Zhong H, Beaulaurier J, Lum PY, Molony C, Yang X, Macneil DJ, et al. Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet. 2010;6:e1000932. doi: 10.1371/journal. pgen.1000932.
19. Zhong H, Yang X, Kaplan LM, Molony C, Schadt EE. Integrating pathway analysis and genetics of gene expression for genome-wide association studies. Am J Hum Genet. 2010;86:581-591. doi: 10.1016/j. ajhg.2010.02.020.
20. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25-29. doi: 10.1038/75556.
21. Skogsberg J, Lundström J, Kovacs A, Nilsson R, Noori P, Maleki S, et al. Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes. PLoS Genet. 2008;4:e1000036. doi: 10.1371/journal.pgen.1000036.
22. Greenawalt DM, Dobrin R, Chudin E, Hatoum IJ, Suver C, Beaulaurier J, et al. A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res. 2011;21:1008-1016. doi: 10.1101/gr.112821.110.
23. Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, et al. Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet. 2012;44:502-510. doi: 10.1038/ng.2205.
24. Fu J, Wolfs MG, Deelen P, Westra HJ, Fehrmann RS, Te Meerman GJ, et al. Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet. 2012;8:e1002431. doi: 10.1371/journal.pgen.1002431.
25. Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A, Keildson S, et al; Multiple Tissue Human Expression Resource (MuTHER) Consortium. Mapping cis-and trans-regulatory effects across multiple tissues in twins. Nat Genet. 2012;44:1084-1089. doi: 10.1038/ng.2394.
26. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, et al. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science. 2009;325:1246-1250. doi: 10.1126/science.1174148.
27. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012;22:1748-1759. doi: 10.1101/gr.136127.111.
28. Becker KG, Barnes KC, Bright TJ, Wang SA. The genetic association database. Nat Genet. 2004;36:431-432. doi: 10.1038/ng0504-431.
29. McDonough CW, Gong Y, Padmanabhan S, Burkley B, Langaee TY, Melander O, et al. Pharmacogenomic association of nonsynonymous SNPs in SIGLEC12, A1BG, and the selectin region and cardiovascular outcomes. Hypertension. 2013;62:48-54. doi: 10.1161/HYPERTENSIONAHA.111.00823.