SNP-SNP interactions dominate the genetic architecture of candidate genes associated with left ventricular mass in african-americans of the GENOA study

BMC Medical Genetics

Volumn 11, Issue 1, 2010, Pages

  Meyers, Kristin J ^a   Chu, Jian ^b   Mosley, Thomas H ^c   Kardia, Sharon L R ^d  

^a UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^b WASHINGTON UNIVERSITY   (United States)

^c UNIVERSITY OF MISSISSIPPI SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHOLESTEROL; LOW DENSITY LIPOPROTEIN CHOLESTEROL; TRIACYLGLYCEROL;

AFRICAN AMERICAN; AGE; ARTICLE; BODY HEIGHT; BODY WEIGHT; CHOLESTEROL BLOOD LEVEL; DIABETES MELLITUS; DIASTOLIC BLOOD PRESSURE; DISEASE DURATION; DRUG USE; FALSE POSITIVE RESULT; GENDER; GENE INTERACTION; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC RISK; GENOTYPE; HEART INFARCTION; HEART LEFT VENTRICLE MASS; HUMAN; HYPERTENSION; LINEAR REGRESSION ANALYSIS; MAJOR CLINICAL STUDY; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM; SMOKING; SYSTOLIC BLOOD PRESSURE; TRIACYLGLYCEROL BLOOD LEVEL; ETHNOLOGY; FEMALE; GENE REGULATORY NETWORK; GENETICS; HEART LEFT VENTRICLE HYPERTROPHY; RISK FACTOR; STATISTICAL MODEL;

AFRICAN AMERICANS; FEMALE; GENE REGULATORY NETWORKS; HUMANS; HYPERTROPHY, LEFT VENTRICULAR; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS;

EID: 78149257657     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-11-160     Document Type: Article

References (51)

1. National Center for Health Statistics. 2006, Health, 2006: with chartbook on trends in the health of Americans.
2. 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. 10.1056/NEJM199005313222203, 2139921.
3. 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.
4. Benjamin EJ, Levy D. Why is left ventricular hypertrophy so predictive of morbidity and mortality?. Am J Med Sci 1999, 317:168-175. 10.1097/00000441-199903000-00006, 10100690.
5. Kizer JR, Arnett DK, Bella JN, Paranicas M, Rao DC, Province MA, Oberman A, Kitzman DW, Hopkins PN, Liu JE, Devereux RB. Differences in left ventricular structure between black and white hypertensive adults: the Hypertension Genetic Epidemiology Network study. Hypertension 2004, 43:1182-1188. 10.1161/01.HYP.0000128738.94190.9f, 15123573.
6. Galderisi M, Anderson KM, Wilson PW, Levy D. Echocardiographic evidence for the existence of a distinct diabetic cardiomyopathy (the Framingham Heart Study). Am J Cardiol 1991, 68:85-89. 10.1016/0002-9149(91)90716-X, 2058564.
7. Bella JN, Wachtell K, Palmieri V, Liebson PR, Gerdts E, Ylitalo A, Koren MJ, Pedersen OL, Rokkedal J, Dahlof B, Roman MJ, Devereux RB. Relation of left ventricular geometry and function to systemic hemodynamics in hypertension: the LIFE Study. Losartan Intervention For Endpoint Reduction in Hypertension Study. J Hypertens 2001, 19:127-134. 10.1097/00004872-200101000-00017, 11204292.
8. du Cailar G, Ribstein J, Mimran A. Dietary sodium and target organ damage in essential hypertension. Am J Hypertens 2002, 15:222-229. 10.1016/S0895-7061(01)02287-7, 11939611.
9. Arnett DK, Hong Y, Bella JN, Oberman A, Kitzman DW, Hopkins PN, Rao DC, Devereux RB. Sibling correlation of left ventricular mass and geometry in hypertensive African Americans and whites: the HyperGEN study. Hypertension Genetic Epidemiology Network. Am J Hypertens 2001, 14:1226-1230. 10.1016/S0895-7061(01)02200-2, 11775131.
10. Bella JN, MacCluer JW, Roman MJ, Almasy L, North KE, Best LG, Lee ET, Fabsitz RR, Howard BV, Devereux RB. Heritability of left ventricular dimensions and mass in American Indians: The Strong Heart Study. J Hypertens 2004, 22:281-286. 10.1097/00004872-200402000-00011, 15076185.
11. de Simone G, Tang W, Devereux RB, Hunt SC, Kitzman DW, Rao DC, Arnett DK. Assessment of the interaction of heritability of volume load and left ventricular mass: the HyperGEN offspring study. J Hypertens 2007, 25:1397-1402. 10.1097/HJH.0b013e328126851e, 17563561.
12. Sharma P, Middelberg RP, Andrew T, Johnson MR, Christley H, Brown MJ. Heritability of left ventricular mass in a large cohort of twins. J Hypertens 2006, 24:321-324. 10.1097/01.hjh.0000202815.18083.03, 16508579.
13. Sing CF, Stengard JH, Kardia SL. Dynamic relationships between the genome and exposures to environments as causes of common human diseases. World Rev Nutr Diet 2004, 93:77-91. full_text, 15496802.
14. Wade MJ. Epistasis, complex traits, and mapping genes. Genetica 2001, 112-113:59-69. 10.1023/A:1013316611768, 11838787.
15. Greene CS, Penrod NM, Williams SM, Moore JH. Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS ONE 2009, 4(6):e5639. 10.1371/journal.pone.0005639, 2685469, 19503614.
16. Sillanpaa MJ, Auranen K. Replication in genetic studies of complex traits. Ann Hum Genet 2004, 68:646-657. 10.1046/j.1529-8817.2004.00122.x, 15598223.
17. Chobanian AV, Bakris GL, Black HR, Cushman WC, Green LA, Izzo JL, Jones DW, Materson BJ, Oparil S, Wright JT, Roccella EJ, . Joint National Committee on Prevention, Detection, Evaluation and Treatment of High Blood Pressure. National Heart, Lung, and Blood Institute, National High Blood Pressure Education Program Coordinating Committee Seventh report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure. Hypertension 2003, 42:1206-1252. 10.1161/01.HYP.0000107251.49515.c2, 14656957, Joint National Committee on Prevention, Detection, Evaluation and Treatment of High Blood Pressure. National Heart, Lung, and Blood Institute, National High Blood Pressure Education Program Coordinating Committee.
18. Lang RM, Bierig M, Devereux RB, Flachskampf FA, Foster E, Pellikka PA, Picard MH, Roman MJ, Seward J, Shanewise JS, Solomon SD, Spencer KT, Sutton MS, Stewart WJ, . Chamber Quantification Writing Group, American Society of Echocardiography's Guidelines and Standards Committee, European Association of Echocardiography Recommendations for chamber quantification: a report from the American Society of Echocardiography's Guidelines and Standards Committee and the Chamber Quantification Writing Group. J Am Soc Echocardiogr 2005, 18:1440-1463. 10.1016/j.echo.2005.10.005, 16376782, Chamber Quantification Writing Group, American Society of Echocardiography's Guidelines and Standards Committee, European Association of Echocardiography.
19. Devereux RB, Alonso DR, Lutas EM, Gottlieb GJ, Campo E, Sachs I, Reichek N. Echocardiographic assessment of left ventricular hypertrophy: comparison to necropsy findings. Am J Cardiol 1986, 57:450-458. 10.1016/0002-9149(86)90771-X, 2936235.
20. Palmieri V, Dahlof B, DeQuattro V, Sharpe N, Bella JN, de Simone G, Paranicas M, Fishman D, Devereux RB. Reliability of echocardiographic assessment of left ventricular structure and function: the PRESERVE study. Prospective Randomized Study Evaluating Regression of Ventricular Enlargement. J Am Coll Cardiol 1999, 34:1625-1632. 10.1016/S0735-1097(99)00396-4, 10551715.
21. Barkley RA, Chakravarti A, Cooper RS, Ellison RC, Hunt SC, PRovince MA, Turner ST, Weder AB, Boerwinkle E, . Family Blood Pressure Program Positional identification of hypertension susceptibility genes on chromosome 2. Hypertension 2004, 43(2):477-482. 10.1161/01.HYP.0000111585.76299.f7, 14732741, Family Blood Pressure Program.
22. NCBI Entrez dbSNP. , http://www.ncbi.nlm.nih.gov/SNP/
23. SeattleSNPs. , http://pga.mbt.washington.edu
24. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM. Control of confounding of genetic associations in stratified populations. Am J Hum Genet 2003, 72:1492-1504. 10.1086/375613, 1180309, 12817591.
25. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, Patterson N, Gabriel SB, Topol EJ, Smoller JW, Pato CN, Pato MT, Petryshen TL, Kolonel LN, Lander ES, Sklar P, Henderson B, Hirschhorn JN, Altshuler D. Assessing the impact of population stratification on genetic association studies. Nat Genet 2004, 36:388-393. 10.1038/ng1333, 15052270.
26. Thomas DC, Witte JS. Point: population stratification: a problem for case-control studies of candidate-gene associations?. Cancer Epidemiol Biomarkers Prev 2002, 11:505-512.
27. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science 2002, 298:2381-2385. 10.1126/science.1078311, 12493913.
28. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959. 1461096, 10835412.
29. Menozzi P, Piazza A, Cavalli-Sforza L. Synthetic maps of human gene frequencies in Europeans. Science 1978, 201:786-792. 10.1126/science.356262, 356262.
30. Price A, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 2006, 38:904-909. 10.1038/ng1847, 16862161.
31. R Core Development Team R: A language and environment for statistical computing. 2007, version 2.6.0, R Core Development Team.
32. Weir BS. Genetic data analysis II: Methods for discrete population genetic data. 1996, Sudnerland, MA: Sinauer Associates, Inc.
33. Kardia SLR, Greene MT, Boerwinkle E, Turner ST, Kullo IJ. Investigating the complex genetic architecture of ankle-brachial index, a measure of peripheral arterial disease, in non-Hispanic whites. BMC Medical Genomics 2008, 15:1-16.
34. Smith JA, Turner ST, Sun YV, Fornage M, Kelly RJ, Mosley TH, Jack CR, Kullo IJ, Karida SLR. Complexity in the genetic architecture of leukoaraiosis in hypertensive sibships from the GENOA study. BMC Medical Genomics 2009, 7:2-16.
35. Kleinbaum D, Kupper L, Muller K, Nizam A. Applied Regression Analysis and Other Multivariate Methods. 1998, Pacific Grove, CA: Brooks/Cole Publishing Company.
36. Cordell HJ. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 2002, 11:2463-2468. 10.1093/hmg/11.20.2463, 12351582.
37. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100:9440-9445. 10.1073/pnas.1530509100, 170937, 12883005.
38. Molinaro AM, Simon R, Pfeiffer RM. Prediction error estimation: a comparison of resampling methods. Bioinformatics 2005, 21:3301-3307. 10.1093/bioinformatics/bti499, 15905277.
39. Marchini J, Donnelly P, Cardon LR. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005, 37:413-417. 10.1038/ng1537, 15793588.
40. Musani SK, Shriner D, Liu N, Feng R, Coffey CS, Yi N, Tiwari HK, Allison DB. Detection of gene × gene interactions in genome-wide association studies of human population data. Hum Hered 2007, 63:67-84. 10.1159/000099179, 17283436.
41. Putt W, Palmen J, Nicaud V, Tregouet DA, Tahri-Daizadeh N, Flavell DM, Humphries SE, Talmud PJ, . EARSII group: Variation in USF1 shows haplotype effects, gene gene and gene: environment associations with glucose and lipid parameters in the European Atherosclerosis Research Study II. Hum Mol Genet 2004, 13:1587-1597. 10.1093/hmg/ddh168, 15175273, EARSII group: Variation in USF1 shows haplotype effects, gene.
42. Tsai CT, Lai LP, Lin JL, Chiang FT, Hwang JJ, Ritchie MD, Moore JH, Hsu KL, Tseng CD, Liau CS, Tseng YZ. Renin-angiotensin system gene polymorphisms and atrial fibrillation. Circulation 2004, 109:1640-1646. 10.1161/01.CIR.0000124487.36586.26, 15023884.
43. Nelson MR, Kardia SL, Ferrell RE, Sing CF. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 2001, 11:458-470. 10.1101/gr.172901, 311041, 11230170.
44. Zollner S, Pritchard JK. Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet 2007, 80:605-615. 10.1086/512821, 1852705, 17357068.
45. Ioannidis JP. Why most discovered true associations are inflated. Epidemiology 2008, 19:640-648. 10.1097/EDE.0b013e31818131e7, 18633328.
46. Steffens M, Becker T, Sander T, Fimmers R, Herold C, Holler DA, Leu C, Herms S, Cichon S, Bohn B, Gerstner T, Griebel M, Nothen MM, Wienker TF, Baur MP. Feasible and Successful: Genome-wide interaction analysis involving all 1.9 × 10 pair-wise interaction tests. Hum Hered 2010, 69(4):268-284. 10.1159/000295896, 20357478.
47. Michigan Molecular Interactions (MiMI). , http://mimi.ncibi.org/MimiWeb/main-page.jsp
48. NCBI Entrez PubMed. , http://www.ncbi.nlm.nih.gov/pubmed/
49. Moore JH, Williams SM. Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. Bioessays 2005, 27:637-64. 10.1002/bies.20236, 15892116.
50. Vasilyev N, Williams T, Brennan ML, Unzek S, Zhou X, Heinecke JW, Spitz DR, Topol EJ, Hazen SL, Penn MS. Myeloperozidase-generated oxidants modulate left ventricular remodeling but not infarct size after myocardial infarction. Circulation 2005, 112(18):2812-20. 10.1161/CIRCULATIONAHA.105.542340, 16267254.
51. Ng LL, Pathik B, Loke IW, Squire IB, Davies JE. Myeloperoxidase and C-reactive protein augment the specificity of B-type natriuretic peptide in community screening for systolic heart failure. Am Heart J 2006, 152(1):94-101. 10.1016/j.ahj.2005.09.020, 16824837.