Extremes of unexplained variation as a phenotype: An efficient approach for genome-wide association studies of cardiovascular disease

Circulation: Cardiovascular Genetics

Volumn 3, Issue 2, 2010, Pages 215-221

  Lanktree, Matthew B ^a   Hegele, Robert A ^a   Schork, Nicholas J ^b   Spence, J David ^a  

^a WESTERN UNIVERSITY   (Canada)

^b Scripps Translational Sciences Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; ATHEROSCLEROSIS; ATHEROSCLEROTIC PLAQUE; CARDIOVASCULAR DISEASE; CARDIOVASCULAR RISK; CONTROLLED STUDY; FEMALE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; PHENOTYPIC VARIATION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RISK ASSESSMENT;

AGED; CARDIOVASCULAR DISEASES; FEMALE; GENE FREQUENCY; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MIDDLE AGED; ODDS RATIO; PHENOTYPE; REGRESSION ANALYSIS;

EID: 77953664953     PISSN: 1942325X     EISSN: 19423268     Source Type: Journal    
DOI: 10.1161/CIRCGENETICS.109.934505     Document Type: Article

References (42)

1. Yusuf S, Reddy S, Ounpuu S, Anand S. Global burden of cardiovascular diseases, I: general considerations, the epidemiologic transition, risk factors, and impact of urbanization. Circulation. 2001;104:2746-2753.
2. Dawber TR, Meadors GF, Moore FE Jr. Epidemiological approaches to heart disease: the Framingham Study. Am J Public Health Nations Health. 1951;41:279-281.
3. Helgadottir A, Thorleifsson G, Manolescu A, Gretarsdottir S, Blondal T, Jonasdottir A, Sigurdsson A, Baker A, Palsson A, Masson G, Gudbjartsson DF, Magnusson KP, Andersen K, Levey AI, Backman VM, Matthiasdottir S, Jonsdottir T, Palsson S, Einarsdottir H, Gunnarsdottir S, Gylfason A, Vaccarino V, Hooper WC, Reilly MP, Granger CB, Austin H, Rader DJ, Shah SH, Quyyumi AA, Gulcher JR, Thorgeirsson G, Thorsteinsdottir U, Kong A, Stefansson K. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science. 2007; 316:1491-1493. (Pubitemid 46906618)
4. McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, Hinds DA, Pennacchio LA, Tybjaerg-Hansen A, Folsom AR, Boerwinkle E, Hobbs HH, Cohen JC. A common allele on chromosome 9 associated with coronary heart disease. Science. 2007;316:1488-1491. (Pubitemid 46906617)
5. Samani NJ, Erdmann J, Hall AS, Hengstenberg C, Mangino M, Mayer B, Dixon RJ, Meitinger T, Braund P, Wichmann HE, Barrett JH, Konig IR, Stevens SE, Szymczak S, Tregouet DA, Iles MM, Pahlke F, Pollard H, Lieb W, Cambien F, Fischer M, Ouwehand W, Blankenberg S, Balmforth AJ, Baessler A, Ball SG, Strom TM, Braenne I, Gieger C, Deloukas P, Tobin MD, Ziegler A, Thompson JR, Schunkert H. Genomewide association analysis of coronary artery disease. N Engl J Med. 2007;357: 443-453. (Pubitemid 47204873)
6. Welcome 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.
7. Lanktree M, Oh J, Hegele RA. Genetic testing for atherosclerosis risk: inevitability or pipe dream? Can J Cardiol. 2008;24:851-854.
8. Plomin R, Haworth CM, Davis OS. Common disorders are quantitative traits. Nat Rev Genet. 2009;10:872-878.
9. Lander ES, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989;121:185-199.
10. Carey G, Williamson J. Linkage analysis of quantitative traits: increased power by using selected samples. Am J Hum Genet. 1991;49:786-796.
11. Risch N, Zhang H. Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science. 1995;268:1584-1589.
12. Schork NJ, Nath SK, Fallin D, Chakravarti A. Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects. Am J Hum Genet. 2000;67: 1208-1218.
13. Abecasis GR, Cookson WO, Cardon LR. The power to detect linkage disequilibrium with quantitative traits in selected samples. Am J Hum Genet. 2001;68:1463-1474.
14. Tenesa A, Knott SA, Carothers AD, Visscher PM. Power of linkage disequilibrium mapping to detect a quantitative trait locus (QTL) in selected samples of unrelated individuals. Ann Hum Genet. 2003;67: 557-566.
15. Jawaid A, Bader JS, Purcell S, Cherny SS, Sham P. Optimal selection strategies for QTL mapping using pooled DNA samples. Eur J Hum Genet. 2002;10:125-132.
16. Pollex RL, Spence JD, House AA, Fenster A, Hanley AJ, Zinman B, Harris SB, Hegele RA. A comparison of ultrasound measurements to assess carotid atherosclerosis development in subjects with and without type 2 diabetes. Cardiovasc Ultrasound. 2005;3:15.
17. de Labriolle A, Mohty D, Pacouret G, Giraudeau B, Fichet J, Fremont B, Fauchier L, Charbonnier B, Arbeille P. Comparison of degree of stenosis and plaque volume for the assessment of carotid atherosclerosis using 2-D ultrasound. Ultrasound Med Biol. 2009;35:1436-1442.
18. Spence JD, Hegele RA. Noninvasive phenotypes of atherosclerosis: similar windows but different views. Stroke. 2004;35:649-653.
19. Al-Shali K, House AA, Hanley AJ, Khan HM, Harris SB, Mamakeesick M, Zinman B, Fenster A, Spence JD, Hegele RA. Differences between carotid wall morphological phenotypes measured by ultrasound in one, two and three dimensions. Atherosclerosis. 2005;178:319-325.
20. Johnsen SH, Mathiesen EB, Joakimsen O, Stensland E, Wilsgaard T, Lochen ML, Njolstad I, Arnesen E. Carotid atherosclerosis is a stronger predictor of myocardial infarction in women than in men: a 6-year follow-up study of 6226 persons: the Tromso Study. Stroke. 2007;38: 2873-2880.
21. Ebrahim S, Papacosta O, Whincup P, Wannamethee G, Walker M, Nicolaides AN, Dhanjil S, Griffin M, Belcaro G, Rumley A, Lowe GD. Carotid plaque, intima media thickness, cardiovascular risk factors, and prevalent cardiovascular disease in men and women: the British Regional Heart Study. Stroke. 1999;30:841-850.
22. Spence JD, Barnett PA, Bulman DE, Hegele RA. An approach to ascertain probands with a non-traditional risk factor for carotid atherosclerosis. Atherosclerosis. 1999;144:429-434.
23. Spence JD, Eliasziw M, DiCicco M, Hackam DG, Galil R, Lohmann T. Carotid plaque area: a tool for targeting and evaluating vascular preventive therapy. Stroke. 2002;33:2916-2922.
24. Dupont WD, Plummer WD Jr. Power and sample size calculations for studies involving linear regression. Control Clin Trials. 1998;19: 589-601.
25. Purcell S, Cherny SS, Sham PC. Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics. 2003;19:149-150.
26. Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet. 2006;7:781-791.
27. Wallace C, Chapman JM, Clayton DG. Improved power offered by a score test for linkage disequilibrium mapping of quantitative-trait loci by selective genotyping. Am J Hum Genet. 2006;78:498-504.
28. Huang BE, Lin DY. Efficient association mapping of quantitative trait loci with selective genotyping. Am J Hum Genet. 2007;80:567-576.
29. Manichaikul A, Palmer AA, Sen S, Broman KW. Significance thresholds for quantitative trait locus mapping under selective genotyping. Genetics. 2007;177:1963-1966. (Pubitemid 350277087)
30. Tenesa A, Visscher PM, Carothers AD, Knott SA. Mapping quantitative trait loci using linkage disequilibrium: marker- versus trait-based methods. Behav Genet. 2005;35:219-228.
31. Reich DE, Lander ES. On the allelic spectrum of human disease. Trends Genet. 2001;17:502-510.
32. Pritchard JK. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet. 2001;69:124-137.
33. Schork NJ, Murray SS, Frazer KA, Topol EJ. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev. 2009;19: 212-219.
34. Aulchenko YS, Ripatti S, Lindqvist I, Boomsma D, Heid IM, Pramstaller PP, Penninx BW, Janssens AC, Wilson JF, Spector T, Martin NG, Pedersen NL, Kyvik KO, Kaprio J, Hofman A, Freimer NB, Jarvelin MR, Gyllensten U, Campbell H, Rudan I, Johansson A, Marroni F, Hayward C, Vitart V, Jonasson I, Pattaro C, Wright A, Hastie N, Pichler I, Hicks AA, Falchi M, Willemsen G, Hottenga JJ, de Geus EJ, Montgomery GW, Whitfield J, Magnusson P, Saharinen J, Perola M, Silander K, Isaacs A,Sijbrands EJ, Uitterlinden AG, Witteman JC, Oostra BA, Elliott P,Ruokonen A, Sabatti C, Gieger C, Meitinger T, Kronenberg F, Doring A, Wichmann HE, Smit JH, McCarthy MI, van Duijn CM, Peltonen L. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet. 2009;41:47-55.
35. Kathiresan S, Willer CJ, Peloso GM, Demissie S, Musunuru K, Schadt EE, Kaplan L, Bennett D, Li Y, Tanaka T, Voight BF, Bonnycastle LL, Jackson AU, Crawford G, Surti A, Guiducci C, Burtt NP, Parish S, Clarke R, Zelenika D, Kubalanza KA, Morken MA, Scott LJ, Stringham HM, Galan P, Swift AJ, Kuusisto J, Bergman RN, Sundvall J, Laakso M, Ferrucci L, Scheet P, Sanna S, Uda M, Yang Q, Lunetta KL, Dupuis J, de Bakker PI, O'Donnell CJ, Chambers JC, Kooner JS, Hercberg S, Meneton P, Lakatta EG, Scuteri A, Schlessinger D, Tuomilehto J, Collins FS, Groop L, Altshuler D, Collins R, Lathrop GM, Melander O, Salomaa V, Peltonen L, Orho-Melander M, Ordovas JM, Boehnke M, Abecasis GR, Mohlke KL, Cupples LA. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet. 2009;41:56-65.
36. Sabatti C, Service SK, Hartikainen AL, Pouta A, Ripatti S, Brodsky J, Jones CG, Zaitlen NA, Varilo T, Kaakinen M, Sovio U, Ruokonen A, Laitinen J, Jakkula E, Coin L, Hoggart C, Collins A, Turunen H, Gabriel S, Elliot P, McCarthy MI, Daly MJ, Jarvelin MR, Freimer NB, Peltonen L. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet. 2009;41:35-46.
37. Hegele RA, Ban MR, Hsueh N, Kennedy BA, Cao H, Zou GY, Anand S, Yusuf S, Huff MW, Wang J. A polygenic basis for four classical Fredrickson hyperlipoproteinemia phenotypes that are characterized by hypertriglyceridemia. Hum Mol Genet. 2009;18:4189-4194.
38. Wang J, Cao H, Ban MR, Kennedy BA, Zhu S, Anand S, Yusuf S, PollexRL, Hegele RA. Resequencing genomic DNA of patients with severe hypertriglyceridemia (MIM 144650). Arterioscler Thromb Vasc Biol. 2007;27:2450-2455.
39. Hegele RA. Plasma lipoproteins: genetic influences and clinical implications. Nat Rev Genet. 2009;10:109-121.
40. Cotsapas C, Speliotes EK, Hatoum IJ, Greenawalt DM, Dobrin R, Lum PY, Suver C, Chudin E, Kemp D, Reitman M, Voight BF, Neale BM, Schadt EE, Hirschhorn JN, Kaplan LM, Daly MJ. Common body mass index-associated variants confer risk of extreme obesity. Hum Mol Genet. 2009;18:3502-3507.
41. Ji W, Foo JN, O'Roak BJ, Zhao H, Larson MG, Simon DB, Newton-Cheh C, State MW, Levy D, Lifton RP. Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet. 2008;40:592-599.
42. Rana BK, Insel PA, Payne SH, Abel K, Beutler E, Ziegler MG, Schork NJ, O'Connor DT. Population-based sample reveals gene-gender interactions in blood pressure in White Americans. Hypertension. 2007;49: 96-106.