MASTOR: Mixed-model association mapping of quantitative traits in samples with related individuals

American Journal of Human Genetics

Volumn 92, Issue 5, 2013, Pages 652-666

  Jakobsdottir, Johanna ^a,b   McPeek, Mary Sara ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b ICELANDIC HEART ASSOCIATION   (Iceland)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH DENSITY LIPOPROTEIN CHOLESTEROL;

ARTICLE; COMPUTER PROGRAM; EPISTASIS; GENE LOCUS; GENETIC ASSOCIATION; GENETIC MODEL; GENOTYPE; HERITABILITY; MIXED MODEL ASSOCIATION SCORE TEST ON RELATED INDIVIDUALS; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; SIMULATION;

COMPUTER SIMULATION; GENETIC ASSOCIATION STUDIES; HUMANS; INHERITANCE PATTERNS; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT, HERITABLE; SOFTWARE;

EID: 84877260532     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2013.03.014     Document Type: Article

References (29)

1. G.L. Splansky, D. Corey, Q. Yang, L.D. Atwood, L.A. Cupples, E.J. Benjamin, R.B. D'Agostino Sr., C.S. Fox, M.G. Larson, and J.M. Murabito 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 2007 1328 1335
2. D.L. Newman, M. Abney, M.S. McPeek, C. Ober, and N.J. Cox The importance of genealogy in determining genetic associations with complex traits Am. J. Hum. Genet. 69 2001 1146 1148
3. T. Thornton, and M.S. McPeek Case-control association testing with related individuals: a more powerful quasi-likelihood score test Am. J. Hum. Genet. 81 2007 321 337
4. M. Abney, C. Ober, and M.S. McPeek Quantitative-trait homozygosity and association mapping and empirical genomewide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites Am. J. Hum. Genet. 70 2002 920 934
5. H.M. Kang, J.H. Sul, S.K. Service, N.A. Zaitlen, S.Y. Kong, N.B. Freimer, C. Sabatti, and E. Eskin Variance component model to account for sample structure in genome-wide association studies Nat. Genet. 42 2010 348 354
6. H.M. Kang, N.A. Zaitlen, C.M. Wade, A. Kirby, D. Heckerman, M.J. Daly, and E. Eskin Efficient control of population structure in model organism association mapping Genetics 178 2008 1709 1723
7. X. Zhou, and M. Stephens Genome-wide efficient mixed-model analysis for association studies Nat. Genet. 44 2012 821 824
8. C. Lippert, J. Listgarten, Y. Liu, C.M. Kadie, R.I. Davidson, and D. Heckerman FaST linear mixed models for genome-wide association studies Nat. Methods 8 2011 833 835
9. W.-M. Chen, and G.R. Abecasis Family-based association tests for genomewide association scans Am. J. Hum. Genet. 81 2007 913 926
10. G.R. Abecasis, L.R. Cardon, and W.O.C. Cookson A general test of association for quantitative traits in nuclear families Am. J. Hum. Genet. 66 2000 279 292
11. C. Lange, D.L. DeMeo, and N.M. Laird Power and design considerations for a general class of family-based association tests: quantitative traits Am. J. Hum. Genet. 71 2002 1330 1341
12. Z. Feng, W.W. Wong, X. Gao, and F. Schenkel Generalized genetic association study with samples of related individuals Ann. Appl. Stat. 5 2011 2109 2130
13. C. Bourgain, S. Hoffjan, R. Nicolae, D. Newman, L. Steiner, K. Walker, R. Reynolds, C. Ober, and M.S. McPeek Novel case-control test in a founder population identifies P-selectin as an atopy-susceptibility locus Am. J. Hum. Genet. 73 2003 612 626
14. L. Han, and M. Abney Identity by descent estimation with dense genome-wide genotype data Genet. Epidemiol. 35 2011 557 567
15. T. Thornton, and M.S. McPeek ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure Am. J. Hum. Genet. 86 2010 172 184
16. M.S. McPeek BLUP genotype imputation for case-control association testing with related individuals and missing data J. Comput. Biol. 19 2012 756 765
17. M.S. McPeek, X. Wu, and C. Ober Best linear unbiased allele-frequency estimation in complex pedigrees Biometrics 60 2004 359 367
18. Z. Wang, and M.S. McPeek An incomplete-data quasi-likelihood approach to haplotype-based genetic association studies on related individualst J. Am. Stat. Assoc. 104 2009 1251 1260
19. S.J. Welham, and R. Thompson Likelihood ratio tests for fixed model terms using residual maximum likelihood J. Royal Stat. Soc. Ser. B 59 1997 701 714
20. L.A. Weiss, L. Pan, M. Abney, and C. Ober The sex-specific genetic architecture of quantitative traits in humans Nat. Genet. 38 2006 218 222
21. S. Kathiresan, A.K. Manning, S. Demissie, R.B. D'Agostino, A. Surti, C. Guiducci, L. Gianniny, N.P. Burtt, O. Melander, and M. Orho-Melander A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study BMC Med. Genet. 8 Suppl 1 2007 S17
22. C.J. Willer, S. Sanna, A.U. Jackson, A. Scuteri, L.L. Bonnycastle, R. Clarke, S.C. Heath, N.J. Timpson, S.S. Najjar, and H.M. Stringham Newly identified loci that influence lipid concentrations and risk of coronary artery disease Nat. Genet. 40 2008 161 169
23. C. Wallace, S.J. Newhouse, P. Braund, F. Zhang, M. Tobin, M. Falchi, K. Ahmadi, R.J. Dobson, A.C. Marçano, and C. Hajat Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia Am. J. Hum. Genet. 82 2008 139 149
24. L. Ma, J. Yang, H.B. Runesha, T. Tanaka, L. Ferrucci, S. Bandinelli, and Y. Da Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham heart study data BMC Med. Genet. 11 2010 55
25. S. Kathiresan, O. Melander, C. Guiducci, A. Surti, N.P. Burtt, M.J. Rieder, G.M. Cooper, C. Roos, B.F. Voight, and A.S. Havulinna Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans Nat. Genet. 40 2008 189 197
26. Y.S. Aulchenko, S. Ripatti, I. Lindqvist, D. Boomsma, I.M. Heid, P.P. Pramstaller, B.W.J.H. Penninx, A.C.J.W. Janssens, J.F. Wilson, T. Spector ENGAGE Consortium Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts Nat. Genet. 41 2009 47 55
27. S. Kathiresan, C.J. Willer, G.M. Peloso, S. Demissie, K. Musunuru, E.E. Schadt, L. Kaplan, D. Bennett, Y. Li, and T. Tanaka Common variants at 30 loci contribute to polygenic dyslipidemia Nat. Genet. 41 2009 56 65
28. J. Yu, G. Pressoir, W.H. Briggs, I. Vroh Bi, M. Yamasaki, J.F. Doebley, M.D. McMullen, B.S. Gaut, D.M. Nielsen, and J.B. Holland A unified mixed-model method for association mapping that accounts for multiple levels of relatedness Nat. Genet. 38 2006 203 208
29. G.M. Peloso, J. Dupuis, and K.L. Lunetta Evaluation of methods accounting for population structure with pedigree data and continuous outcomes Genet. Epidemiol. 35 2011 427 436