Testing for genetic associations in arbitrarily structured populations

Nature Genetics

Volumn 47, Issue 5, 2015, Pages 550-554

  Song, Minsun ^a,b   Hao, Wei ^a   Storey, John D ^a  

^a PRINCETON UNIVERSITY   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

C REACTIVE PROTEIN; GLUCOSE; HIGH DENSITY LIPOPROTEIN CHOLESTEROL; INSULIN; LOW DENSITY LIPOPROTEIN CHOLESTEROL; TRIACYLGLYCEROL;

ARTICLE; BODY HEIGHT; BODY MASS; COHORT ANALYSIS; DIASTOLIC BLOOD PRESSURE; FINLAND; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC SCREENING; GENETIC TRAIT; GENOTYPE; HUMAN; POPULATION GENETIC STRUCTURE; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; SYSTOLIC BLOOD PRESSURE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENOME-WIDE ASSOCIATION STUDY; PRINCIPAL COMPONENT ANALYSIS; STATISTICAL MODEL;

COMPUTER SIMULATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINEAR MODELS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS;

EID: 84929130444     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3244     Document Type: Article

References (24)

1. McCarthy, M.I. et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 9, 356-369 (2008
2. Frazer, K.A., Murray, S.S., Schork, N.J. & Topol, E.J. Human genetic variation and its contribution to complex traits. Nat. Rev. Genet. 10, 241-251 (2009
3. Wellcome Trust Case Control Consortium. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 447, 661-678 (2007
4. Pritchard, J.K. & Rosenberg, N.A. Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet. 65, 220-228 (1999
5. Astle, W. & Balding, D.J. Population structure and cryptic relatedness in genetic association studies. Stat. Sci. 24, 451-471 (2009
6. Price, A.L., Zaitlen, N.A., Reich, D. & Patterson, N. New approaches to population stratification in genome-wide association studies. Nat. Rev. Genet. 11, 459-463 (2010
7. Zhang, S., Zhu, X. & Zhao, H. On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet. Epidemiol. 24, 44-56 (2003
8. Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909 (2006
9. Yu, J. et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 203-208 (2006
10. Kang, H.M. et al. Variance component model to account for sample structure in genome-wide association studies. Nat. Genet. 42, 348-354 (2010
11. Wang, K., Hu, X. & Peng, Y. An analytical comparison of the principal component method and the mixed effects model for association studies in the presence of cryptic relatedness and population stratification. Hum. Hered. 76, 1-9 (2013
12. Sabatti, C. et al. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat. Genet. 41, 35-46 (2009
13. Soranzo, N. et al. Meta-Analysis of genome-wide scans for human adult stature identifies novel loci and associations with measures of skeletal frame size. PLoS Genet. 5, e1000445 (2009
14. Hao, W., Song, M. & Storey, J.D. Probabilistic models of genetic variation in structured populations applied to global human studies. arXiv, http: //arxiv.org/abs/1312.2041 (2013
15. Zhou, X. & Stephens, M. Genome-wide efficient mixed-model analysis for association studies. Nat. Genet. 44, 821-824 (2012
16. Dudbridge, F. & Gusnanto, A. Estimation of significance thresholds for genomewide association scans. Genet. Epidemiol. 32, 227-234 (2008
17. Sandhu, M.S. et al. LDL-cholesterol concentrations: a genome-wide association study. Lancet 371, 483-491 (2008
18. Prokopenko, I. et al. Variants in MTNR1B influence fasting glucose levels. Nat. Genet. 41, 77-81 (2009
19. Devlin, B. & Roeder, K. Genomic control for association studies. Biometrics 55, 997-1004 (1999
20. Yang, J. et al. Genomic inflation factors under polygenic inheritance. Eur. J. Hum. Genet. 19, 807-812 (2011
21. Witten, D.M., Tibshirani, R. & Hastie, T. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10, 515-534 (2009
22. Baglama, J. & Reichel, L. Restarted block Lanczos bidiagonalization methods. Num. Algo. 43, 251-272 (2006
23. Balding, D.J. & Nichols, R.A. A method for quantifying differentiation between populations at multi-Allelic loci and its implications for investigating identity and paternity. Genetica 96, 3-12 (1995
24. Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945-959 (2000