A mixed-model approach for genome-wide association studies of correlated traits in structured populations (original) (raw)

• Platt, A., Vilhjálmsson, B.J. & Nordborg, M. Conditions under which genome-wide association studies will be positively misleading. Genetics 186, 1045–1052 (2010).
  Article Google Scholar
• Kang, H.M. et al. Variance component model to account for sample structure in genome-wide association studies. Nat. Genet. 42, 348–354 (2010).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Hamza, T.H. et al. Genome-wide gene environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee. PLoS Genet. 7, e1002237 (2011).
  Article CAS Google Scholar
• Lynch, M. & Walsh, B. Genetics and Analysis of Quantitative Traits (Sinauer Associates, Sunderland, Massachusetts, 1997).
• Jiang, C. & Zeng, Z.B. Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140, 1111–1127 (1995).
  Article CAS Google Scholar
• Ferreira, M.A. & Purcell, S.M. A multivariate test of association. Bioinformatics 25, 132–133 (2009).
  Article CAS Google Scholar
• Zhang, L., Pei, Y.F., Li, J., Papasian, C.J. & Deng, H.W. Univariate/multivariate genome-wide association scans using data from families and unrelated samples. PLoS ONE 4, e6502 (2009).
  Article Google Scholar
• Knott, S.A. & Haley, C.S. Multitrait least squares for quantitative trait loci detection. Genetics 156, 899–911 (2000).
  Article CAS Google Scholar
• Henderson, C.R. Application of Linear Models in Animal Breeding (University of Guelph, Guelph, Canada, 1984).
• Thomas, D. Gene–environment-wide association studies: emerging approaches. Nat. Rev. Genet. 11, 259–272 (2010).
  Article CAS Google Scholar
• Ober, C. & Vercelli, D. Gene-environment interactions in human disease: nuisance or opportunity? Trends Genet. 27, 107–115 (2011).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Atwell, S. et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627–631 (2010).
  Article CAS Google Scholar
• Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961–967 (2010).
  Article CAS Google Scholar
• Olsen, H.G. et al. Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12. Anim. Genet. 42, 466–474 (2011).
  Article CAS Google Scholar
• Tian, F. et al. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43, 159–162 (2011).
  Article CAS Google Scholar
• Zhao, K. et al. An Arabidopsis example of association mapping in structured samples. PLoS Genet. 3, e4 (2007).
  Article Google Scholar
• Kang, H.M. et al. Efficient control of population structure in model organism association mapping. Genetics 178, 1709–1723 (2008).
  Article Google Scholar
• Zhang, Z. et al. Mixed linear model approach adapted for genome-wide association studies. Nat. Genet. 42, 355–360 (2010).
  Article CAS Google Scholar
• Idaghdour, Y. et al. Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nat. Genet. 42, 62–67 (2010).
  Article CAS Google Scholar
• International Multiple Sclerosis Genetics Consortium and Wellcome Trust Case Control Consortium 2. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 476, 214–219 (2011).
• Stich, B., Piepho, H.P., Schulz, B. & Melchinger, A.E. Multitrait association mapping in sugar beet (Beta vulgaris L.). Theor. Appl. Genet. 117, 947–954 (2008).
  Article Google Scholar
• Lee, S.H., Wray, N.R., Goddard, M.E. & Visscher, P.M. Estimating missing heritability for disease from genome-wide association studies. Am. J. Hum. Genet. 88, 294–305 (2011).
  Article Google Scholar
• Yang, J., Lee, S.H., Goddard, M.E. & Visscher, P.M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76–82 (2011).
  Article CAS Google Scholar
• Lee, S.H. et al. Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nat. Genet. 44, 247–250 (2012).
  Article CAS Google Scholar
• Deary, I.J. et al. Genetic contributions to stability and change in intelligence from childhood to old age. Nature 482, 212–215 (2012).
  Article CAS Google Scholar
• Kim, S. & Xing, E.P. Statistical estimation of correlated genome associations to a quantitative trait network. PLoS Genet. 5, e1000587 (2009).
  Article Google Scholar
• Manning, A.K. et al. Meta-analysis of gene-environment interaction: joint estimation of SNP and SNP × environment regression coefficients. Genet. Epidemiol. 35, 11–18 (2011).
  Article Google Scholar
• Horton, M.W. et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat. Genet. 44, 212–216 (2012).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Li, Y., Huang, Y., Bergelson, J., Nordborg, M. & Borevitz, J.O. Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 107, 21199–21204 (2010).
  Article CAS Google Scholar
• Kathiresan, S. et al. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. BMC Med. Genet. 8 (suppl. 1) S17 (2007).
  Article Google Scholar
• Teslovich, T.M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707–713 (2010).
  Article CAS Google Scholar
• Lin, R. & Wang, H. Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development. Plant Physiol. 136, 4010–4022 (2004).
  Article CAS Google Scholar
• Fisher, R. The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinburgh 52, 399–433 (1918).
  Article Google Scholar
• Price, A.L. et al. Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet. 7, e1001317 (2011).
  Article CAS Google Scholar
• Buckler, E.S. et al. The genetic architecture of maize flowering time. Science 325, 714–718 (2009).
  Article CAS Google Scholar
• Valdar, W. et al. Genetic and environmental effects on complex traits in mice. Genetics 174, 959–984 (2006).
  Article CAS Google Scholar
• Smith, E.N. & Kruglyak, L. Gene-environment interaction in yeast gene expression. PLoS Biol. 6, e83 (2008).
  Article Google Scholar
• Gilmour, A., Gogel, B., Cullis, B., Welham, S.J. & Thompson, R. ASReml User Guide Release 1.0 (VSN International, Hemel Hempstead, UK, 2002).
• Henderson, C. & Quaas, R.L. Multiple trait evaluation using relatives' records. J. Anim. Sci. 43, 1188–1197 (1976).
  Article Google Scholar