title: A randomization test for controlling population stratification in whole-genome association studies.
abstract: Population stratification can be a serious obstacle in the analysis of genomewide association studies. We propose a method for evaluating the significance of association scores in whole-genome cohorts with stratification. Our approach is a randomization test akin to a standard permutation test. It conditions on the genotype matrix and thus takes into account not only the population structure but also the complex linkage disequilibrium structure of the genome. As we show in simulation experiments, our method achieves higher power and significantly better control over false-positive rates than do existing methods. In addition, it can be easily applied to whole-genome association studies.
authors.affiliation: Computer Science Division, University of California Berkeley, Berkeley, CA 94720, USA. kimmel@cs.berkeley.edu
authors.forename: Gad
authors.initials: G
authors.lastname: Kimmel
authors.forename: Michael I
authors.initials: MI
authors.lastname: Jordan
authors.forename: Eran
authors.initials: E
authors.lastname: Halperin
authors.forename: Ron
authors.initials: R
authors.lastname: Shamir
authors.forename: Richard M
authors.initials: RM
authors.lastname: Karp
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D020022:Genetic Predisposition to Disease; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide / Q000235:genetics