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FaST linear mixed models for genome-wide association studies

C Lippert, J Listgarten, Y Liu, CM Kadie, RI Davidson, and D Heckerman

Abstract

We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algorithms. Our algorithm can analyze data for 120,000 individuals in just a few hours, whereas current algorithms fail on data for even 20,000 individuals (http://mscompbio.codeplex.com/).

Details

Publication typeArticle
Published inNature Methods
URL10.1038/nmeth.1681
Pages833–835
Volume8
Number10
> Publications > FaST linear mixed models for genome-wide association studies