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. 2011 Sep 4;8(10):833-5.
doi: 10.1038/nmeth.1681.

FaST linear mixed models for genome-wide association studies

Christoph Lippert  1 , Jennifer Listgarten, Ying Liu, Carl M Kadie, Robert I Davidson, David Heckerman
Affiliations

FaST linear mixed models for genome-wide association studies

Christoph Lippert et al. Nat Methods. .

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/).

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