FaST linear mixed models for genome-wide association studies

  • Christoph Lippert ,
  • Jennifer Listgarten ,
  • Ying Liu ,
  • Carl Kadie ,
  • Bob Davidson ,

Nature Methods | , Vol 8: pp. 833-835

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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/).