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FaST linear mixed models for genome-wide association studies
FaST linear mixed models for genome-wide association studies
Journal Article

FaST linear mixed models for genome-wide association studies

2011
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Overview
An algorithm for linear mixed models substantially reduces memory usage and run time for genome-wide association studies. The improved algorithm scales linearly in cohort size, allowing the application of these models to much larger samples. 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/ ).