FaST linear mixed models for genome-wide association studies - PubMed (original) (raw)
. 2011 Sep 4;8(10):833-5.
doi: 10.1038/nmeth.1681.
Affiliations
- PMID: 21892150
- DOI: 10.1038/nmeth.1681
FaST linear mixed models for genome-wide association studies
Christoph Lippert et al. Nat Methods. 2011.
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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References
- BMC Genet. 2005 Dec 30;6 Suppl 1:S2 - PubMed
- Nat Genet. 2010 Apr;42(4):348-54 - PubMed
- Nat Rev Genet. 2006 Oct;7(10):781-91 - PubMed
- Genet Res (Camb). 2009 Feb;91(1):47-60 - PubMed
- Nat Genet. 2010 Apr;42(4):355-60 - PubMed
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