FaST linear mixed models for genome-wide association studies
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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- Authors
- Lippert, C., Listgarten, J., Liu, Y., Kadie, C. M., Davidson, R. I., & Heckerman, D.
- Affiliations
- Microsoft (United States) (US)
- Corresponding author
- Lippert, Christoph
- Listgarten, Jennifer
- Heckerman, David
- Venue
- Nature Methods
- Published
- 2011-09-04
- Volume
- 8
- Issue
- 10
- Pages
- 833-835
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2079927753
- Cited by
- 1,209
- References
- 2
- Citations by year
- 2026: 45 · 2025: 72 · 2024: 104 · 2023: 83 · 2022: 111 · 2021: 113 · 2020: 114 · 2019: 92 · 2018: 102 · 2017: 76 · 2016: 93 · 2015: 75 · 2014: 62 · 2013: 45 · 2012: 15
- FWCI
- 23.46
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Wellcome Trust (085475, 076113)
- National Institutes of Health
- National Institute on Alcohol Abuse and Alcoholism (U10AA008401)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- linear mixed models, genome-wide association study, computational scalability, memory efficiency, computation time reduction, spectral transformation, genetic association
- MeSH terms
- Algorithms, Computer Simulation, Models, Genetic, Software, Genome-Wide Association Study
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