scholarly journals Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Christian Widmer ◽  
Christoph Lippert ◽  
Omer Weissbrod ◽  
Nicolo Fusi ◽  
Carl Kadie ◽  
...  
Keyword(s):  
Mixed Models ◽  
Association Studies ◽  
Linear Mixed Models ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Ludicrous Speed Linear Mixed Models for Genome-Wide Association Studies

2017 ◽  
Author(s):  
Carl Kadie ◽  
David Heckerman
Keyword(s):  
Mixed Models ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Association Studies ◽  
Linear Mixed Models ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Confounding Factors ◽  
Genome Wide ◽  
A Genome

AbstractWe have developed Ludicrous Speed Linear Mixed Models, a version of FaST-LMM optimized for the cloud. The approach can perform a genome-wide association analysis on a dataset of one million SNPs across one million individuals at a cost of about 868 CPU days with an elapsed time on the order of two weeks. A Python implementation is available at https://fastlmm.github.io/.SignificanceIdentifying SNP-phenotype correlations using GWAS is difficult because effect sizes are so small for common, complex diseases. To address this issue, institutions are creating extremely large cohorts with sample sizes on the order of one million. Unfortunately, such cohorts are likely to contain confounding factors such as population structure and family/cryptic relatedness. The linear mixed model (LMM) can often correct for such confounding factors, but is too slow to use even with algebraic speedups known as FaST-LMM. We present a cloud implementation of FaST-LMM, called Ludicrous Speed LMM, that can process one million samples and one million test SNPs in a reasonable amount of time and at a reasonable cost.

scholarly journals Improved linear mixed models for genome-wide association studies

2012 ◽  
Vol 9 (6) ◽  
pp. 525-526 ◽  
Author(s):  
Jennifer Listgarten ◽  
Christoph Lippert ◽  
Carl M Kadie ◽  
Robert I Davidson ◽  
Eleazar Eskin ◽  
...  
Keyword(s):  
Mixed Models ◽  
Association Studies ◽  
Linear Mixed Models ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

FaST linear mixed models for genome-wide association studies

2011 ◽  
Vol 8 (10) ◽  
pp. 833-835 ◽  
Author(s):  
Christoph Lippert ◽  
Jennifer Listgarten ◽  
Ying Liu ◽  
Carl M Kadie ◽  
Robert I Davidson ◽  
...  
Keyword(s):  
Mixed Models ◽  
Association Studies ◽  
Linear Mixed Models ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide
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