MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies

Author:

Burch Myson,Bose Aritra,Dexter Gregory,Parida LaxmiORCID,Drineas PetrosORCID

Abstract

AbstractLinear mixed models (LMMs) have been widely used in genome-wide association studies (GWAS) to control for population stratification and cryptic relatedness. Unfortunately, estimating LMM parameters is computationally expensive, necessitating large-scale matrix operations to build the genetic relatedness matrix (GRM). Over the past 25 years, Randomized Linear Algebra has provided alternative approaches to such matrix operations by leveragingmatrix sketching, which often results in provably accurate fast and efficient approximations. We leveragematrix sketchingto develop a fast and efficient LMM method calledMatrix-SketchingLMM(MaSk-LMM) by sketching the genotype matrix to reduce its dimensions and speed up computations. Our framework comes with both theoretical guarantees and a strong empirical performance compared to current state-of-the-art.

Publisher

Cold Spring Harbor Laboratory

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