An expression-directed linear mixed model discovering low-effect genetic variants

• Published in: Genetics (Austin) Vol. 226; no. 4
• Main Authors: Li, Qing, Bian, Jiayi, Qian, Yanzhao, Kossinna, Pathum, Gau, Cooper, Gordon, Paul M K, Zhou, Xiang, Guo, Xingyi, Yan, Jun, Wu, Jingjing, Long, Quan
• Format: Journal Article
• Language: English
• Published: United States 03-04-2024
• Subjects: Genome-Wide Association Study; Humans; Linear Models; Models, Genetic; Multifactorial Inheritance; Phenotype; Polymorphism, Single Nucleotide; Sample Size; human diseases; linear mixed model; gene expression; low-effect genetic variants
• ISSN: 1943-2631; 1943-2631
• DOI: 10.1093/genetics/iyae018

Detecting genetic variants with low-effect sizes using a moderate sample size is difficult, hindering downstream efforts to learn pathology and estimating heritability. In this work, by utilizing informative weights learned from training genetically predicted gene expression models, we formed an alternative approach to estimate the polygenic term in a linear mixed model. Our linear mixed model estimates the genetic background by incorporating their relevance to gene expression. Our protocol, expression-directed linear mixed model, enables the discovery of subtle signals of low-effect variants using moderate sample size. By applying expression-directed linear mixed model to cohorts of around 5,000 individuals with either binary (WTCCC) or quantitative (NFBC1966) traits, we demonstrated its power gain at the low-effect end of the genetic etiology spectrum. In aggregate, the additional low-effect variants detected by expression-directed linear mixed model substantially improved estimation of missing heritability. Expression-directed linear mixed model moves precision medicine forward by accurately detecting the contribution of low-effect genetic variants to human diseases.