TY - JOUR
T1 - A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits
AU - Pazokitoroudi, Ali
AU - Liu, Zhengtong
AU - Dahl, Andrew
AU - Zaitlen, Noah
AU - Rosset, Saharon
AU - Sankararaman, Sriram
N1 - Publisher Copyright:
© 2024 The Authors
PY - 2024/7/11
Y1 - 2024/7/11
N2 - Understanding the contribution of gene-environment interactions (GxE) to complex trait variation can provide insights into disease mechanisms, explain sources of heritability, and improve genetic risk prediction. While large biobanks with genetic and deep phenotypic data hold promise for obtaining novel insights into GxE, our understanding of GxE architecture in complex traits remains limited. We introduce a method to estimate the proportion of trait variance explained by GxE (GxE heritability) and additive genetic effects (additive heritability) across the genome and within specific genomic annotations. We show that our method is accurate in simulations and computationally efficient for biobank-scale datasets. We applied our method to common array SNPs (MAF ≥1%), fifty quantitative traits, and four environmental variables (smoking, sex, age, and statin usage) in unrelated white British individuals in the UK Biobank. We found 68 trait-E pairs with significant genome-wide GxE heritability (p<0.05/200) with a ratio of GxE to additive heritability of ≈6.8% on average. Analyzing ≈8 million imputed SNPs (MAF ≥0.1%), we documented an approximate 28% increase in genome-wide GxE heritability compared to array SNPs. We partitioned GxE heritability across minor allele frequency (MAF) and local linkage disequilibrium (LD) values, revealing that, like additive allelic effects, GxE allelic effects tend to increase with decreasing MAF and LD. Analyzing GxE heritability near genes highly expressed in specific tissues, we find significant brain-specific enrichment for body mass index (BMI) and basal metabolic rate in the context of smoking and adipose-specific enrichment for waist-hip ratio (WHR) in the context of sex.
AB - Understanding the contribution of gene-environment interactions (GxE) to complex trait variation can provide insights into disease mechanisms, explain sources of heritability, and improve genetic risk prediction. While large biobanks with genetic and deep phenotypic data hold promise for obtaining novel insights into GxE, our understanding of GxE architecture in complex traits remains limited. We introduce a method to estimate the proportion of trait variance explained by GxE (GxE heritability) and additive genetic effects (additive heritability) across the genome and within specific genomic annotations. We show that our method is accurate in simulations and computationally efficient for biobank-scale datasets. We applied our method to common array SNPs (MAF ≥1%), fifty quantitative traits, and four environmental variables (smoking, sex, age, and statin usage) in unrelated white British individuals in the UK Biobank. We found 68 trait-E pairs with significant genome-wide GxE heritability (p<0.05/200) with a ratio of GxE to additive heritability of ≈6.8% on average. Analyzing ≈8 million imputed SNPs (MAF ≥0.1%), we documented an approximate 28% increase in genome-wide GxE heritability compared to array SNPs. We partitioned GxE heritability across minor allele frequency (MAF) and local linkage disequilibrium (LD) values, revealing that, like additive allelic effects, GxE allelic effects tend to increase with decreasing MAF and LD. Analyzing GxE heritability near genes highly expressed in specific tissues, we find significant brain-specific enrichment for body mass index (BMI) and basal metabolic rate in the context of smoking and adipose-specific enrichment for waist-hip ratio (WHR) in the context of sex.
KW - UK Biobank
KW - complex traits
KW - gene-context interaction
KW - gene-drug interaction
KW - gene-environment interaction
KW - genetic architecture of gene-environment interactions
KW - noise heterogeneity
KW - patitioning GxE heritability
KW - scalable variance component analysis
UR - http://www.scopus.com/inward/record.url?scp=85197087294&partnerID=8YFLogxK
U2 - 10.1016/j.ajhg.2024.05.015
DO - 10.1016/j.ajhg.2024.05.015
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C2 - 38866020
AN - SCOPUS:85197087294
SN - 0002-9297
VL - 111
SP - 1462
EP - 1480
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
IS - 7
ER -