Detecting Genotype-Population Interaction Effects by Ancestry Principal Components

Title
Detecting Genotype-Population Interaction Effects by Ancestry Principal Components
Publication Date
2020-04-21
Author(s)
Yu, Chenglong
Ni, Guiyan
Van Der Werf, Julius
( author )
OrcID: https://orcid.org/0000-0003-2512-1696
Email: jvanderw@une.edu.au
UNE Id une-id:jvanderw
Lee, S Hong
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Frontiers Research Foundation
Place of publication
Switzerland
DOI
10.3389/fgene.2020.00379
UNE publication id
une:1959.11/51489
Abstract

Heterogeneity in the phenotypic mean and variance across populations is often observed for complex traits. One way to understand heterogeneous phenotypes lies in uncovering heterogeneity in genetic effects. Previous studies on genetic heterogeneity across populations were typically based on discrete groups in populations stratified by different countries or cohorts, which ignored the difference of population characteristics for the individuals within each group and resulted in loss of information. Here, we introduce a novel concept of genotype-by-population (G × P) interaction where population is defined by the first and second ancestry principal components (PCs), which are less likely to be confounded with country/cohort-specific factors. We applied a reaction norm model fitting each of 70 complex traits with significant SNP-heritability and the PCs as covariates to examine G × P interactions across diverse populations including white British and other white Europeans from the UK Biobank (N = 22,229). Our results demonstrated a significant population genetic heterogeneity for behavioral traits such as age at first sexual intercourse and academic qualification. Our approach may shed light on the latent genetic architecture of complex traits that underlies the modulation of genetic effects across different populations.

Link
Citation
Frontiers in Genetics, v.11, p. 1-12
ISSN
1664-8021
Pubmed ID
32373165
Start page
1
End page
12
Rights
Attribution 4.0 International

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