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Open Access Highly Accessed Research article

Genotype-environment interactions for quantitative traits in Korea Associated Resource (KARE) cohorts

Jaemin Kim1, Taeheon Lee2, Hyun-Jeong Lee123* and Heebal Kim124*

Author Affiliations

1 Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea

2 Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea

3 Division of Animal Genomics and Bioinformatics, National Institute of Animal science, #564 Omockchun-dong, Suwon 441-706, Republic of Korea

4 CHO&KIM Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea

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BMC Genetics 2014, 15:18  doi:10.1186/1471-2156-15-18

Published: 4 February 2014

Abstract

Background

Due to the lack of statistical power and confounding effects of population structure in human population data, genotype-environment interaction studies have not yielded promising results and have provided only limited knowledge for exploring how genotype and environmental factors interact to in their influence onto risk.

Results

We analyzed 49 human quantitative traits in 7,170 unrelated Korean individuals on 326,262 autosomal single nucleotide polymorphisms (SNPs) collected from the KARE (Korean Association Resource) project, and we estimated the statistically significant proportion of variance that could be explained by genotype-area interactions in the supra-iliac skinfold thickness trait (<a onClick="popup('http://www.biomedcentral.com/1471-2156/15/18/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/15/18/mathml/M1">View MathML</a> = 0.269 and P = 0.00032), which is related to abdominal obesity. Data suggested that the genotypes could have different effects on the phenotype (supra-iliac skinfold thickness) in different environmental settings (rural vs. urban areas). We then defined the genotype groups of individuals with similar genetic profiles based on the additive genetic relationships among individuals using SNPs. We observed the norms of reaction, and the differential phenotypic response of a genotype to a change in environmental exposure. Interestingly, we also found that the gene clusters responsible for cell-cell and cell-extracellular matrix interactions were enriched significantly for genotype-area interaction.

Conclusions

This significant heritability estimate of genotype-environment interactions will lead to conceptual advances in our understanding of the mechanisms underlying genotype-environment interactions, and could be ultimately applied to personalized preventative treatments based on environmental exposures.

Keywords:
Genotype-environment interaction; Heritability; Obesity; Supra-iliac skinfold thickness