Increasing the power of GxE detection by using multi-locus genome-wide predictors

Harvard Medical School, Boston MA

Investigators

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Abstract

DESCRIPTION (provided by applicant): It is intuitive that the genetic risk for human disease depends on the environment, or that the effect of an exposure in disease is not identical across human populations of different genetic backgrounds. This concept is known as gene-by-environment interaction (GxE) and it is hypothesized that disease risk can be better explained by identifying GxE. Despite the importance in understanding GxE in human disease, there have been few studies that have documented the concept. There are a number of explanations for few-recorded GxE. First, there a few ways to measure standardized indicators of the environment (unlike single nucleotide polymorphisms [SNPs]). When GxE are investigated, environmental factors are selected without sufficient evidence of their prior association in disease traits. Second, investigating GxE requires large sample sizes to identify interactions between individual SNPs and environmental factors. The problem is exacerbated when accounting for multiple tests of millions of SNPs with small main effects. Using current day methods and unstandardized environmental data, it is difficult to collect evidence for interactions between millions of specific SNPs and environmental factors. It is now possible to detect GxE in complex disease traits that contribute to significant disease burden, such as body mass index (BMI) and blood pressure (BP), by developing new methods in quantitative genetics and leveraging existing methods in environmental exposure bioinformatics. This project has four aims to achieve this goal. First, the investigators will develop and validate genome-wide polygenic prediction scores to summarize the contribution of all common SNPs in BMI and BP. The investigators will develop and validate the scores in preexisting genome-wide association study (GWAS) consortia data. In the second aim, the investigators will standardize environmental variables from 7 independent cohort studies deposited in the Database of Genotypes and Phenotypes (dbGaP) to build a large cohort of N ~ 30K for GxE testing. Third, the investigators will develop methods to detect and validate GxE between polygenic trait scores and specific environmental factors selected from Environment-Wide Association Studies (EWAS) in BMI and BP with the combined dbGaP cohorts. Fourth, the investigators will estimate the proportion of variation in BMI and BP due to GxE interaction. The methods proposed in the R21 provide a new paradigm for GxE estimation by taking advantage of all SNPs on the genome while considering a larger number of environmental factors with robust support from EWAS. This will lead to a more complete picture of variability ascribed to genes and environment in complex traits of highest disease burden. If successful, the methods will enable the rapid documentation of reproducible GxE, a need in the human genetics and environmental health fields.