paperKB
coga / coga-kb
Help
Sign in

Chunk #27 — Materials and Method — Analytic Plan — G×E analyses

Source
Incorporating Functional Genomic Information to Enhance Polygenic Signal and Identify Variants Involved in Gene-by-Environment Interaction for Young Adult Alcohol Problems.
Embedded
yes

Text

are most likely to be observed for SNPs with smaller p-values (Thomas, 2010). This threshold was arbitrary, but was selected in an attempt to balance testing a large enough number of “top” SNPs with the computational resources required for such tests. For each SNP, we then examined gene-environment interaction effects in a linear model where relationship status was the moderator and frequency of alcohol intoxication was the outcome. G×E models were run using the lme4 package in R in order to account for familial nesting. G×E was tested using a parameterization method that takes into account effects between three gene levels in order to accurately capture interactions that can otherwise be misrepresented when using a single cross-product term (Aliev et al., 2014). The method checks the additive interaction between any two of the three gene levels and corrects for the number of tests. The resulting p-value corresponds to the difference between at least two of the gene levels. Sex and age were included as covariates. Preliminary analyses indicated only a modest association between relationship status and intoxication frequency (r = −.10), and no association between the GW- and DHS-scores and relationship status (range rpb = −0.04 to 0.004, all p