Question asked via email:

I am currently working on a project with a binary outcome, and need to report beta coefficients (representing the log-odds increase per copy of the minor allele), confidence intervals, and odds ratios for each variant. I am using a SeqVarGDSClass object with a SeqVarIterator, and have run fitNullModel and assocTestSingle with no problems. Since my outcome is binary and I am using the “family=binomial” option in fitNullModel, the association test produces Score test statistics only.

My question is – do you know if it is possible to get beta coefficients and standard errors for an additive model with a binary outcome using GENESIS?

You have two options for calculating betas for binary outcomes.

Option 1) refit the null model including the genotypes for the variant of interest as a covariate. This is a good option if you only need betas for a small number of variants. You can use SeqVarTools::altDosage to get the alternate allele dosage for a given variant or set of variants.

Option 2) approximate the betas based on the Score test, using the method in Zhou, Shi, and Whittemore 2011 (https://www.ncbi.nlm.nih.gov/pubmed/21922536).

assoc <- assocTestSingle(iterator, nullmod)
assoc$beta <- assoc$Score/(assoc$Score.SE)^2
assoc$beta.SE <- 1/assoc$Score.SE