Using the SNPs and subjects that passed QC, investigators generally use logistic regression with case-control status as the dependent variable and a single SNP as the predictor. The SNP is coded as 0, 1, or 2 (i.e., the number of copies of one of the two alleles) for an additive test with one degree of freedom. This analysis is repeated for each SNP for a million or more statistical tests. Some investigators include covariates in the logistic regression model like age, sex, or indicators of ancestry. In some instances, alternative genetic models are used (e.g., recessive or dominant) but most studies use a 1 degree of freedom additive test as the primary statistical test.
