Age and gender were regressed before genetic analysis of the P3 amplitude of the ERP. The quantitative transmission disequilibrium test (QTDT) (Abecasis et al., 2000) was used to test population stratification, total association, and within-family association with each of the SNPs and the P3 amplitude of the ERP. QTDT, one of the most popular family-based linkage disequilibrium tests, is able to avoid spurious evidence of association in the presence of population stratification. In the QTDT framework, association effects are partitioned into orthogonal between-family and within-family components. The between-family association can be impacted by population structure. Within-family association, however, is significant only if there is linkage disequilibrium and is robust to population stratification/admixture. The total association tests use all information including within-family and between-family components, and are proper only if there is no population stratification/admixture. The within-family association results were reported if the test of population stratification was significant, otherwise, the total association (i.e., measured genotype; Boerwinkle et al., 1986) results were reported.
