Abstract
Knowledge of simulated genetic effects facilitates interpretation of methodological studies. Genetic interactions for common disorders are likely numerous and weak. Using the 200 replicates of the Genetic Analysis Workshop 16 (GAW16) Problem 3 simulated data, we compared the statistical power to detect weak gene-gene interactions using a haplotype-based test in the UNPHASED software with genotypic mixed model (GMM) and additive mixed model (AMM) mixed linear regression model in SAS. We assumed a candidate-gene approach where a single-nucleotide polymorphism (SNP) in one gene is fixed and multiple SNPs are at the second gene. We analyzed the quantitative low-density lipoprotein trait (heritability 0.7%), modulated by simulated interaction of rs4648068 from 4q24 and another gene on 8p22, where we analyzed seven SNPs. We generally observed low power calculated per SNP (