Forward LASSO analysis for high-order interactions in genome-wide association study

Previous genome-wide association study (GWAS) focused on low-order interactions between pairwise single-nucleotide polymorphisms (SNPs) with significant main effects. Little is known how high-order interactions effect, especially one among the SNPs without main effects regulates quantitative traits. Within the frameworks of linear model and generalized linear model, the LASSO with coordinate descent step can be used to simultaneously analyze thousands and thousands of SNPs for normal and discrete traits. With consideration of high-order interactions among SNPs, a huge number of genetic effects make the LASSO failing to work under the presented condition of computation. Forward LASSO analysis is, therefore, proposed to shrink most of genetic effects to be zeros stage by stage. Simulation demonstrates that our proposed method could be used instead of the LASSO method for full model in mapping high-order interactions. Application of forward LASSO method is provided to GWAS for carcass traits and meat quality traits in beef cattle.