Two-phase stratified sampling designs for regional sequencing

By systematic examination of common tag single-nucleotide polymorphisms (SNPs) across the genome, the genome-wide association study (GWAS) has proven to be a successful approach to identify genetic variants that are associated with complex diseases and traits. Although the per base pair cost of sequencing has dropped dramatically with the advent of the next-generation technologies, it may still only be feasible to obtain DNA sequence data for a portion of available study subjects due to financial constraints. Two-phase sampling designs have been used frequently in large-scale surveys and epidemiological studies where certain variables are too costly to be measured on all subjects. We consider two-phase stratified sampling designs for genetic association, in which tag SNPs for candidate genes or regions are genotyped on all subjects in phase 1, and a proportion of subjects are selected into phase 2 based on genotypes at one or more tag SNPs. Deep sequencing in the region is then applied to genotype phase 2 subjects at sequence SNPs. We investigate alternative sampling designs for selection of phase 2 subjects within strata defined by tag SNP genotypes and develop methods of inference for sequence SNP variant associations using data from both phases. In comparison to methods that use data from phase 2 alone, the combined analysis improves efficiency.