Many of today's researchers are generating DNA sequence data for large numbers of samples in population-based experiments. This may include whole genomes, exomes, or targeted regions. The Golden Helix SNP and Variation Suite (SVS) provides a powerful computing environment for analyzing these data and performing association tests at the gene and/or variant level. In this presentation, Dr. Christensen will review fundamentals of population-based variant analysis and demonstrate some of the tools available in SVS for analysis of both common and rare variants. The presentation will feature the recently implemented SKAT-O method, as well as other functions for annotation, visualization, quality control and statistical analysis of DNA sequence variants.