CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies

We have developed two software tools, CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait), which enable efficient large-scale analysis of low frequency and rare variants. Both programs implement a collapsing method examining the accumulation of low frequency and rare variants across a locus of interest that has more power than single variant analysis. CCRaVAT carries out case-control analyses whereas QuTie has been developed for continuous trait analysis.CCRaVAT and QuTie are easy to use software tools that allow users to perform genome-wide association analysis on low frequency and rare variants for both binary and quantitative traits. The software is freely available and provides the genetics community with a resource to perform association analysis on rarer genetic variants.Recent advances in high-throughput genotyping have made large-scale genetic association studies possible. Genome-wide association studies (GWAS) for complex disease have met with unprecedented success in identifying common susceptibility variants. However, the discovered common-frequency single nucleotide polymorphism (SNP) associations do not account for a large proportion of the genetic component of disease. The field is now focusing on the analysis of low frequency and rare variants (i.e. minor allele frequency (MAF) ≤0.05) to investigate if they will help explain the missing heritability in complex trait etiology [1,2]. While the sample sizes currently investigated are large enough for a well-powered GWAS of common variants, they are not large enough to provide sufficient power for the single-point analysis of low frequency/rare variants with small to moderate effect sizes [3]. We have developed association analysis software, CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait), which allow the large-scale analysis of low frequency/rare polymorphisms. The software increases power over single marker analysis of these variants by pooli