Application of noncollapsing methods to the gene-based association test: a comparison study using Genetic Analysis Workshop 18 data

Rare variants have been proposed to play a significant role in the onset and development of common diseases. However, traditional analysis methods have difficulties in detecting association signals for rare causal variants because of a lack of statistical power. We propose a two-stage, gene-based method for association mapping of rare variants by applying four different noncollapsing algorithms. Using the Genome Analysis Workshop18 whole genome sequencing data set of simulated blood pressure phenotypes, we studied and contrasted the false-positive rate of each algorithm using receiver operating characteristic curves. The statistical power of these methods was also evaluated and compared through the analysis of 200 simulated replications in a smaller genotype data set. We showed that the Fisher's method was superior to the other 3 noncollapsing methods, but was no better than the standard method implemented with famSKAT. Further investigation is needed to explore the potential statistical properties of these approaches.