Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.

ABSTRACT: Integrating single nucleotide polymorphism (SNP) p-values from genome-wide association studies (GWAS) across genes and pathways is a strategy to improve statistical power and gain biological insight. Here, we present Pascal (Pathway scoring algorithm), a powerful tool for computing gene and pathway scores from SNP-phenotype association summary statistics. For gene score computation, we implemented analytic and efficient numerical solutions to calculate test statistics. We examined in particular the sum and the maximum of chi-squared statistics, which measure the strongest and the average association signals per gene, respectively. For pathway scoring, we use a modified Fisher method, which offers not only significant power improvement over more traditional enrichment strategies, but also e

SUBMITTER: Lamparter D 

PROVIDER: S-EPMC4726509 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature