FastEpistasis: a high performance computing solution for quantitative trait epistasis.

ABSTRACT:

Motivation

Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously.

Results

We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and off

SUBMITTER: Schupbach T 

PROVIDER: S-EPMC2872003 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature