High-throughput analysis of epistasis in genome-wide association studies with BiForce.

ABSTRACT:

Motivation

Gene-gene interactions (epistasis) are thought to be important in shaping complex traits, but they have been under-explored in genome-wide association studies (GWAS) due to the computational challenge of enumerating billions of single nucleotide polymorphism (SNP) combinations. Fast screening tools are needed to make epistasis analysis routinely available in GWAS.

Results

We present BiForce to support high-throughput analysis of epistasis in GWAS for either quantitative or binary disease (case-control) traits. BiForce achieves great computational efficiency by using memory efficient data structures, Boolean bitwise operations and multithreaded parallelization. It performs a full pair-wise genome scan to detect interactions involving SNPs with or without significan

SUBMITTER: Gyenesei A 

PROVIDER: S-EPMC3400955 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature