Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2011 Jul 1;27(13):i214-21. doi: 10.1093/bioinformatics/btr218.

Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs.

Author information

  • 1Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany. tony@mpipsykl.mpg.de

Abstract

MOTIVATION:

In recent years, numerous genome-wide association studies have been conducted to identify genetic makeup that explains phenotypic differences observed in human population. Analytical tests on single loci are readily available and embedded in common genome analysis software toolset. The search for significant epistasis (gene-gene interactions) still poses as a computational challenge for modern day computing systems, due to the large number of hypotheses that have to be tested.

RESULTS:

In this article, we present an approach to epistasis detection by exhaustive testing of all possible SNP pairs. The search strategy based on the Hilbert-Schmidt Independence Criterion can help delineate various forms of statistical dependence between the genetic markers and the phenotype. The actual implementation of this search is done on the highly parallelized architecture available on graphics processing units rendering the completion of the full search feasible within a day.

AVAILABILITY:

The program is available at http://www.mpipsykl.mpg.de/epigpuhsic/.

CONTACT:

tony@mpipsykl.mpg.de.

[PubMed - indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk