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Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs




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.

Author(s): Kam-Thong, T. and Pütz, B. and Karbalai, N. and Müller-Myhsok, B. and Borgwardt, K.
Journal: Bioinformatics
Volume: 27
Number (issue): 13: ISMB/ECCB 2011
Pages: i214-i221
Year: 2011
Month: July
Day: 0

Department(s): Empirical Inference
Bibtex Type: Article (article)

DOI: 10.1093/bioinformatics/btr218

Links: Web


  title = {Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs},
  author = {Kam-Thong, T. and P{\"u}tz, B. and Karbalai, N. and M{\"u}ller-Myhsok, B. and Borgwardt, K.},
  journal = {Bioinformatics},
  volume = {27},
  number = {13: ISMB/ECCB 2011},
  pages = {i214-i221},
  month = jul,
  year = {2011},
  month_numeric = {7}