ArticleBioinformatics (Oxford, England)2011
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic interaction effects.Nature genetics · 2025Article
- Review on GPU accelerated methods for genome-wide SNP-SNP interactions.Molecular genetics and genomics : MGG · 2024Review
- Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis.Plant physiology · 2024Article
- Exploring Machine Learning Algorithms to Unveil Genomic Regions Associated With Resistance to Southern Root-Knot Nematode in Soybeans.Frontiers in plant science · 2022Article
- High performance computing enabling exhaustive analysis of higher order single nucleotide polymorphism interaction in Genome Wide Association Studies.Health information science and systems · 2015Article
- Practical aspects of genome-wide association interaction analysis.Human genetics · 2014Review
- EPIQ-efficient detection of SNP-SNP epistatic interactions for quantitative traits.Bioinformatics (Oxford, England) · 2014Article
- Discovering epistasis in large scale genetic association studies by exploiting graphics cards.Frontiers in genetics · 2013Review
- Screening-testing approaches for gene-gene and gene-environment interactions using independent statistics.Frontiers in genetics · 2013Article
- The advantages and limitations of trait analysis with GWAS: a review.Plant methods · 2013Review
- GWIS--model-free, fast and exhaustive search for epistatic interactions in case-control GWAS.BMC genomics · 2013Article
- A comparison of internal model validation methods for multifactor dimensionality reduction in the case of genetic heterogeneity.BMC research notes · 2012Article
- Natural variation in Arabidopsis: from molecular genetics to ecological genomics.Plant physiology · 2012Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationIn 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.
resultsIn 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.
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