{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T16:00:12Z","timestamp":1768924812147,"version":"3.49.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Hundreds of genome-wide association studies have been performed over the last decade, but as single nucleotide polymorphism (SNP) chip density has increased so has the computational burden to search for epistasis [for n SNPs the computational time resource is O(n(n\u22121)\/2)]. While the theoretical contribution of epistasis toward phenotypes of medical and economic importance is widely discussed, empirical evidence is conspicuously absent because its analysis is often computationally prohibitive. To facilitate resolution in this field, tools must be made available that can render the search for epistasis universally viable in terms of hardware availability, cost and computational time.<\/jats:p>\n               <jats:p>Results: By partitioning the 2D search grid across the multicore architecture of a modern consumer graphics processing unit (GPU), we report a 92\u00d7 increase in the speed of an exhaustive pairwise epistasis scan for a quantitative phenotype, and we expect the speed to increase as graphics cards continue to improve. To achieve a comparable computational improvement without a graphics card would require a large compute-cluster, an option that is often financially non-viable. The implementation presented uses OpenCL\u2014an open-source library designed to run on any commercially available GPU and on any operating system.<\/jats:p>\n               <jats:p>Availability: The software is free, open-source, platform-independent and GPU-vendor independent. It can be downloaded from http:\/\/sourceforge.net\/projects\/epigpu\/.<\/jats:p>\n               <jats:p>Contact: \u00a0gib.hemani@roslin.ed.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr172","type":"journal-article","created":{"date-parts":[[2011,4,7]],"date-time":"2011-04-07T00:42:01Z","timestamp":1302136921000},"page":"1462-1465","source":"Crossref","is-referenced-by-count":80,"title":["EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards"],"prefix":"10.1093","volume":"27","author":[{"given":"Gibran","family":"Hemani","sequence":"first","affiliation":[{"name":"1 Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG and 2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK"}]},{"given":"Athanasios","family":"Theocharidis","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG and 2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK"}]},{"given":"Wenhua","family":"Wei","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG and 2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK"}]},{"given":"Chris","family":"Haley","sequence":"additional","affiliation":[{"name":"1 Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG and 2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK"},{"name":"1 Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG and 2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,4,6]]},"reference":[{"key":"2023012511152409500_B1","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1534\/genetics.107.075614","article-title":"Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis","volume":"177","author":"Aulchenko","year":"2007","journal-title":"Genetics"},{"key":"2023012511152409500_B2","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/nrg1407","article-title":"Epistasis: too often neglected in complex trait studies?","volume":"5","author":"Carlborg","year":"2004","journal-title":"Nat. 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