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Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test

BACKGROUND: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. FINDINGS: We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphi...

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Autores principales: Al-jouie, Abdulrhman, Esfandiari, Mohammadreza, Ramakrishnan, Srividya, Roshan, Usman
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568583/
https://www.ncbi.nlm.nih.gov/pubmed/26369336
http://dx.doi.org/10.1186/s13104-015-1392-5
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author Al-jouie, Abdulrhman
Esfandiari, Mohammadreza
Ramakrishnan, Srividya
Roshan, Usman
author_facet Al-jouie, Abdulrhman
Esfandiari, Mohammadreza
Ramakrishnan, Srividya
Roshan, Usman
author_sort Al-jouie, Abdulrhman
collection PubMed
description BACKGROUND: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. FINDINGS: We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit. We analyze each of the seven WTCCC genome-wide association studies that have about 5000 total case and controls and 400,000 SNPs in an average of 9.6 h on a single GPU. We also study the power, false positives, and area under curve of our program on simulated data and provide a comparison to the GBOOST program. Our program source code is freely available from http://www.cs.njit.edu/usman/Chi8. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-015-1392-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-45685832015-09-15 Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test Al-jouie, Abdulrhman Esfandiari, Mohammadreza Ramakrishnan, Srividya Roshan, Usman BMC Res Notes Technical Note BACKGROUND: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. FINDINGS: We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit. We analyze each of the seven WTCCC genome-wide association studies that have about 5000 total case and controls and 400,000 SNPs in an average of 9.6 h on a single GPU. We also study the power, false positives, and area under curve of our program on simulated data and provide a comparison to the GBOOST program. Our program source code is freely available from http://www.cs.njit.edu/usman/Chi8. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-015-1392-5) contains supplementary material, which is available to authorized users. BioMed Central 2015-09-14 /pmc/articles/PMC4568583/ /pubmed/26369336 http://dx.doi.org/10.1186/s13104-015-1392-5 Text en © Al-jouie et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Technical Note
Al-jouie, Abdulrhman
Esfandiari, Mohammadreza
Ramakrishnan, Srividya
Roshan, Usman
Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
title Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
title_full Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
title_fullStr Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
title_full_unstemmed Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
title_short Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
title_sort chi8: a gpu program for detecting significant interacting snps with the chi-square 8-df test
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568583/
https://www.ncbi.nlm.nih.gov/pubmed/26369336
http://dx.doi.org/10.1186/s13104-015-1392-5
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