Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
| Autor: | Srividya Ramakrishnan, Usman Roshan, Abdulrhman Aljouie, Mohammadreza Esfandiari |
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| Rok vydání: | 2014 |
| Předmět: |
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media_common.quotation_subject Graphics processing unit Single-nucleotide polymorphism Biology Chi-square 8 degrees of freedom computer.software_genre Polymorphism Single Nucleotide General Biochemistry Genetics and Molecular Biology Computer graphics Interacting SNPs Area under curve Databases Genetic False positive paradox Chi-square test Computer Graphics Technical Note Humans Computer Simulation media_common Genetics Medicine(all) Chi-Square Distribution Biochemistry Genetics and Molecular Biology(all) Epistasis Genetic General Medicine Genome wide association studies Test (assessment) Area Under Curve Epistasis Data mining computer Algorithms Graphics Processing Unit Genome-Wide Association Study |
| Zdroj: | BMC Research Notes |
| ISSN: | 1756-0500 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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