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Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS.
Greene, Casey S; Sinnott-Armstrong, Nicholas A; Himmelstein, Daniel S; Park, Paul J; Moore, Jason H; Harris, Brent T.
Afiliação
  • Greene CS; Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA.
Bioinformatics ; 26(5): 694-5, 2010 Mar 01.
Article em En | MEDLINE | ID: mdl-20081222
MOTIVATION: Epistasis, the presence of gene-gene interactions, has been hypothesized to be at the root of many common human diseases, but current genome-wide association studies largely ignore its role. Multifactor dimensionality reduction (MDR) is a powerful model-free method for detecting epistatic relationships between genes, but computational costs have made its application to genome-wide data difficult. Graphics processing units (GPUs), the hardware responsible for rendering computer games, are powerful parallel processors. Using GPUs to run MDR on a genome-wide dataset allows for statistically rigorous testing of epistasis. RESULTS: The implementation of MDR for GPUs (MDRGPU) includes core features of the widely used Java software package, MDR. This GPU implementation allows for large-scale analysis of epistasis at a dramatically lower cost than the standard CPU-based implementations. As a proof-of-concept, we applied this software to a genome-wide study of sporadic amyotrophic lateral sclerosis (ALS). We discovered a statistically significant two-SNP classifier and subsequently replicated the significance of these two SNPs in an independent study of ALS. MDRGPU makes the large-scale analysis of epistasis tractable and opens the door to statistically rigorous testing of interactions in genome-wide datasets. AVAILABILITY: MDRGPU is open source and available free of charge from http://www.sourceforge.net/projects/mdr.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Epistasia Genética / Estudo de Associação Genômica Ampla / Esclerose Lateral Amiotrófica Limite: Humans Idioma: En Ano de publicação: 2010 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Epistasia Genética / Estudo de Associação Genômica Ampla / Esclerose Lateral Amiotrófica Limite: Humans Idioma: En Ano de publicação: 2010 Tipo de documento: Article