FastEpistasis: a high performance computing solution for quantitative trait epistasis.

Détails

Ressource 1Télécharger: BIB_CC4EF3D71E98.P001.pdf (74.39 [Ko])
Etat: Public
Version: de l'auteur
ID Serval
serval:BIB_CC4EF3D71E98
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
FastEpistasis: a high performance computing solution for quantitative trait epistasis.
Périodique
Bioinformatics
Auteur(s)
Schüpbach T., Xenarios I., Bergmann S., Kapur K.
ISSN
1367-4811[electronic], 1367-4803[linking]
Statut éditorial
Publié
Date de publication
2010
Volume
26
Numéro
11
Pages
1468-1469
Langue
anglais
Résumé
Motivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously.
Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism ( SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.
Mots-clé
Computing Methodologies, Epistasis, Genetic/genetics, Genome-Wide Association Study, Genomics/methods, Humans, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Software
Pubmed
Web of science
Open Access
Oui
Création de la notice
11/03/2011 12:34
Dernière modification de la notice
20/08/2019 15:47
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