title: FastEpistasis: a high performance computing solution for quantitative trait epistasis.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  FastEpistasis is open source and available free of charge only for non-commercial users from http://www.vital-it.ch/software/FastEpistasis.
authors.affiliation: Vital-IT Group, Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Thierry
authors.initials: T
authors.lastname: Schüpbach
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Sven
authors.initials: S
authors.lastname: Bergmann
authors.forename: Karen
authors.initials: K
authors.lastname: Kapur
mesh_terms: D003205:Computing Methodologies; D004843:Epistasis, Genetic / Q000235:genetics*; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012984:Software