title: Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.
abstract: BACKGROUND
  Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics.
  
  
  RESULTS
  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.
authors.affiliation: King Abdullah Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, P.O. Box 22490, Riyadh, 11426, Saudi Arabia. aljouieab@ngha.med.sa.|Department of Computer Science, New Jersey Institute of Technology, GITC 4400, University Heights, Newark, NJ, 07102, USA. aljouieab@ngha.med.sa.
authors.forename: Abdulrhman
authors.initials: A
authors.lastname: Al-jouie
authors.affiliation: Department of Computer Science, New Jersey Institute of Technology, GITC 4400, University Heights, Newark, NJ, 07102, USA. me76@njit.edu.
authors.forename: Mohammadreza
authors.initials: M
authors.lastname: Esfandiari
authors.affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA. sramakri@cshl.edu.
authors.forename: Srividya
authors.initials: S
authors.lastname: Ramakrishnan
authors.affiliation: Department of Computer Science, New Jersey Institute of Technology, GITC 4400, University Heights, Newark, NJ, 07102, USA. usman@njit.edu.
authors.forename: Usman
authors.initials: U
authors.lastname: Roshan
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D016009:Chi-Square Distribution; D003196:Computer Graphics; D003198:Computer Simulation; D030541:Databases, Genetic; D004843:Epistasis, Genetic; D055106:Genome-Wide Association Study; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*