title: Automated construction and testing of multi-locus gene-gene associations.
abstract: It has been argued that the missing heritability in common diseases may be in part due to rare variants and gene-gene effects. Haplotype analyses provide more power for rare variants and joint analyses across genes can address multi-gene effects. Currently, methods are lacking to perform joint multi-locus association analyses across more than one gene/region. Here, we present a haplotype-mining gene-gene analysis method, which considers multi-locus data for two genes/regions simultaneously. This approach extends our single region haplotype-mining algorithm, hapConstructor, to two genes/regions. It allows construction of multi-locus SNP sets at both genes and tests joint gene-gene effects and interactions between single variants or haplotype combinations. A Monte Carlo framework is used to provide statistical significance assessment of the joint and interaction statistics, thus the method can also be used with related individuals. This tool provides a flexible data-mining approach to identifying gene-gene effects that otherwise is currently unavailable.
  
  
  BACKGROUND
  http://bioinformatics.med.utah.edu/Genie/hapConstructor.html.
authors.affiliation: Department of Biomedical Informatics, University of Utah School of Medicine, UT, USA. ryan.abo@hsc.utah.edu
authors.forename: Ryan
authors.initials: R
authors.lastname: Abo
authors.forename: Stacey
authors.initials: S
authors.lastname: Knight
authors.forename: Alun
authors.initials: A
authors.lastname: Thomas
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Camp
mesh_terms: D000465:Algorithms; D005796:Genes; D056726:Genetic Association Studies / Q000379:methods*; D056426:Genetic Loci; D006239:Haplotypes; D009010:Monte Carlo Method; D020641:Polymorphism, Single Nucleotide; D012984:Software