INTERSNP is a software for genome-wide interaction analysis (GWIA) of case-control SNP data and quantitative traits. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). Our software product implements

• A logistic regression framework as well as log-linear models for joint analysis of multiple SNPs.

• Automatic handling of SNP annotation and pathway information

• Methods to account for multiple testing, in particular, Monte-Carlo simulations to judge genome-wide significance.
• A linear regression framework for analysis of quantitative traits
• Pathway Association Analysis (SNP ratio, Fisher score, Gene ratio, Fisher Max, Fisher MaxPlus)
• Genome-wide Haplotype Analysis
• Pre-tests for quick analysis

• New features:

• • Pathway Association Analysis with interaction-ratio
  • Case-Only analysis
    

Herold C, Steffens M, Brockschmidt FF, Baur MP, Becker T (2009) INTERSNP: Genome-wide Interaction Analysis Guided by A Priori Information. Bioinformatics. 2009 Dec 15;25(24):3275-81