imbie intersnp uni

Software from IMBIE
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).

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New Version: v1.15 (22 January 2015).

To compile INTERSNP-RARE, change #RARE 0 to #RARE 1 in intersnp.cpp.

New features:

  • Methods for stratified analysis

Recent features:

  • Output of the covariance matrix for regression models to enable meta-analysis of GWAS results.

  • Regression rare variant association tests
  • Adaptive permutation testing
  • Streamlined and simplified bin handling
  • Compatibility with SetID files. Ability to create SetID files from interval files.
  • Gene reference interval file updated to Ensembl Release 75.
  • Contact: drichel(at)

Our software product INTERSNP implements:
  • A logistic regression framework as well as log-linear models for joint analysis of multiple SNPs
  • All PLINK input formats (ped/map, tped/tfam, bed/bim/fam) can be used
  • 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
  • Pathway Association Analysis with interaction-ratio
  • Case-Only-Analysis
  • ... and more

INTERSNP started as a project of the Institute f. Medical Biometry, Informatics and Epidemiology, University of Bonn, Germany, and is now maintained and extended by the AG Genomic Mathematics in Neuroepidemiology at the German Center for Neurodegenerative Diseases, DZNE

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

Herold C, Mattheisen M, Lacour A, Vaitsiakhovich T, Angisch M, Drichel D, Becker T (2012) Integrated genome-wide pathway association analysis with INTERSNP. Hum Hered. 2012;73(2):63-72.

Herold C, Ramirez A, Drichel D, Lacour A, Vaitsiakhovich T, Noethen MM, Jessen F, Maier W, Becker T (2013) A one-degree-of-freedom test for supra-multiplicativity of SNP effects. PLoS One. 2013 Oct 30;8(10):e78038.

Drichel D, Herold C, Lacour A, Ramirez A, Jessen F, Maier W, Noethen MM, Leber M, Vaitsiakhovich T, Becker T (2014) Rare variant testing of imputed data: an analysis pipeline typified. Hum Hered. 2014;78(3-4):164-78.