IBDFinder

About this program

This program is designed to aid the identification of regions of Identity By Descent (IBD) in consanguineous individuals by visually presenting the SNP genotype data ordered by physical or genetic distances.

The program uses the text files (with a *.xls file extension) created by Affymetrix, however it may be a relatively simple process upgrade the program to use data from other sources.

Non IBD control images

When analysing SNP data with IBDFinder a number of unusual features can be seen. Some of these will be due to common IBD regions in the affected individuals, while some are just features commonly seen in normal individuals. To help you pick out important regions from the background noise look at these images of 29 sets of NSP and STY SNP chip data.

AutoSNPa versus IBDFinder

Unlike AutoSNPa this program is designed to work with unrelated individuals possibly from different ethnic origins. It is also possible to compare results from different SNP datasets. This means that it will allow you to analyse data from singletons with different disease haplotypes rather than pedigrees. Also, since it can analyse a mixture of different SNP datasets (i.e. 10k Xba, 50k Hind and 250k NSP files) it can use data that has been obtained over an extended period of time and does not require the patients to be reanalysed.

This program and its instruction file is currently hosted on mirror of my old department web site and can obtained from here. A copy of the user guide is also kept on this site here.

IBDFinder along with SNPSetter has been published by Human Mutation

Citation

Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT (2009). IBDfinder and SNPsetter: tools for pedigree-independent identification of autozygous regions in individuals with recessive inherited disease. Human Mutation, 30:960-7

Computer requirements

This program runs on Microsoft Windows, using the .NET 2.0 environment which can be obtained from here.