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SAMPLE

Shadow Autozygosity MaPping by Linkage Exclusion

About this program

This program is designed to identify regions that are linked to a recessive disease by analysing genotype data from the parents and unaffected sibs of affected individuals. Since the analysis does not use data from affected patients it makes it an ideal method to find lethal recessive genes where the patients have died before DNA samples could be obtained.

The program uses the files created by the Affymetrix Genotyping console and annotated by SNP6Annotator, however it may be a relatively simple process to upgrade the program to use data from other sources.

Since the majority of SNPs are uninformative this programe works best with the very high density SNP sets such as SNP5 and SNP6 data sets.

SAMPLE versus AutoSNPa and IBDFinder

Ths program works by looking for a lack of homozygous regions in the families of affected individuals and so works in a completely different way to AutoSNPa and IBDFinder and as very different data requirements. This makes SAMPLE and AutoSNPa/IBDFinder mutually exclusive methods

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

Citation

Carr, IM, Szymanska K,Sheridan E, Markham AF, Bonthron DT, Johnson CA (2009) Shadow autozygosity mapping by linkage exclusion (SAMPLE): A simple strategy to identify the genetic basis of lethal autosomal recessive disorders. Human Mutation, Accepted Article Online: Aug 14

Computer requirements

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



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