GIST: Genotype-IBD Sharing Test

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GIST is a method for detecting association between marker genotypes and IBD sharing at the marker locus. Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal. In a nutshell, GIST essentially tests if there is correlation between the dosage of a marker allele among the affected in a family and the family's linkage result at the same locus. If the marker is unlinked to disease gene or linked but not in LD with the disease gene, there will be no correlation. If the marker is linked and in LD with the disease gene, this often is a positive correlation. Thus, testing for such correlation gives you information on whether the marker is close enough to the disease gene.

The software can be used to analyze affected sibship data. Two versions of the software are available.

Windows version: GIST_WIN.exe is a self-installation executable file that will install GIST on your Windows computer. See instructions here.

Linux/Unix version: gist.tar.gz is a gzipped archive of necessary files. Once you have uncompressed the files, you can install the program by compiling the C program. See instructions here.

The paper that describes the method is:

Li C, Scott LJ, Boehnke M. (2004) Assessing whether an allele can account in part for a linkage signal: The genotype-IBD sharing test (GIST). Am. J. Hum. Genet. 74:418-431 (GIST.pdf)

Topic revision: r3 - 28 Apr 2009, ChunLi

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