Germline Mosaicism (GM) is a genetic condition in which some germ cells of an individual carry a mutation.
Individuals with germline mosaicism may give birth to affected children and unaffected
children that carry the same measured markers in the vicinity of the trait locus.
This condition violates some of the assumptions underlying standard genetic linkage analysis.
Consequently, there is relatively low power to detect genes created by GM using standard genetic
Superlink-GM is a software that performs genetic linkage analysis in the presence of GM. The software extends the standard model used for genetic linkage analysis in order to incorporate GM.
Superlink-GM is composed of three parts.
In order to use the software one must follow the following steps:|
1. Create a .csv file with the pedigree data. An example .csv file is available in the package. A description of the file format is provided in the readme file.
2. Convert the .csv file to a .xmlbif file using the Python script csvToGMPed.py. .
3. Compute the likelihood of evidence in the .xmlfile file with the program BayesNetPlus.bin.
Please refer to the readme file for detailed instructions
|Code and Executables|
BayesNetPlus was developed by Mark Silberstein.
It uses the program Orderfinder, developed by Nickolay Dovgolevsky and Maayan Fishelson.
BayesNetGeneration was developed by Andrei Anisenia and is based on algorithms developed by Maayan Fishelson and Allen and Darwiche (2008).
The script csvToGMPed was written by Omer Weissbrod under the supervision of Dan Geiger.
|Any comments or bug reports should be directed to Omer Weissbrod.|
|Allen, D. and Darwiche, A. (2008). "RC Link: Genetic linkage analysis using Bayesian networks." International journal of approximate reasoning, 48(2), 499.525.|
|Weissbrod, Omer and Geiger, Dan (2011): "Genetic Linkage Analysis in the Presence of Germline Mosaicism," Statistical Applications in Genetics and Molecular Biology: Vol. 10: Iss. 1, Article 46.|