CCB » Software » BRCA diagnostic software

A computational diagnostic test for mutations in the human breast-cancer genes BRCA1 and BRCA2


Here we provide a computational screening test that takes the raw DNA sequence data from a whole-genome sequence of an individual human and tests for each of 68 known mutations in the BRCA1 and BRCA2 genes. The system uses the very fast Bowtie  alignment program to align all the reads from a deeply-sequenced human genome in just a few hours. For each mutation that it finds, the software reports whether the individual is homozygous or heterozygous for that mutation. This method represents a template that can easily be modified to test for almost any known human genetic mutation.

Obtaining the software

The software is released as perl source code, and is  OSI Certified Open Source Software .

To download it, just click here .

After downloading, uncompress the distribution file by typing:

% tar -xzf brca_diagnostic.tar.gz

A directory named 'brca_diagnostic/' will be created which contains the software, and other supporting files. Please consult the README file in that directory for further information.

Contact Information

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Steven L Salzberg, Mihaela Pertea Do-it-yourself genetic testing Genome Biology 2010, 11:404 (7 October 2010)

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