GenePool

About GenePool

GenePool is a software package that provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays. Funding of GenePool is made possible through a National Institutes of Health ENDGAME grant (U01-HL086528-421-43401).

The GenePool system consists of two executable programs, gpextract and gpanalyze and one perl script gpcommand The first GenePool script gpextract uses the Affymetrix Fusion SDK library to extract intensity values from Affymetrix CEL files and write them to a customized, more compact binary file format. The new files have the same name as the original CEL file but with the string .gpb appended to each filename. gpanalyze takes the intensity values from the .gpb files and uses a variety of distance measures to assign a probability score to each SNP where the score indicates how unlikely is the observed difference in allele frequency between the hybridizations for the two DNA pools.

The primary documentation for GenePool is the man pages that accompany the distributions. The genepool man page is the primary project documentation and should be used as the jumping-off point for anyone looking for information about how to use GenePool. It contains installation instructions for the binary and source code distributions of GenePool as well as Known Issues and a To Do section that outlines major areas of development effort.

A full copy of the man pages for all executables and scripts in PDF and HTML format is available online. If you are using a unix-based operating system for development, once GenePool is installed the man pages should be viewable using the standard man command.

Release Numbers

GenePool will use the odd-even system to denote development and stable releases. Stable releases will be made periodically and will end in an even digit, for example 0.12, 0.16.2, 1.06. The current development code will also be periodically copied to the download site and will end in an odd number, for example 0.13, 0.17, 1.07.

Copyright and Licensing

GenePool is copyright 2006-2008 by The Translational Genomics Research Institute. All rights reserved. This License is limited to, and you may use the Software solely for, your own internal and non-commercial use for academic and research purposes. Without limiting the foregoing, you may not use the Software as part of, or in any way in connection with the production, marketing, sale or support of any commercial product or service. For commercial use, please contact licensing@tgen.org. By installing this Software you are agreeing to the terms of the LICENSE file distributed with this software.

In any work or product derived from the use of this Software, proper attribution of the authors as the source of the software or data must be made. The following publication should be cited:

Pearson JV, Huentelman MJ, Halperin RF, Tembe WD, Melquist S, Homer N, Brun M, Szelinger S, Coon KD, Zismann VL, Webster JA, Beach T, Sando SB, Aasly JO, Heun R, Jessen F, Kolsch H, Tsolaki M, Daniilidou M, Reiman EM, Papassotiropoulos A, Hutton ML, Stephan DA, Craig DW. Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies. Am J Hum Genet. 2007 Jan;80(1):126-39.