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Bioinformatics Advance Access originally published online on September 14, 2007
Bioinformatics 2007 23(22):3105-3107; doi:10.1093/bioinformatics/btm458
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

IGG: A tool to integrate GeneChips for genetic studies

M.-X. Li 1, L. Jiang 6, S.-L. Ho 3, Y.-Q. Song 1,4,5,* and P.-C. Sham 2,4,5

1Department of Biochemistry, 2Department of Psychiatry, 3Department of Medicine, 4The Centre for Reproduction, Development and Growth, 5Genome Research Center, The University of Hong Kong, Pokfulam, Hong Kong and 6Hunan Business College, Changsha, Hunan 410205, China

*To whom correspondence should be addressed.


  Abstract

Summary: To facilitate genetic studies using high-throughput genotyping technologies, we have developed an open source tool to integrate genotype data across the Affymetrix and Illumina platforms. It can efficiently integrate a large amount of data from various GeneChips, add genotypes of the HapMap Project into a specific project, flexibly trim and export the integrated data with different formats of popular genetic analysis tools, and highly control the quality of genotype data. Furthermore, this tool has sufficiently simplified its usage through its user-friendly graphic interface and is independent of third-party databases. IGG has successfully been applied to a genome-wide linkage scan in a Charcot-Marie-Tooth disease pedigree by integrating three types of GeneChips and HapMap project genotypes.

Availability: http://bioinfo.hku.hk/iggweb (version 0.9).

Contact: limx54{at}yahoo.com and songy{at}hku.hk

Associate Editor: Martin Bishop

Received on June 22, 2007; revised on August 10, 2007; accepted on September 3, 2007

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