GeneChips for CMT: IGG: A Tool to Integrate GeneChips for Genetic Studies

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IGG: A Tool to Integrate GeneChips for Genetic Studies

Li Miao-Xin 1, Jiang Lin 6, Ho S.L. 4, Song You-Qiang 1,4,* and Sham

Pak C. 2,4,5

Department of 1Biochemistry, 2Psychiatry and 3Medicine, 4the Centre

for Reproduction, Development and Growth, and 5Genome Research

Center, The University of Hong Kong, Pokfulam, Hong Kong and 6Hunan

Business College, Changsha, Hunan 410205, China

http://bioinformatics.oxfordjournals.org/cgi/content/short/btm458v1

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.