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Bioinformatics Advance Access originally published online on March 7, 2006
Bioinformatics 2006 22(9):1147-1149; doi:10.1093/bioinformatics/btl080
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data

David C. Walley 1, Ben W. Tripp 1, Young C. Song 1, Keith R. Walley 1 and Scott J. Tebbutt 1,*

1 James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St. Paul's Hospital, University of British Columbia Vancouver, V6Z 1Y6, Canada

*To whom correspondence should be addressed.

Summary: Multi-dimensional Automated Clustering Genotyping Tool (MACGT) is a Java application that clusters complex multi-dimensional vector data derived from single nucleotide polymorphism (SNP) genotyping experiments using mini-sequencing based microarray chemistries such as arrayed primer extension (APEX). Spot intensity output files from microarray experiments across multiple samples are imported into MACGT. The datasets can include four channels of intensity data for each spot, replica spots for each SNP probe and multiple probe types (APEX and allele-specific APEX probes) on both DNA strands for each SNP. MACGT automatically clusters these multi-dimensionality datasets for each SNP across multiple samples. Incorporation of additional array datasets from known samples that have previously validated SNP genotype calls allows unknown samples to be automatically assigned a genotype based on the clustering, along with numerical measures of confidence for each genotype call. Calling accuracy by MACGT exceeds 98% when applied to genotyping data from APEX microarrays, and can be increased to >99.5% by applying thresholds to the confidence measures.

Availability: MACGT is open source and is freely available (under a GNU General Public License) from the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.

Contact: stebbutt{at}mrl.ubc.ca

Supplementary information: Additional information, including Supplementary Figure S1, test data and a user's manual, is available from the iCAPTURE Centre web site (see above).

Received on January 13, 2006; revised on February 16, 2006; accepted on March 2, 2006

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