Skip Navigation



Bioinformatics Advance Access published online on March 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl080
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
22/9/1147    most recent
btl080v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Walley, D. C.
Right arrow Articles by Tebbutt, S. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Walley, D. C.
Right arrow Articles by Tebbutt, S. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 13, 2006
Revised February 16, 2006
Accepted March 2, 2006

Applications note

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.
Scott J. Tebbutt, E-mail: stebbutt{at}mrl.ubc.ca


  Abstract

Summary: 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 data sets can include four channels of intensity data for each spot, replica spots for each SNP probe, and multiple probe types (APEX and allele-specific [AS] APEX probes) on both DNA strands for each SNP. MACGT automatically clusters these multi-dimensionality data sets for each SNP across multiple samples. Incorporation of additional array data sets 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.

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).

Associate Editor: Martin Bishop
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.