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Bioinformatics Advance Access published online on February 19, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp091
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution

Björn Nilsson 1,2,3,*, Mikael Johansson 4, Fatima Al-Shahrour 1,3, Anne E. Carpenter 1 and Benjamin L. Ebert 3

1Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
2Department of Hematology and Transfusion Medicine, Lund University Hospital, SE-221 85 Lund, Sweden
3Hematology Division, Brigham and Women's Hospital, Harvard Medical School, One Blackfan Circle, Boston, MA 02115, USA
4Department of Automatic Control, Royal Institute of Technology, SE-100 44 Stockholm, Sweden.

*To whom correspondence should be addressed. Dr. Bjorn Nilsson, E-mail: bnilsson{at}broad.mit.edu, bjorn.nilsson{at}med.lu.se


  Abstract

Motivation: Multimillion-probe microarrays allow detection of gains and losses of chromosomal material at unprecedented resolution. However, the data generated by these arrays are several-fold larger than data from earlier platforms, creating a need for efficient analysis tools that scale robustly with data size.

Results: We developed a new aberration caller, Ultrasome, that delineates genomic changes-of-interest with dramatically improved efficiency. Ultrasome shows near-linear computational complexity and processes latest-generation copy number arrays about 10,000 times faster than standard methods with preserved analytic accuracy.

Availability: www.broad.mit.edu/~bnilsson/ultrasome.zip.

Contact: bnilsson{at}broad.mit.edu

Associate Editor: Prof. Alfonso Valencia

Received on January 12, 2009; revised on February 6, 2009; accepted on February 13, 2009

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