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Bioinformatics 2007 23(2):e77-e83; doi:10.1093/bioinformatics/btl316
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Computational Genomics

Optimization of probe coverage for high-resolution oligonucleotide aCGH

Doron Lipson 1,*, Zohar Yakhini 1,2 and Yonatan Aumann 3

1 Computer Science Department Technion, Israel
2 Agilent Laboratories CA, USA
3 Computer Science Department, Bar-Ilan University Israel

*To whom correspondence should be addressed.


  Abstract

Motivation: The resolution at which genomic alterations can be mapped by means of oligonucleotide aCGH (array-based comparative genomic hybridization) is limited by two factors: the availability of high-quality probes for the target genomic sequence and the array real-estate. Optimization of the probe selection process is required for arrays that are designed to probe specific genomic regions in very high resolution without compromising probe quality constraints.

Results: In this paper we describe a well-defined optimization problem associated with the problem of probe selection for high-resolution aCGH arrays. We propose the whenever possible isin-cover as a formulation that faithfully captures the requirement of probe selection problem, and provide a fast randomized algorithm that solves the optimization problem in O(n logn) time, as well as a deterministic algorithm with the same asymptotic performance. We apply the method in a typical high-definition array design scenario and demonstrate its superiority with respect to alternative approaches.

Availability: Address requests to the authors.

Contact: dlipson{at}cs.technion.ac.il


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