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 in-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.
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 in-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.
Authors: Viren C Patel; Kajari Mondal; Amol Carl Shetty; Vanessa L Horner; Jirair K Bedoyan; Donna Martin; Tamara Caspary; David J Cutler; Michael E Zwick Journal: Open Access Bioinformatics Date: 2010-11-01
Authors: Yann S Dufour; Gary E Wesenberg; Andrew J Tritt; Jeremy D Glasner; Nicole T Perna; Julie C Mitchell; Timothy J Donohue Journal: Nucleic Acids Res Date: 2010-06-06 Impact factor: 16.971
Authors: Laurent Jourdren; Aurélie Duclos; Christian Brion; Thomas Portnoy; Hugues Mathis; Antoine Margeot; Stéphane Le Crom Journal: Nucleic Acids Res Date: 2010-02-21 Impact factor: 16.971
Authors: Cali E Willet; Laura Bunbury-Cruickshank; Diane van Rooy; Georgina Child; Mohammad R Shariflou; Peter C Thomson; Claire M Wade Journal: BMC Bioinformatics Date: 2013-07-22 Impact factor: 3.169