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 withthe problem of probe selectionfor high-resolution aCGH
arrays. We propose the whenever possible 2-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.
| Original language | American English |
|---|---|
| Title of host publication | 5thAnuual European Conference on Computational Biology (ECCB) |
| Publisher | Oxford University Press |
| State | Published - 2006 |