Functional performance of aCGH test

Tomasz Gambin

Abstract

Array-comparative genomic hybridization (aCGH) technology enables rapid, high-resolution analysis of genomic rearrangements. With the use of it, genome copy number changes and rearrangement breakpoints can be detected and analyzed at resolutions down to a few kilobases. An exon array CGH approach proposed recently accurately measures copy-number changes of individual exons in the human genome. The crucial and highly non-trivial starting task is the design of an array, i.e. the choice of appropriate (multi)set of oligos. The success of the whole high-level analysis depends on the quality of the design. Also, the comparison of several alternative designs of array CGH constitutes an important step in development of new diagnostic chip. In this paper, we deal with these two often neglected issues. We propose a new approach to measure the quality of array CGH designs. Our measures reflect the robustness of rearrangements detection to the noise (mostly experimental measurement error). The method is parametrized by the segmentation algorithm used to identify aberrations. We implemented the efficient Monte Carlo method for testing noise robustness within DNAcopy procedure. Developed framework has been applied to evaluation of functional quality of several optimized array designs.
Author Tomasz Gambin II
Tomasz Gambin,,
- The Institute of Computer Science
Journal seriesComputers in Biology and Medicine, ISSN 0010-4825
Issue year2011
Vol43
NoIssue 6
Pages775-785
Keywords in EnglishaCGH, Custom array design, Functional performance, Design optimization
DOIDOI:10.1016/j.compbiomed.2013.02.008
Languageen angielski
Score (nominal)20
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