ROBUSTNESS OF EXON CGH ARRAY DESIGNS

Tomasz Gambin, Pawel Stankiewicz, Maciej Sykulski, Anna Gambin

2011

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 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.

Paper Citation

in Harvard Style

Gambin T., Stankiewicz P., Sykulski M. and Gambin A. (2011). ROBUSTNESS OF EXON CGH ARRAY DESIGNS . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 173-182. DOI: 10.5220/0003153201730182

in Bibtex Style

@conference{bioinformatics11,
author={Tomasz Gambin and Pawel Stankiewicz and Maciej Sykulski and Anna Gambin},
title={ROBUSTNESS OF EXON CGH ARRAY DESIGNS},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={173-182},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003153201730182},
isbn={978-989-8425-36-2},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - ROBUSTNESS OF EXON CGH ARRAY DESIGNS
SN - 978-989-8425-36-2
AU - Gambin T.
AU - Stankiewicz P.
AU - Sykulski M.
AU - Gambin A.
PY - 2011
SP - 173
EP - 182
DO - 10.5220/0003153201730182