loading
Documents

Research.Publish.Connect.

Paper

Paper Unlock

Authors: Tomasz Gambin 1 ; Pawel Stankiewicz 2 ; Maciej Sykulski 3 and Anna Gambin 3

Affiliations: 1 Warsaw University of Technology, Poland ; 2 Baylor College of Medicine, United States ; 3 University of Warsaw, Poland

ISBN: 978-989-8425-36-2

Keyword(s): aCGH, Segmentation, Noise robustness, Design optimization, DNA copy.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Model Design and Evaluation ; Structural Variations

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 meth od 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. (More)

PDF ImageFull Text

Download
Sign In Guest: Register as new SciTePress user now for free.

Sign In SciTePress user: please login.

PDF ImageMy Papers

You are not signed in, therefore limits apply to your IP address 3.88.156.58

In the current month:
Recent papers: 100 available of 100 total
2+ years older papers: 200 available of 200 total

Paper citation in several formats:
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

@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},
}

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

Login or register to post comments.

Comments on this Paper: Be the first to review this paper.