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A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data.


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Authors

Roberts, Ian 
Carter, Stephanie A 
Scarpini, Cinzia G 
Karagavriilidou, Konstantina 
Barna, Jenny CJ 

Abstract

Reliable identification of copy number aberrations (CNA) from comparative genomic hybridization data would be improved by the availability of a generalised method for processing large datasets. To this end, we developed swatCGH, a data analysis framework and region detection heuristic for computational grids. swatCGH analyses sequentially displaced (sliding) windows of neighbouring probes and applies adaptive thresholds of varying stringency to identify the 10% of each chromosome that contains the most frequently occurring CNAs. We used the method to analyse a published dataset, comparing data preprocessed using four different DNA segmentation algorithms, and two methods for prioritising the detected CNAs. The consolidated list of the most commonly detected aberrations confirmed the value of swatCGH as a simplified high-throughput method for identifying biologically significant CNA regions of interest.

Description

Keywords

0604 Genetics, Biotechnology, Genetics, Human Genome

Journal Title

Adv Bioinformatics

Conference Name

Journal ISSN

1687-8027
1687-8035

Volume Title

Publisher

Hindawi Limited
Sponsorship
Cancer Research Uk (None)