A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data.pdfVIP

Hindawi Publishing Corporation Advances in Bioinformatics Volume 2012, Article ID 876976, 12 pages doi:10.1155/2012/876976 Research Article A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data Ian Roberts,1 Stephanie A. Carter,1 Cinzia G. Scarpini,1 Konstantina Karagavriilidou,1 Jenny C. J. Barna,2 Mark Calleja,3 and Nicholas Coleman1 1 Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK 2 Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK 3 The Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, UK Correspondence should be addressed to Nicholas Coleman, nc109@cam.ac.uk Received 14 March 2012; Revised 22 June 2012; Accepted 26 June 2012 Academic Editor: Yves Van de Peer Copyright © 2012 Ian Roberts et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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