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Updated: Jun 23, 2026

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
CGHregions: dimension reduction for array CGH data with minimal information loss
Mark A van de Wiel1, Wessel N van Wieringen
1Department of Pathology and Department of Biostatistics (KEB), VU University Medical Center, Amsterdam, The Netherlands. mark.vdwiel@vumc.nl
Abstract:
An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is explained using a small example. The potential beneficial effects of the algorithm for downstream analysis are illustrated by re-analysis of previously published colorectal cancer data. Using multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R.
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