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Updated: Jun 7, 2026

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number
M Ortiz-Estevez1, J De Las Rivas, C Fontanillo
1Department of Electronics and Communication, CEIT and TECNUN (Univeristy of Navarra), Paseo Manuel Lardizabal 15, 20009, San Sebastian, Spain.
Abstract:
DNA copy number aberrations (CNAs) are genetic alterations common in cancer cells. Their transcriptional consequences are still poorly understood. Based on the fact that DNA copy number (CN) is highly correlated with the genomic position, we have applied a segmentation algorithm to gene expression (GE) to explore its relation with CN. We have found a strong correlation between segmented CN (sCN) and segmented GE (sGE), corroborating that CNAs have clear effects on genome-wide expression. We have found out that most of the recurrent regions of sGE are common to those obtained from sCN analysis. Results for two cancer datasets confirm the known targets of aberrations and provide new candidates to study. The suggested methodology allows to find recurrent aberrations specific to sGE, revealing loci where the expression of the genes is independent from their CNs. R code and additional files are available as supplementary material.
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