Using expression arrays for copy number detection: an example from E. coli

Background: The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. While many of the methods and algorithms developed for the analysis microarrays have focused on expression analysis, the same technology can be used to detect genetic alterations, using for example standard commercial Affymetrix arrays. Due to the nature of the resultant data, standard techniques for processing GeneChip expression experiments are inapplicable. Results: We have developed a robust and flexible methodology for high-resolution analysis of DNA copy number of whole genomes, using Affymetrix high-density expression oligonucleotide microarrays. Copy number is obtained from fluorescence signals after processing with novel normalization, spatial artifact correction,...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Dmitriy Skvortsov, Diana Abdueva, Michael E. Stitzer, Steven E. Finkel, Simon Tavaré
• Keywords: Array Cgh, BMCBI 2007, Comparative Genomic Hybridization, Copy Number