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Genome Res. 14:287-295, 2004
©2004 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/04 $5.00
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Methods

High-Resolution Analysis of DNA Copy Number Using Oligonucleotide Microarrays

Graham R. Bignell1, Jing Huang2, Joel Greshock3, Stephen Watt1, Adam Butler1, Sofie West1, Mira Grigorova4, Keith W. Jones2, Wen Wei2, Michael R. Stratton1, P. Andrew Futreal1,5, Barbara Weber3, Michael H. Shapero2 and Richard Wooster1

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK 2 Affymetrix, Inc., Santa Clara, California 95051, USA 3 University of Pennsylvania Cancer Center, Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA 4 Department of Pathology, University of Cambridge, Hutchison/MRC Research Centre, Addenbrooke's Hospital, Cambridge CB2 2XZ, UK

Genomic copy number alterations are a feature of many human diseases including cancer. We have evaluated the effectiveness of an oligonucleotide array, originally designed to detect single-nucleotide polymorphisms, to assess DNA copy number. We first showed that fluorescent signal from the oligonucleotide array varies in proportion to both decreases and increases in copy number. Subsequently we applied the system to a series of 20 cancer cell lines. All of the putative homozygous deletions (10) and high-level amplifications (12; putative copy number >4) tested were confirmed by PCR (either qPCR or normal PCR) analysis. Low-level copy number changes for two of the lines under analysis were compared with BAC array CGH; 77% (n = 44) of the autosomal chromosomes used in the comparison showed consistent patterns of LOH (loss of heterozygosity) and low-level amplification. Of the remaining 10 comparisons that were discordant, eight were caused by low SNP densities and failed in both lines. The studies demonstrate that combining the genotype and copy number analyses gives greater insight into the underlying genetic alterations in cancer cells with identification of complex events including loss and reduplication of loci.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2012304.

5 Corresponding author.
E-MAIL paf{at}sanger.ac.uk; FAX 44-1223-494919.

[Supplemental material is available online at www.genome.org and ftp.sanger.pub/p501. The data from all 70 arrays (29 normals, 20 cancer lines, 3 X-copy number, and 18 "spike" DNAs) used in this study will also be made available initially on ftp.sanger.pub/p501, until submission to Array Express is arranged.]


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