RT Journal
A1 Bignell, Graham R.
A1 Huang, Jing
A1 Greshock, Joel
A1 Watt, Stephen
A1 Butler, Adam
A1 West, Sofie
A1 Grigorova, Mira
A1 Jones, Keith W.
A1 Wei, Wen
A1 Stratton, Michael R.
A1 Futreal, P. Andrew
A1 Weber, Barbara
A1 Shapero, Michael H.
A1 Wooster, Richard
T1 High-Resolution Analysis of DNA Copy Number Using Oligonucleotide Microarrays
JF Genome Research 
JO Genome Research 
YR 2004 
FD February 01 
VO 14 
IS 2 
SP 287 
OP 295 
DO 10.1101/gr.2012304 
UL http://genome.cshlp.org/content/14/2/287.abstract 
AB 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.