High-resolution analysis of DNA copy number using oligonucleotide microarrays.
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.
Bignell
Graham R
GR
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Huang
Jing
J
Greshock
Joel
J
Watt
Stephen
S
Butler
Adam
A
West
Sofie
S
Grigorova
Mira
M
Jones
Keith W
KW
Wei
Wen
W
Stratton
Michael R
MR
Futreal
P Andrew
PA
Weber
Barbara
B
Shapero
Michael H
MH
Wooster
Richard
R
D002460:Cell Line; D045744:Cell Line, Tumor; D004247:DNA / Q000235:genetics*; D004273:DNA, Neoplasm / Q000235:genetics*; D018628:Gene Dosage; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D019656:Loss of Heterozygosity / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000639:trends; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
D004273:DNA, Neoplasm; D004247:DNA