Bignell Graham R, Huang Jing, Greshock Joel, Watt Stephen, Butler Adam, West Sofie, Grigorova Mira, Jones Keith W, Wei Wen, Stratton Michael R, Futreal P Andrew, Weber Barbara, Shapero Michael H, Wooster Richard
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Genome Res. 2004 Feb;14(2):287-95. doi: 10.1101/gr.2012304.
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.
基因组拷贝数改变是包括癌症在内的许多人类疾病的一个特征。我们评估了一种最初设计用于检测单核苷酸多态性的寡核苷酸阵列评估DNA拷贝数的有效性。我们首先表明,来自寡核苷酸阵列的荧光信号随拷贝数的减少和增加成比例变化。随后,我们将该系统应用于一系列20个癌细胞系。所有测试的假定纯合缺失(10个)和高水平扩增(12个;假定拷贝数>4)均通过PCR(定量PCR或普通PCR)分析得到证实。将分析中的两个细胞系的低水平拷贝数变化与BAC阵列比较基因组杂交(CGH)进行比较;在比较中使用的常染色体中,77%(n = 44)显示出一致的杂合性缺失(LOH)和低水平扩增模式。在其余10个不一致的比较中,8个是由低SNP密度引起的,并且在两个细胞系中均失败。这些研究表明,将基因型和拷贝数分析相结合,能够更深入地了解癌细胞中潜在的基因改变,包括识别基因座的缺失和重复等复杂事件。