DNA copy-number changes

Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. This study is described more fully in Pollack JR et al.(1999) Nat Genet 23:41-6 Keywords: other

基因扩增与缺失常促进肿瘤发生。对这类DNA拷贝数改变（DNA copy-number changes）的特征进行解析，对于癌症的基础研究与临床诊断均具有重要价值。

比较基因组杂交（Comparative Genomic Hybridization）技术最初被开发用于全基因组范围的DNA拷贝数变异（DNA copy-number variation）筛查。采用CGH时，将经差异标记的待测基因组DNA与对照基因组DNA共同杂交于正常中期染色体，沿染色体长度分布的荧光比值可直观反映DNA拷贝数变异的细胞遗传学特征。

然而，CGH的定位分辨率有限（约20 Mb）；而诸如荧光原位杂交（Fluorescence In Situ Hybridization）这类更高分辨率的技术，在基因组规模下开展实验时，工作量大到难以承受。

基于阵列的CGH（array-based CGH）通过阵列化DNA元件的荧光比值实现逐位点的DNA拷贝数变异定量检测，是另一种提升定位分辨率的技术途径。

已发表的阵列CGH方法多以大片段基因组克隆（如细菌人工染色体（Bacterial Artificial Chromosome））作为阵列靶标，仅覆盖人类基因组的极小一部分。

涵盖超过30000个经辐射杂交（radiation-hybrid，RH）定位的人类基因的cDNA序列，可为DNA拷贝数改变的定位分析提供一种替代性且易于获取的基因组资源。

尽管cDNA微阵列（cDNA microarray）已被广泛用于人类基因表达变异的特征解析，但人类基因组DNA的混合物复杂度远高于人类细胞的mRNA转录本混合物。因此，利用cDNA微阵列开展DNA拷贝数变异分析，所需的检测灵敏度需比常规报道的水平高出一个数量级。

本研究介绍了一种基于cDNA微阵列的CGH方法，并将其应用于乳腺癌细胞系及肿瘤组织的DNA拷贝数变异分析。本研究的详细内容参见Pollack JR等（1999）《自然·遗传学》23卷：41-6 关键词：其他。