Analysis of chromosome copy number in leukemic cells by different microarray platforms
Analysis of chromosome copy number in leukemic cells by different microarray platforms
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DOI：
10.1038/sj.leu.2404636
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发表时间：
2007-06
期刊：
影响因子：
11.4
通讯作者：
Y. Yamashita;K. Minoura;T. Taya;Shin-ichiro Fujiwara;K. Kurashina;Hideki Watanabe;Y. L. Choi;M. Soda;Hisashi Hatanaka;Munehiro Enomoto;Shuji Takada;Hiroyuki Mano
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文献类型：
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作者：
Y. Yamashita;K. Minoura;T. Taya;Shin-ichiro Fujiwara;K. Kurashina;Hideki Watanabe;Y. L. Choi;M. Soda;Hisashi Hatanaka;Munehiro Enomoto;Shuji Takada;Hiroyuki Mano
染色体拷贝数的变化或拷贝数改变（CNA）在癌细胞的基因组中经常是明显的，并且可能导致癌基因的扩增或肿瘤抑制基因的缺失。1这种CNA的大小范围从整个染色体到几个酶对，其中许多较小的变化是传统的细菌人工染色体比较基因组杂交（CGH）无法检测到的，其分辨率为几百个酶对。[2]这一局限性最近已经被高密度寡核苷酸微阵列所克服，这种微阵列最初是为单核苷酸多态性（SNP）分型而开发的，现在已经用于CNA的评估。3用于这种分析的复杂软件，包括dChip（http：//biosun 1.哈佛edu/complab/dchip）和CNAG（http：//www.cNAG.org）。基因组乌敏。jp/CNAG.尽管高密度SNP分型阵列允许以100 kbp的分辨率确定CNA，但将这些数据与相应基因数量的变化联系起来并不是一项简单的任务。由Affytechnology（USA）制造的HGU 133 Plus 2.0（HGU 133 P2）微阵列被设计用于定量> 47000个人类转录物的丰度，并且已被广泛用于基因表达谱分析。阵列上的大多数探针序列靶向对应于每个转录物的非翻译区的外显子。虽然，据我们所知，还没有关于使用这种微阵列进行CNA评估或CGH的报道，但我们认为HGU 133 P2可能是评估CNA的有用平台，因为（1）cDNA序列是人类基因组最新和最全面的信息之一，（2）可以直接计算每个基因的拷贝数值。此外，通过基因组DNA和mRNA与阵列的单独杂交来比较给定基因的拷贝数和表达水平将是直接的。为此目的，我们修改了由Affytechnology提供的标记和杂交基因组DNA的方案（补充信息）。
Changes in the copy number of chromosomes, or copy number alterations (CNAs), are frequently apparent in the genome of cancer cells and may result in the amplification of oncogenes or deletion of tumor suppressor genes. 1 Such CNAs range in size from an entire chromosome to several kilobase pairs, with many of the smaller changes being undetectable by conventional bacterial artificial chromosome-based comparative genomic hybridization (CGH), which has a resolution of several hundred kilobase pairs. 2 This limitation has recently been overcome by the adaptation of high-density oligonucleotide microarrays that were originally developed for typing of single nucleotide polymorphisms (SNPs) to the evaluation of CNAs. 3 Sophisticated software for such analysis, including dChip (http://biosun1. harvard. edu/complab/dchip) and CNAG (http://www. genome. umin. jp/CNAG. html), is now available online.Although high-density SNP-typing arrays allow determination of CNAs at a resolution of o100kbp, it is not a simple task to link such data to changes in the number of the corresponding genes. The HGU133 Plus 2.0 (HGU133P2) microarray manufactured by Affymetrix (USA) was designed to quantitate the abundance of> 47 000 human transcripts and has been widely used for gene expression profiling. Most of the probe sequences on the array are targeted to exons corresponding to the 30 untranslated region of each transcript. Although, as far as we are aware, there have been no reports on the use of this microarray for CNA assessment or CGH, we reasoned that HGU133P2 may be a useful platform for evaluation of CNAs because (1) cDNA sequences are one of the most updated and comprehensive information for human genome, and (2) copy number values could be calculated directly for each gene. Furthermore, it would be straightforward to compare the copy number and expression level of a given gene through separate hybridization of genomic DNA and mRNA to the array. For this purpose, we modified a protocol for labeling and hybridizing genomic DNA, provided by Affymetrix (Supplementary Information).