Notl subtraction and Notl-specific microarrays to detect copy number and methylation changes in whole genomes
Notl subtraction and Notl-specific microarrays to detect copy number and methylation changes in whole genomes
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DOI：
10.1073/pnas.132271699
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发表时间：
2002-08-06
影响因子：
11.1
通讯作者：
Zabarovsky, ER
中科院分区：
文献类型：
--
作者：
Li, JF;Protopopov, A;Zabarovsky, ER
癌基因的甲基化、缺失和扩增构成了癌发生的重要机制。对于这些变化的全基因组分析，我们建议使用Nod克隆微阵列和基因组减法，因为Not！识别位点与CpG岛和基因密切相关。我们在这里表明，CODE（删除序列的克隆）基因组扣除程序可以适应节点侧翼序列和CpG岛。由于该过程的序列复杂度大大降低，因此仅需要两个减法循环。Nod-CODE程序可用于制备含有总DNA的0.1-0.5%的Nod表示（NR）。NR包含的重复序列平均比整个人类基因组少10倍，并且可以用作与Nod微阵列杂交的探针。当用NR探测时，这些微阵列可以同时检测拷贝数变化和甲基化。Nod微阵列为研究致癌作用提供了一个强有力的工具。
Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of Nod clone microarrays and genomic subtraction, because Not! recognition sites are closely associated with CpG islands and genes. We show here that the CODE (Cloning Of DEleted sequences) genomic subtraction procedure can be adapted to Nod flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A Nod-CODE procedure can be used to prepare Nod representations (NRs) containing 0.1-0.5% of the total DNA. The NRs contain, on average, 10-fold less repetitive sequences than the whole human genome and can be used as probes for hybridization to Nod microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation. Nod microarrays offer a powerful tool with which to study carcinogenesis.