Comparative genomic hybridization data and web-based tool for the NCI-60

NCI-60 的比较基因组杂交数据和基于网络的工具

• 批准号: 8763782
• 负责人: William Reinhold
• 金额: $ 4.51万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8763782
• 关键词: Communities; Copy Number Polymorphism; DNA; Data; Databases; Drug Compounding; Gene Chips; Gene Dosage; Gene Expression; Genes; Human; Human Genome; Maps; Measures; Methods; MicroRNAs; Nature; Online Systems; RNA; Resolution; Techniques; Transcript; Tumor Suppressor Genes; Tumor Suppressor Proteins; base; cancer cell; comparative genomic hybridization; novel; tool

Array-based comparative genomic hybridization (aCGH) is a powerful technique for detecting gene copy number variation. It is generally considered to be a less variable parameter than gene expression since it measures the more consistent DNA, rather than the condition dependent and labile RNA. In the current study, we combine copy number estimates from four different platforms (Agilent 44K, Nimblegen 385K, Affymetrix 500K and Illumina Human1Mv1_C) to compute a high-resolution measure of copy number changes in the 60 cancer cells of the NCI-DTP (the NCI-60). We will plan to release that database on CellMiner (http://discover.nci.nih.gov/cellminer), the host for our web-based tools. This should facilitate easy access, interpretation and comparison of this information to our pre-existing transcript expression data for 26,065 genes and 360 microRNAs, and the activity of 20,602 compounds and drugs for the scientific community. Initial comparisons of copy number and expression levels indicates an overall medium correlation (median r=0.247), with significantly higher correlations (median r=0.408) for the known tumor suppressor genes. This is consistent with gene loss being an important mechanism for tumor suppressor inactivation. Using the parameter of the focal nature of the DNA gains or losses, in tandem with changes in transcript expression, it may be used to identify novel candidate tumor suppressors.

基于阵列的比较基因组杂交（aCGH）是检测基因拷贝数变异的有效技术。它通常被认为是比基因表达可变性更小的参数，因为它测量更一致的DNA，而不是条件依赖性和不稳定的RNA。在目前的研究中，我们结合了来自四个不同平台（Agilent 44 K，Nimblegen 385 K，Affyphase 500 K和Illumina Human1Mv1_C）的联合收割机拷贝数估计值，以计算NCI-DTP（NCI-60）的60个癌细胞中拷贝数变化的高分辨率测量。我们将计划在CellMiner（http：//www.nci.nih.gov/cellminer）上发布该数据库，CellMiner是我们基于网络的工具的主机。这将有助于轻松访问，解释和比较这些信息与我们先前存在的26，065个基因和360个microRNA的转录表达数据，以及科学界20，602种化合物和药物的活性。拷贝数和表达水平的初步比较表明，总体中等相关性（中位数r=0.247），具有显着较高的相关性（中位数r=0.408）为已知的肿瘤抑制基因。这与基因丢失是肿瘤抑制因子失活的重要机制相一致。使用DNA获得或损失的焦点性质的参数，与转录本表达的变化相结合，它可以用于鉴定新的候选肿瘤抑制剂。