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）是一种用于检测基因拷贝数变化的强大技术。它通常被认为是基因表达的可变参数，因为它测量了较一致的DNA，而不是条件依赖性和不稳定的RNA。在当前的研究中，我们结合了来自四个不同平台的拷贝数估计值（Agilent 44K，Nimblegen 385K，Affymetrix 500K和Illumina Human1MV1_C），以计算NCI-DTP的60个癌细胞的高分辨率衡量尺寸衡量标准（NCI-DTP）（NCI-60）。我们计划在Cellminer（http://discover.nci.nih.gov/cellminer）上发布该数据库，该数据库是我们基于Web的工具的主机。这应该有助于将这些信息与我们的26,065个基因和360个microRNA的先前的成绩单表达数据进行易于访问，解释和比较，以及科学界的20,602种化合物和药物的活性。拷贝数和表达水平的初始比较表明已知抑制基因的总体培养基相关性（中位r = 0.247），相关性明显更高（中位r = 0.408）。这与基因丧失是抑制肿瘤灭活的重要机制。使用DNA收益或损失的焦点性质的参数，随着转录表表达的变化，它可用于鉴定新型候选肿瘤抑制子。