Amplicon Profiling by Array CGH

通过阵列 CGH 进行扩增子分析

• 批准号: 6441297
• 负责人: Donna G Albertson
• 金额: $ 28.97万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-05-01 至 2005-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6441297
• 关键词: artificial chromosomes; breast neoplasms; clinical research; comparative genomic hybridization; drug resistance; esophagus neoplasm; fluorescent in situ hybridization; functional /structural genomics; gene expression; genetic mapping; genome; microarray technology; neoplasm /cancer genetics; nucleic acid amplification techniques; oncogenes; polymerase chain reaction; stomach neoplasms; tissue /cell culture; tumor suppressor genes

Losses and gains of multiple portions of the genome occur in tumor cells, and in some cases amplifications, or high level copy number increases of portions of chromosomes are observed. Alterations in gene expression that result from these copy number aberrations provide a selective advantage to the tumor cells and specific copy number aberrations have been associated with inactivation of tumor suppressor genes or overexpression of oncogenes. The driver genes for many regions of recurrent amplification have not been identified and methods to facilitate their identification would be broadly applicable to increasing knowledge of the genetic events involved in cancer development. Recent implementation of a high resolution form of comparative genomic hybridization (CGH) using microarrays allows quantitative mapping of copy number across an amplicon such that the magnitude of the copy number increase and the extent of the amplicon can be mapped relative to the physical map of the human genome. The goal of this project is to further develop our understanding of the information that can be obtained from array CGH copy number profiles. In particular, we will determine if the copy number maxima as mapped by array CGH can be used to identify the driver gene(s) for an amplicon. This investigation was motivated by the observation that array CGH copy number profiles displayed peaks mapping to the locus of candidate oncogenes amplified at 20q13 in breast cancer, suggesting that these peaks in the copy number profile may result from selection for highest copy number of the genes conferring growth advantage. Therefore, quantitative mapping of amplicon structure by array CGH may provide a powerful new way to identify oncogenes in regions of recurrent amplification in tumors. In order to establish the generality of these observations, in this project, we will use array CGH to quantitatively map the amplicon structure of three well-established oncogenes, CMYC, ERBB2 and CCND1 in different tumor types. We will also map amplicons arising in cells in culture in response to selection for drug resistance. We will determine (a) the extent to which amplicon boundaries are clustered in the genome around these genes, (b) where amplification maxima occur in relation to the locus of the oncogene and (c) the similarities of differences in the amplicons as a function of tissue type. Characterization of the copy number profiles of amplicons containing these known oncogenes and drug resistance genes will provide the information required for interpretation of amplicon structure in other regions of the genome and facilitate identification of the critical genes they contain.

在肿瘤细胞中发生基因组的多个部分的丢失和获得，在某些情况下，观察到部分染色体的扩增或高水平拷贝数增加。这些拷贝数异常导致的基因表达变化为肿瘤细胞提供了选择性优势，而特定的拷贝数异常与肿瘤抑制基因的失活或癌基因的过度表达有关。许多重复扩增区域的驱动基因尚未被识别，促进它们识别的方法将广泛适用于增加对参与癌症发展的遗传事件的了解。最近使用微阵列实现的高分辨率形式的比较基因组杂交(CGH)允许跨扩增子的拷贝数的定量映射，使得拷贝数增加的幅度和扩增子的范围可以相对于人类基因组的物理图谱来映射。这个项目的目标是进一步加深我们对可以从阵列CGH拷贝数配置文件中获得的信息的理解。特别是，我们将确定是否可以使用阵列CGH定位的拷贝数最大值来识别扩增子的驱动基因(S)。这项研究的动机是观察到阵列CGH拷贝数谱显示的峰映射到乳腺癌中20q13扩增的候选癌基因的位置，表明拷贝数谱中的这些峰可能是对具有生长优势的基因的最高拷贝数的选择。因此，利用阵列CGH定量定位扩增子结构可能为识别肿瘤复发扩增区域的癌基因提供一种强有力的新途径。为了建立这些观察结果的共性，在本项目中，我们将使用阵列CGH来定量地定位cMYC、ERBB2和CCND1这三个已确立的癌基因在不同肿瘤类型中的扩增结构。我们还将绘制培养细胞中出现的扩增片段，以响应对耐药性的选择。我们将确定(A)扩增子边界在基因组中围绕这些基因聚集的程度，(B)扩增最大值发生在与癌基因位置有关的地方，以及(C)扩增子差异作为组织类型的函数的相似性。对含有这些已知癌基因和耐药基因的扩增产物的拷贝数谱进行表征，将为解释基因组其他区域的扩增产物结构提供必要的信息，并有助于鉴定它们所包含的关键基因。