Development of ESP: Structural & Functional Oncogenomics

ESP 的发展：结构

• 批准号: 6932479
• 负责人: COLIN C COLLINS
• 金额: $ 34.32万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-08-01 至 2007-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6932479
• 关键词: artificial chromosomes; bioengineering /biomedical engineering; biotechnology; breast neoplasms; clinical research; fluorescent in situ hybridization; functional /structural genomics; fusion gene; gene expression; gene rearrangement; genetic library; genetic mapping; genome; human tissue; method development; microarray technology; molecular biology information system; molecular cloning; molecular oncology; neoplasm /cancer; neoplasm /cancer genetics; nucleic acid sequence; solid state

DESCRIPTION (provided by applicant): The long-term objective of this proposal is to gain an enhanced understanding of the structural genomics of solid tumors through development of a novel, sequence-based method capable of identifying all types of structural rearrangements that occur in tumor genomes. Genome rearrangements can promote cancer development, progression and/or resistance to therapy by altering gene regulation and/or function, and the involved genes are potential therapeutic targets. This is well established in leukemia and lymphoma, but less so in solid tumors, in part because of the difficulty of identifying the genes involved in complex structural rearrangements. We describe here a powerful and high resolution, sequence-based analytical approach called End Sequence Profiling (ESP). ESP maps copy number aberrations and directly identifies and clones en masse genome breakpoints associated with genome rearrangements such as inversions, translocations, deletions and amplifications. ESP is accomplished by constructing a BAC library of a tumor genome, end sequencing a larger number of BAC clones, and mapping the BAC end sequences (BES) onto the normal genome sequence. Paired BES that map to different parts of the normal genome span structural rearrangements. Sequencing these clones will reveal exact breakpoints and involved genes. In Specific Aim 1 we will: Implement ESP as a cost effective sequence-based technology for determining the structural organization of tumor genomes and clone rearrangement breakpoints en masse. Determine the minimum sequencing depth needed to yield the maximum structural information. Determine if ESP can reproducibly identify recurrent rearrangements between tumors, and if so, whether specific sequence elements are associated with these rearrangements. In Specific Aim 2 we will: Develop robust computational methods for the analysis, visual representation, and integration of ESP data with the human reference sequence, making possible comparison of ESP data from independent tumors. Knowledge of how genome rearrangements such as inversions and translocations impact local gene expression is critical. Thus, we will integrate ESP-based structure data with expression microarray data and co-localize aberrantly expressed genes with genome rearrangement breakpoints. In Specific Aim 3: We will biologically and clinically validate key ESP findings. We believe ESP provides a rational framework for sequencing tumor genomes. In fact, ( 100 tumor genomes can be analyzed at ( 10 kb resolution for less than sequencing a single 3000 Mb genome yielding hundreds of novel biomarkers and therapeutic targets associated with translocations, inversions, and complex rearrangements. This is important because, just as a comprehensive systems-based knowledge of human biology is predicated on the structural organization and sequence of the human genome, a structure-based view of tumor genomes is essential for a comprehensive understanding of tumor biology.

描述（由申请人提供）： 该提案的长期目标是通过开发一种基于序列的新方法，能够鉴定出在肿瘤基因组中发生的所有类型的结构重排，从而增强对实体瘤的结构基因组学的了解。基因组重排可以通过改变基因调节和/或功能来促进癌症的发展，进展和/或对治疗的抵抗，而所涉及的基因是潜在的治疗靶标。这在白血病和淋巴瘤中已经很好地确定，但在实体瘤中却较少，部分原因是很难鉴定出复杂的结构重排中所涉及的基因。我们在这里描述了一种强大而高分辨率的基于序列的分析方法，称为最终序列分析（ESP）。 ESP映射拷贝数畸变并直接识别和克隆与基因组重排相关的基因组断点，例如反转，易位，缺失和扩增。 ESP是通过构造肿瘤基因组的BAC文库，结束较大数量的BAC克隆并将BAC末端序列（BES）映射到正常基因组序列上的方法来完成。将图与正常基因组的不同部分配对结构重排。测序这些克隆将揭示确切的断点和涉及的基因。在特定目标1中，我们将：实施ESP作为基于经济有效的序列技术，用于确定肿瘤基因组和克隆重排断点的结构组织。确定产生最大结构信息所需的最小测序深度。确定ESP是否可以重复识别肿瘤之间的复发重排，如果是的话，是否可以与这些重排相关的特定序列元素。在特定目标2中，我们将：开发可靠的计算方法，用于分析，视觉表示和ESP数据与人类参考序列的集成，从而可以比较独立肿瘤的ESP数据。了解基因组重排如何影响局部基因表达的知识至关重要。因此，我们将将基于ESP的结构数据与表达微阵列数据整合在一起，并与基因组重排断点的异常表达基因共定位。在特定目标3中：我们将在生物学和临床上验证关键的ESP发现。我们认为，ESP为测序肿瘤基因组提供了合理的框架。实际上（可以在100个肿瘤基因组（10 kb分辨率的分辨率）下进行分析，比对单个3000 MB基因组进行测序，产生数百种新型的生物标志物和与易位，倒置和复杂重排相关的新型生物标志物和治疗靶标，这一点很重要。对肿瘤生物学的全面理解。