Genomics Core

摘要 基因组学核心的目标是1）进行前瞻性和回顾性分子分析， 前列腺肿瘤，无细胞DNA（cfDNA）和生殖系DNA，以促进P01和2）的目的，以促进 在P01研究者之间以及与更广泛的 科学界。为了实现这些目标，基因组学核心包括接受过癌症培训的人员 遗传学、外科病理学、生物统计学、生物信息学和基因组数据共享。基因组学核心拥有 三个目标。首先，为了帮助鉴定与遗传风险增加相关的生殖系突变， 由于长期临床结果不佳，基因组学核心将对250个DNA损伤进行靶向测序， 前列腺癌肿瘤的DDR修复（DDR）途径基因或WES和匹配的生殖系DNA（项目1） 我们有长期临床结果数据的前列腺癌患者。进一步方便 鉴定与增加的遗传风险或不良临床结果相关的新的生殖系突变， 作为本P01的一部分生成的所有测序数据将与已发布的数据集实时整合， 来自纪念斯隆-凯特琳癌症中心（MSK-）正在进行的分析计划的未发表基因组数据。 丹娜-法伯癌症研究所（Dana-Farber Cancer Institute，DFCI-Profile）第二，核心将探索机制 通过分析在PARP抑制剂治疗之前和之后收集的肿瘤和cfDNA， 入选MetaCURE临床试验平台（项目2）的患者。后一个目标需要基因组学 核心是开发cfDNA检测试剂盒（MSK-ACCESS），可用于监测患者的最小残留量 还可以鉴定介导对PARP抑制的反应和抗性的突变。三是 核心将促进P01内部以及与更广泛的研究界（包括 NCI所有三个研究项目都与基因组学核心高度整合，并广泛依赖于基因组学核心， 实现他们提出的目标。更具体地说，该核心将通过排序（有针对性和 完整外显子组）种系，并且在某些情况下，匹配来自几个大的注释的肿瘤DNA的队列。 患者样本以鉴定DDR途径基因的改变。该核心还将提供实时访问， 由MSK-IMPACT和DFCI-Profile生成的种系数据。核心将通过筛选协助项目2 对患者的DDR畸变进行分析，并分析在DDR畸变之前和之后收集的肿瘤样品和cfDNA。 PARP抑制剂治疗，以监测治疗反应并探索耐药机制。的 核心将与项目3合作，对含有有害BRCA2的细胞进行分子分析 或ATM等位基因或其中ATM或CDH1已缺失。最后，基因组学核心将帮助所有三个 项目对单个突变的致病性进行预测，以促进数据解释，研究 登记，以及突变体的优先化以用于功能表征。

ABSTRACT The objectives of the Genomics Core are 1) to perform prospective and retrospective molecular analysis of prostate tumors, cell-free DNA (cfDNA) and germline DNA to facilitate the aims of the P01 and 2) to facilitate sharing of genomic data and linked clinical annotation among the P01 investigators and with the broader scientific community. To achieve these objectives, the Genomics Core includes personnel trained in cancer genetics, surgical pathology, biostatistics, bioinformatics, and genomic data sharing. The Genomics Core has three aims. First, to aid in the identification of germline mutations associated with increased heritable risk or poor long-term clinical outcomes, the Genomics Core will conduct targeted sequencing of 250 DNA damage repair (DDR) pathway genes or WES of prostate cancer tumors and matched germline DNA (Project 1) from men with prostate cancer for whom we have long-term clinical outcomes data. To further facilitate the identification of novel germline mutations that associate with increased heritable risk or poor clinical outcomes, all sequencing data generated as part of this P01 will be integrated in real-time with published datasets and unpublished genomic data from ongoing profiling initiatives at Memorial Sloan Kettering Cancer Center (MSK- IMPACT) and Dana-Farber Cancer Institute (DFCI-Profile). Second, the core will explore mechanisms of treatment resistance by analyzing tumors and cfDNA collected before and after PARP inhibitor treatment from patients enrolled on the MetaCURE clinical trial platform (Project 2). This latter aim required the Genomics Core to develop a cfDNA assay (MSK-ACCESS) that could be used to monitor patients for minimal residual disease and could also identify mutations that mediate response and resistance to PARP inhibition. Third, the core will facilitate data sharing both within the P01 and with the broader research community, including the NCI. All three research projects are highly integrated with and rely extensively on the Genomics Core to achieve their proposed aims. More specifically, the core will assist Project 1 by sequencing (targeted and whole exome) germline and, in some cases, matched tumor DNA from several large cohorts of annotated patient samples to identify alterations in DDR pathway genes. The core will also provide real-time access to the germline data generated by MSK-IMPACT and DFCI-Profile. The core will assist Project 2 by screening patients for DDR aberrations and with the analysis of tumor samples and cfDNA collected before and after PARP inhibitor treatment to monitor treatment response and to explore mechanisms of drug resistance. The core will work with Project 3 to perform molecular analyses of cells engineered to harbor deleterious BRCA2 or ATM alleles or in which ATM or CDH1 have been deleted. Finally, the Genomics Core will help all three projects make predictions about the pathogenicity of individual mutations to facilitate data interpretation, study enrollment, and prioritization of mutants for functional characterization.