Genome Characterization Unit

基因组表征单位

• 批准号: 10294015
• 负责人: Li Ding
• 金额: $ 224.23万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10294015
• 关键词: Address; African American; Biocompatible Materials; Biological Assay; CLIA certified; CLIA certified sequencing; Cancer Biology; Cholangiocarcinoma; Clinical; Clinical Data; Clinical Research; Collection; Colorectal Cancer; Communities; Computers; DNA; Data; Data Commons; Data Storage and Retrieval; Databases; Detection; Diagnostic; Disease Progression; Ensure; Equilibrium; Event; Evolution; Gene Fusion; Genes; Genome; Genomic Data Commons; Genomics; Goals; Guidelines; Health Insurance Portability and Accountability Act; Human Resources; Incidence; Individual; Industry Standard; Inherited; Institutes; Libraries; Malignant Neoplasms; Methodology; Methods; Molecular; Monitor; Multiple Myeloma; Mutation; Normal tissue morphology; Nucleic Acids; Participant; Pathogenicity; Pathologist; Patients; Peptides; Physicians; Practice Management; Preparation; Procedures; Process; Prognosis; Proteomics; Published Comment; Publishing; RNA; Recommendation; Reporting; Research; Running; Sampling; Schedule; Secure; Single Nucleotide Polymorphism; Somatic Mutation; Specimen; Structure; Surveys; System; Testing; Time; TimeLine; Tumor Tissue; Universities; Variant; Washington; archive data; archived data; base; bioinformatics tool; cancer genomics; cancer type; cell free DNA; cellular imaging; clinically actionable; clinically relevant; data acquisition; deep sequencing; early onset; exome sequencing; follow-up; genomic data; health disparity; imaging study; immunogenic; indexing; insertion/deletion mutation; mortality; patient engagement; preference; programs; prospective; research study; single-cell RNA sequencing; statistics; targeted sequencing; transcriptome sequencing; tumor; tumor-immune system interactions; web portal

Project Summary - Genome Characterization Unit (GCU) The GCU will provide comprehensive, end-to-end CLIA-compliant genomic testing and cutting-edge research- level analysis of patients with MM, CRC, and CHOL who are engaged by the PEU. This testing will be conducted on diagnostic tumor samples and matched normal tissue from 300 patients for each of the three cancer types during the WU PE-CGS research program. Additional follow-up samples from 150 of these patients will also be analyzed during disease progression. Sample processing by the GCU will include nucleic acid extraction and QC. Diagnostic samples will be analyzed using 250X tumor/normal exome sequencing (WES) with both somatic and germline analysis for gene-level single nucleotide variants (SNV and insertion/deletions (indels). Tumor-only WGS (60X) will be performed to detect tumor-associated structural mutations, and tumor RNA-seq will support, confirm, and extend findings from the DNA-based assays. Tumor tissue and/or cell-free DNA will also be analyzed with targeted deep sequencing (>10,000X) using unique molecular indexes (UMI) for sensitive detection and monitoring of tumor-associated mutations. All of these assays will be performed using CLIA-compliant procedures with integrated quality management practices. The GCU will also conduct research-level scRNA-Seq, proteomics, and cellular imaging studies on selected samples to enhance our understanding of these tumor types. Genomic assays will proceed according to a planned schedule for year-by-year combinations of diagnostic specimens and follow-up collections, with small numbers of candidates selected for research studies. Results from these assays will be returned to participants using a tiered reporting system that will depend on participant preference. Tier 1 results will highlight findings with established clinical relevance obtained from CLIA sequencing of individual participants, including pathogenic, tumor-associated somatic drivers and inherited mutations that are clinically actionable according to published guidelines and that will be reported using established categorization for somatic drivers and pathogenic germline variants, their clinical implications, and possible actions. Participants can also elect to receive Tier 2 results, which will be comprised of additional mutations from the same CLIA-compliant data that are identified with advanced methods and are predicted to be clinically relevant via functional annotation, as well as results from targeted sequencing of follow-up samples for monitoring tumor evolution over time. Research-level Tier 3 molecular studies may also be provided to participants as aggregate, deidentified reports that can be used to enhance and extend interpretations of their individualized CLIA results. These results will also be securely uploaded to the NCI Genomic Data Commons (GDC) for use by the cancer biology community. All GCU activities will be coordinated with the PEU and EOU to ensure clarity and consistency across the WU PE-CGS program.

项目摘要-基因组表征单位(GCU) GCU将提供全面的、符合CLIA的端到端基因组测试和尖端研究- PEU参与MM、CRC和CHOL患者的水平分析。这项测试将是 对来自300名患者的诊断肿瘤样本和匹配的正常组织进行了研究 在吴PE-CGS研究计划期间的癌症类型。其中150个额外的后续样本 患者还将在疾病进展期间进行分析。GCU的样本处理将包括核 酸提和质控。诊断样本将使用250X肿瘤/正常外显子组测序进行分析 (WES)基因水平单核苷酸变异(SNV和SNV)的体细胞和生殖系分析 插入/删除(Indels)。仅肿瘤WGS(60X)将用于检测肿瘤相关结构 突变和肿瘤RNA-seq将支持、确认和扩展基于DNA的分析结果。肿瘤 组织和/或无细胞DNA也将通过使用Unique进行定向深度测序(&gt；10,000X)进行分析 用于灵敏检测和监测肿瘤相关突变的分子指数(UMI)。所有这些都是 分析将使用符合CLIA的程序和综合质量管理实践进行。这个 GCU还将进行研究水平的scRNA-Seq、蛋白质组学和细胞成像研究 样本，以加强我们对这些肿瘤类型的了解。基因组分析将按照 诊断样本和后续采集的逐年组合的计划时间表， 被选入研究性研究的候选人数量。这些化验的结果将返回给参与者 使用分级报告系统，这将取决于参与者的偏好。第1级结果将突出调查结果 从CLIA对个体参与者的测序中获得的已建立的临床相关性，包括 致病的、与肿瘤相关的躯体驱动因素和临床上可操作的遗传突变 发布了指南，并将使用已建立的躯体司机分类进行报告 致病生殖系变异、它们的临床意义和可能的行动。参与者还可以选择 接收第2层结果，该结果将包括来自符合CLIA的相同数据的其他突变 用先进的方法识别，并通过功能注释预测与临床相关，如 以及对后续样本进行定向排序的结果，以监测肿瘤随时间的演变。 研究级别的第三级分子研究也可以作为综合的、已确定的报告提供给参与者 这可用于增强和扩展对其个性化CLIA结果的解释。这些结果将 也被安全地上传到NCI基因组数据共享(GDC)，以供癌症生物学使用 社区。所有GCU活动将与PEU和EOU协调，以确保清晰度和一致性 在吴PE-CGS项目上。