Molecular Diagnostics Core Laboratory

分子诊断科目前是NCI内唯一获得CLIA和美国病理学学会批准的临床实验室，获得认证，可以对NIH患者的病理材料进行分子肿瘤学测试。在20财年(2019年7月至2020年6月)，分子诊断实验室处理了2689份来自NCI/NIH患者的独特临床样本(1619例为FFPE组织病例，1078例为血液、骨髓、脑脊液、多液标本)。该实验室提取了2668个DNA和1025个RNA样本。1055例患者进行了COMPASS NGS检测，其余的临床病例采用传统的分子检测，以满足NCI和其他NIH研究所的临床需要。该实验室利用各种技术进行6377项单一或多重分析，以继续为病理实验室和NIH临床诊断和治疗中心提供服务，包括传统的聚合酶链式反应、逆转录聚合酶链式反应、定量聚合酶链式反应、液滴数字聚合酶链式反应(DdPCR)、毛细管电泳法、焦磷酸测序。我们进行的检测包括确定B和T细胞克隆性、与儿童肉瘤相关的易位、癌症相关病毒(例如EBV、HTLV1、HHV8)、BRAF、来自血液、骨髓和最终针吸活检的MYD88突变，以及胶质母细胞瘤中MGMT甲基化检测。这些分析支持30项NCI临床试验和18项其他NIH研究所试验(来自NHGRI、NHLBI、NINID、NIDDK)。该实验室还进行了1000多项测试，每两年一次的CAP熟练程度或替代熟练程度测试，质量控制(阳性、阴性、无模板对照)，每周一批。临床检测的QC和QM性能约占核心实验室试剂成本的15%-20%。分子实验室负责将分子检测结果提供给病理学家和临床团队进行患者护理，负责对病理住院医师和研究员进行培训和教育。每名第一年的住院医生/研究员轮流到分子实验室工作一个月。分子实验室和血液病理科也参加了每周一次的分子注销会议。分子诊断实验室还支持来自NCI和NIH研究人员的许多翻译研究。我们开发的核心技术之一是癌症患者的无细胞循环肿瘤DNA(CtDNA)检测。实验室继续在翠鸟多原仪上对血液中无细胞DNA的提取、数量和质量进行测试和评估，并用ddPCR和NGS进行超灵敏检测。该计划旨在将ctDNA用作治疗反应和早期发现复发的生物标记物。我们与CCR研究人员一起开始了一些新的研究，涉及各种癌症亚型，包括黑色素瘤、肺癌、膀胱癌和胰腺癌。我们继续与Elaine Jaffe博士合作研究罕见的造血癌，目前正在利用Jaffe博士在她的咨询实践中收集和归档的样本来研究组织细胞肉瘤的分子生物学，并根据基因表达、发病部位和突变状态确定了这些罕见癌症的新亚群。

The Molecular Diagnostics Section is currently the only CLIA and College of American Pathology approved clinical laboratory within the NCI certified for performing molecular oncology testing on pathology materials from NIH patients. In FY20 (July 2019 - June 2020) the molecular diagnostics laboratory processed 2689 unique clinical samples from NCI/NIH patients (1619 are FFPE tissue cases, 1078 are blood, bone marrow, CSF, plural fluid specimens). The lab extracted 2668 DNA and 1025 RNA samples. While 1055 cases were performed with COMPASS NGS assays, the rest of clinical cases were tested with traditional molecular tests to meet clinical needs from NCI and other NIH institutes. The laboratory utilizes a variety of technologies to perform 6377 single or multiplex assays to continue to serve the Lab of Pathology and the NIH Clinical Center for clinical diagnosis and treatments, including conventional PCR, RT-PCR, qPCR, droplet digital PCR (ddPCR), capillary electrophoresis, pyrosequencing. The assays we performed included tests to identify B and T-cell clonality, translocations associated with pediatric sarcomas, cancer associated viruses (e.g., EBV, HTLV1, HHV8), BRAF, MYD88 mutations from blood, bone marrow, and final needle biopsies, and MGMT methylation detection in glioblastoma. These assays support 30 NCI clinical trials and 18 other NIH institutes trials (from NHGRI, NHLBI, NINID, NIDDK). The lab also performed over 1000 tests for bi-annual CAP proficiency or alternative proficiency tests, quality controls (positive, negative, no template controls) for each PCR assay in weekly batch. QC and QM performance for clinical testing took about 15-20% of the core laboratory's reagent costs. With delivering molecular test results to pathologists and clinical teams for patient cares, the molecular lab is responsible for training and education of pathology residents and fellows. Each of the first-year resident/fellows rotated to the molecular lab for one months. The molecular lab and Hematopathology Section also join running a weekly molecular sign-out conference. The molecular diagnostics laboratory also supports many translational researches from NCI and NIH researchers. One of core technologies we developed was cell-free circulating tumor DNA (ctDNA) detection in cancer patients. The laboratory continued to test and evaluate extraction of cell-free DNA from blood on KingFisher Duo Prime instrument, its quantity and quality, and ultrasensitive detection with ddPCR and NGS. The program was to use ctDNA as a biomarker for treatment response and early detection of recurrence. We have initiated some new studies with CCR investigators in diverse cancer subtypes including melanoma, lung, bladder, and pancreatic cancer. We have continued to study rare hematopoietic cancers in collaboration with Dr. Elaine Jaffe and are currently investigating the molecular biology of Histiocytic Sarcoma taking advantage of the samples collected and archived by Dr. Jaffe in her consult practice, and have identified novel subgroups of these rare cancers based on gene expression, disease site and mutational status.