Molecular Diagnostics Core Laboratory

分子诊断科是目前唯一的CLIA和美国病理学院批准的临床实验室，在NCI认证下对来自NIH患者的病理材料进行分子肿瘤学检测。在23财年（2022年7月至2023年6月），分子诊断实验室处理了来自NCI/NIH患者的5553份独特临床样本（4140份是FFPE组织病例，1431份是血液、骨髓、CSF、胸膜液、唾液样本）。实验室提取了4709份DNA和1339份RNA样本。1742例采用COMPASS NGS检测，2725例采用甲基化阵列检测，其余临床病例采用传统分子检测，以满足NCI和其他NIH机构的临床需求。该实验室利用各种技术每年进行近10,000次单次或多次检测，为病理学实验室和NIH临床诊断和治疗临床中心服务，包括传统PCR， RT-PCR, qPCR，液滴数字PCR (ddPCR)，毛细管电泳。我们进行的检测包括鉴定B细胞和t细胞克隆性、癌症相关病毒（如EBV、HTLV1、HHV8）、BRAF、MYD88突变（来自血液、骨髓和最终穿刺活检）的检测。这些分析支持49项NCI临床试验和77项其他NIH研究所试验（来自CC、NEI、NHGRI、NHLBI、NIAID、NIAMS、NICHD、NIDCR、NIDDK、NIEHS、NIMH和NINDS）。该实验室还对每批PCR检测进行了1000多次检测，包括两年一次的CAP熟练度检测或替代熟练度检测、质量控制（阳性、阴性、无模板控制）。临床检测的QC和QM性能约占核心实验室试剂成本的15-20%。分子实验室在向病理学家和临床团队提供分子检测结果以进行患者护理的同时，还负责培训和教育病理学住院医师和研究员。每位第一年住院医师/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科也参加了每周一次的分子签到会议。分子诊断实验室还支持NCI和NIH研究人员的许多转化研究。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。实验室继续测试和评估使用新的QIAsymphony仪器提取的游离DNA，其数量和质量，以及使用ddPCR和NGS进行超灵敏检测。该项目将使用ctDNA作为治疗反应和早期复发检测的生物标志物。我们已经与CCR研究人员在不同的癌症亚型中开展了一些新的研究，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症，目前正在研究组织细胞肉瘤的分子生物学，利用Jaffe博士在她的咨询实践中收集和存档的样本，并根据基因表达，疾病部位和突变状态确定了这些罕见癌症的新亚群。我们还致力于建立一个以临床为重点的肿瘤转录组学项目。该项目（SYNTHESIS: SYNthetic leThality to matcH patiEnts through tranScriptomIcS）将建立在两个现有的基础上：(1)现有的NCICOMPASS项目位于病理学实验室，该项目为CC患者提供clia认证的测序服务；(2)CCR癌症数据科学合成拯救（SR）患者分层方法（SELECT）中开发的计算专业知识。CSDL-LP的密切合作启动了SYNTHESIS项目，为CCR临床研究人员在临床试验中评估和实施基于SL/ sr的转录组学方法提供了一个独特的机会。

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 FY23 (July 2022 - June 2023) the molecular diagnostics laboratory processed 5553 unique clinical samples from NCI/NIH patients (4140 are FFPE tissue cases, 1431 are blood, bone marrow, CSF, pleural fluid, saliva specimens). The lab extracted 4709 DNA and 1339 RNA samples. While 1742 cases were performed with COMPASS NGS assays and 2725 cases were performed with Methylation Arrays, 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 near 10,000 single or multiplex assays every year 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. The assays we performed included tests to identify B and T-cell clonality, cancer associated viruses (e.g., EBV, HTLV1, HHV8), BRAF, MYD88 mutations from blood, bone marrow, and final needle biopsies. These assays support 49 NCI clinical trials and 77 other NIH institutes trials (from CC, NEI, NHGRI, NHLBI, NIAID, NIAMS, NICHD, NIDCR, NIDDK, NIEHS, NIMH, and NINDS. 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 research 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 with the new QIAsymphony 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. We are also working to establish a clinically-focused Tumor Transcriptomics program. This program (SYNTHESIS: SYNthetic leThality to matcH patiEnts through tranScriptomIcS) will build on two existing foundations: (1) the existing NCICOMPASS Program housed in the Laboratory of Pathology, which provides CLIA-certified sequencing services of CC patients and, (2) the computational expertise developed in the CCR Cancer Data Science synthetic rescues (SR) patient stratification approaches (SELECT). The close CSDL-LP collaboration to initiate the SYNTHESIS program provides a unique opportunity for CCR clinician-investigators to evaluate and operationalize SL/SR-based transcriptomics approaches in clinical trials for our patients.