Comprehensive Analysis of Best Practices for Clinical Testing of Malignant Pleural Effusion Specimens

恶性胸腔积液标本临床检测最佳实践综合分析

• 批准号: 10703794
• 负责人: Walter Patrick Devine
• 金额: $ 36.94万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-05 至 2028-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10703794
• 关键词: Advanced Malignant Neoplasm; Affect; Ancillary Study; Area; Benchmarking; Benign; Biological Assay; Biopsy; Blood Tests; Cell Separation; Cells; Centrifugation; Certification; Chemistry; Chest wall structure; Clinical; Collection; Cytology; Cytopathology; DNA; Data; Diagnosis; Diagnostic; Evaluation; Experimental Designs; Formalin; Gene Frequency; Gene Rearrangement; Genes; Goals; Guidelines; Hematoxylin and Eosin Staining Method; Inflammatory; Laboratories; Libraries; Liquid substance; Literature; Lung; Malignant Neoplasms; Malignant Pleural Effusion; Measures; Microsatellite Instability; Molecular; Molecular Analysis; Mutation; Nucleic Acids; Oncogenes; Oncogenic; Paraffin Embedding; Pathologic; Pathologist; Patients; Plasma; Pleural; Pleural effusion disorder; Positioning Attribute; Preparation; Procedures; Process; Protocols documentation; Publishing; Reproducibility; Research; Sampling; Serum; Slide; Source; Specimen; Speed; Stains; Surface; Techniques; Temperature; Testing; Therapeutic; Thoracentesis; Time; Tissues; Tumor Tissue; Urine; Validation; Variant; cancer cell; cell free DNA; clinical practice; detection test; experimental study; gene panel; genetic testing; improved; insertion/deletion mutation; liquid biopsy; molecular pathology; multidisciplinary; mutant; neoplastic cell; next generation sequencing; reduce symptoms; research clinical testing; success; theories; time interval; tumor; tumor heterogeneity

PROJECT SUMMARY/ABSTRACT Patients with advanced cancers often develop malignant pleural effusions (MPEs), a collection of fluid that develops between the surface of the lung and the chest wall that contains malignant tumor cells and benign inflammatory cells. In many cases, percutaneous or transbronchial tissue biopsies may be pauci-cellular or difficult to obtain, thus MPEs may be the only specimen available for pathologic evaluation and molecular testing. Thoracentesis removes this fluid, alleviating symptoms and also providing diagnostic material that can be used for downstream molecular analysis. In current clinical practice, the thoracentesis fluid is typically centrifuged and the cell-rich pellet is used to generate a formalin fixed paraffin embedded (FFPE) cell pellet that is subsequently used to make a hematoxylin & eosin (H&E) stained slide for diagnosis along with additional unstained slides for ancillary studies. Recent studies have highlighted the fact that pleural fluid samples often contain abundant cell- free DNA (cfDNA) within the supernatant fraction and this may represent an alternative source of DNA for molecular testing. Similar to cfDNA isolated from plasma, cfDNA isolated from MPEs could in theory circumvent the problem of intra-tumoral heterogeneity and tissue accessibility while at the same time obviate the time needed to create a cell block and reduce/eliminate the labor-intensive steps of scraping and extracting DNA from unstained slides. Despite its promise, there are no established guidelines for the collection, storage, processing, and molecular testing of cfDNA isolated from MPEs. Our proposal systematically tests several preanalytical variables as well as directly compares three different cfDNA isolation techniques to identify the best practices for processing cfDNA from MPEs. We predict that optimization and harmonization of the these preanalytical steps will lead to reduced false negative results, increased reproducibility, improved efficiency, and reduced turn- around-time in the testing of MPEs. We will leverage our collective expertise in cytopathology, molecular pathology, and test validation to develop standard operating procedures that can be easily adapted into existing clinical workflows. Finally, we will validate these pre-analytical protocols using a CLIA/CAP certified multi-gene sequencing assay.

项目总结/文摘