Evaluation of the effect of patient-context factors and sample acquisition on the quality and analytical performance of cell-free DNA and circulating tumor cells profiling assays in prostate cancer pa

评估患者背景因素和样本采集对前列腺癌患者无细胞 DNA 和循环肿瘤细胞分析测定的质量和分析性能的影响

• 批准号: 10054009
• 负责人: Maria E Arcila
• 金额: $ 40.49万
• 依托单位: SLOAN-KETTERING INST CAN RESEARCH
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-08 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10054009
• 关键词: Address; Affect; Aliquot; Androgen Receptor; Antiemetics; Atlases; Biological Assay; Biological Factors; Biological Markers; Biopsy Specimen; Blood; Cancer Patient; Castration; Cell Count; Cellular Assay; Clinic; Clinical; Clinical Trials; Clinical Trials Design; Collection; Communities; Data; Data Analyses; Detection; Diagnosis; Disease; Early Diagnosis; Evaluation; Fasting; Foundations; Frequencies; Funding; Gene Frequency; Goals; Institutional Review Boards; Knowledge; Liquid substance; Malignant Neoplasms; Malignant neoplasm of prostate; Memorial Sloan-Kettering Cancer Center; Methods; Molecular; Molecular Profiling; Monitor; Mutation; Mutation Detection; Neoplasm Circulating Cells; Noise; Nuclear; Patients; Performance; Pilot Projects; Plasma; Point Mutation; Procedures; Protocols documentation; Receptor Signaling; Relapse; Reporting; Reproducibility; Research; Resistance; Sampling; Science; Ships; Signal Transduction; Specificity; Steroids; Temperature; Testing; Time; Tube; Variant; Work; abiraterone; base; blood-based biomarker; cancer cell; cell free DNA; chemotherapy; clinical implementation; clinical practice; cohort; design; genetic variant; individual patient; inhibitor/antagonist; innovation; liquid biopsy; member; neoplastic cell; outcome forecast; practice setting; predictive marker; preservation; response; taxane; tumor

Summary The analysis of liquid biopsy (eg, cell-free DNA [cfDNA]; circulating tumor cells [CTC]) in blood is increasingly integrated in clinical contexts including diagnosis, disease monitoring, understanding resistance, and early detection of relapse. The key challenge of detecting these analytes is that they are present at a very low proportion of the biospecimens, and therefore are heavily influenced by pre-analytical factors associated with acquisition and processing. Understanding effects of these pre-analytical variables on the quality of data generated in downstream molecular CTC and cfDNA assays is critical for robust clinical implementation of liquid biopsy tests. To date, research efforts have focused on effects of preservation methods, processing time, storage temp, and shipment conditions on quality of CTC and cfDNA in blood plasma. There are no studies reported on effects of patient-specific context such as fasting, administration of anti-emetics, or biospecimen acquisition procedures (eg, order of blood collection aliquots, time of day when blood is drawn, etc.) There is a lack of data on this type of pre-analytical variable that impacts design of clinical trials such as optimal timing for blood draw and interpretation of data to distinguish technical variables introduced by these pre-analytical factors from the biological signals being evaluated. We propose to address this gap by extending the work done by our team members on evaluating effects of sample processing protocols on cfDNA and CTC analysis, to further investigate effect of patient-specific context. Hypothesis: Pre-analytic variables may affect signal-to- noise ratio in cfDNA and CTC analysis and thus have a higher impact on quantification at levels close to the assay limit of detection. Aim 1: Determine the effect of patient-specific context on the quality of cell-free DNA (cfDNA) and circulating tumor cells (CTC) in prostate cancer patients. Aim 2: Evaluate the impact of these variables on the performance of downstream cfDNA and CTC molecular profiling assays. We will apply an adaptive design in which we perform initial analysis with 20 patients per cohort, then adjust as needed. In a foundation-funded pilot study, we focused on one cohort to study effect of draw order. Results confirm the variability of biomarkers quantification as a result of pre-analytical variables. Significance: Results will elucidate effects of multiple pre-analytical variables specific to individual patient context on performance of blood-based biomarker analysis in cfDNA and CTC. These data will inform the design of liquid biopsy-incorporated clinical trials by identifying optimal timing of blood collection to minimize effects of pre-analytical variables. Innovation: This will be the first study to examine the effect of patient- specific context on quality of liquid biopsy data. We will collaborate closely with commercial liquid biopsy test developers as part of the Blood Profiling Atlas in Cancer (BloodPAC) project, with the goal of sharing knowledge across different sectors and working toward harmonization of pre-analytical procedures for liquid biopsy testing.

总结 血液中液体活检（例如，无细胞DNA [cfDNA];循环肿瘤细胞[CTC]）的分析越来越多 整合在临床环境中，包括诊断，疾病监测，了解耐药性， 检测复发。检测这些分析物的关键挑战是它们以非常低的浓度存在。 生物样本的比例，因此受与以下因素相关的分析前因素的严重影响： 采集和处理。了解这些分析前变量对数据质量的影响 在下游分子CTC和cfDNA测定中产生的抗体对于稳健的临床实施至关重要。 液体活组织检查到目前为止，研究工作集中在保存方法，处理时间， 储存温度和运输条件对血浆中CTC和cfDNA质量的影响。没有研究 报告了患者特定环境的影响，如禁食、止吐药给药或生物标本 采集程序（例如，血液采集等分试样的顺序、采血时间等）有一个 缺乏关于这类影响临床试验设计的分析前变量的数据，如最佳时间 抽血和解释数据，以区分这些预分析引入的技术变量 从生物信号的因素被评估。我们建议通过延长工作来解决这一差距 由我们的团队成员完成，用于评估样品处理方案对cfDNA和CTC分析的影响， 以进一步研究患者特定背景的影响。假设：分析前变量可能会影响信号- 在cfDNA和CTC分析中的噪声比，因此在接近于最大值的水平下对定量具有更高的影响。 测定检测限。目的1：确定患者特定环境对游离DNA质量的影响 在前列腺癌患者中检测cfDNA（cfDNA）和循环肿瘤细胞（CTC）。目标2：评估这些措施的影响 下游cfDNA和CTC分子谱分析测定的性能的变量。我们将应用一个 适应性设计，我们对每个队列20名患者进行初始分析，然后根据需要进行调整。中 基金会资助的试点研究，我们专注于一个队列研究抽签顺序的影响。结果证实了 分析前变量导致的生物标志物定量的变异性。 意义：结果将阐明个体患者特定的多个分析前变量的影响 关于cfDNA和CTC中基于血液的生物标志物分析的性能的背景。这些数据将告知 通过确定最佳采血时间设计液体活检结合临床试验， 预分析变量的影响。创新：这将是第一项研究，以检查病人的影响- 液体活检数据质量的具体背景。我们将与商业液体活检检测密切合作 作为癌症血液分析图谱（BloodPAC）项目的一部分， 跨不同部门的知识，并致力于统一液体的预分析程序 活组织检查