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

摘要 血液中液体活检的分析(例如，无细胞DNA[cfDNA]；循环肿瘤细胞[ctc])越来越多。 集成到临床环境中，包括诊断、疾病监测、了解耐药性和早期 检测复发。检测这些分析物的关键挑战是它们的含量非常低 生物检疫剂的比例，因此受到与以下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检测中产生的DNA对于强健的临床应用至关重要 液体活组织检查。到目前为止，研究工作主要集中在保存方法、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。目前还没有研究 报道了患者特定环境的影响，如禁食、服用止吐药物或生物喷雾剂 采集程序(例如，采血量的顺序、一天中的采血时间等)有一个 缺乏这类影响临床试验设计的分析前变量的数据，例如 血样采集和数据解释以区分这些分析前引入的技术变量 来自被评估的生物信号的因素。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，以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到 CfDNA和CTC分析中的噪声比，因此在接近 方法检出限。目的1：确定患者特定环境对无细胞DNA质量的影响 前列腺癌患者外周血中cfDNA和循环肿瘤细胞(CTC)的变化。目标2：评估这些措施的影响 影响下游cfDNA和ctc分子图谱分析性能的变量。我们将应用一个 适应性设计，我们对每个队列中的20名患者进行初步分析，然后根据需要进行调整。在一个 基金资助的先导性研究，我们集中在一个队列来研究抽签顺序的影响。结果证实了 生物标记物量化的可变性是分析前变量的结果。 意义：结果将阐明多个分析前变量对个别患者的影响 基于血液的生物标记物分析在cfDNA和ctc中的表现。这些数据将向 液体活组织检查结合临床试验的设计--通过确定最佳采血时间将 分析前变量的影响。创新：这将是第一个研究患者- 关于液体活组织检查数据质量的具体背景。我们将与商业化液体活组织检查密切合作 作为癌症血液图谱项目的一部分的开发人员，目标是分享 跨不同部门的知识，并努力统一液体的分析前程序 活组织检查。

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.