Assay Validation of Cell-Free DNA Shallow Whole Genome Sequencing To Determine 'Tumor Fraction' in Advanced Cancers

游离 DNA 浅全基因组测序的测定验证以确定晚期癌症的“肿瘤部分”

• 批准号: 9976072
• 负责人: Viktor Adalsteinsson
• 金额: $ 21.49万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9976072
• 关键词: Advanced Malignant Neoplasm; Androgen Receptor; Biological Assay; Biopsy; Blood; Blood Circulation; Blood Tests; Blood specimen; Breast; Cell Fraction; Clinical; Collaborations; Collection; DNA; DNA sequencing; Detection; Development; Estrogen receptor positive; Genes; Goals; Hemorrhage; Infection; Knowledge; Libraries; MEKs; Malignant Neoplasms; Malignant neoplasm of prostate; Manuscripts; Metastatic breast cancer; Multiple Myeloma; Mutate; Mutation; Pain; Patients; Performance; Plasma; Ploidies; Process; Proto-Oncogene Proteins c-akt; Protocols documentation; Publications; Quality of life; Reproducibility; Research; Research Personnel; Risk; Role; Running; Sampling; Sensitivity and Specificity; Specimen; Testing; Therapeutic; Therapeutic Clinical Trial; Therapeutic Trials; Time; Tissue Banks; Tube; Tumor-Derived; Validation; Work; assay development; base; cancer type; castration resistant prostate cancer; cell free DNA; computational pipelines; cost effective; genome sequencing; genomic biomarker; improved; ineffective therapies; inhibitor/antagonist; innovation; liquid biopsy; malignant breast neoplasm; minimally invasive; outcome forecast; patient oriented; patient response; prospective; response; success; survival outcome; therapy outcome; time interval; triple-negative invasive breast carcinoma; tumor; tumor DNA; whole genome

PROJECT SUMMARY The overarching goal of this research is to utilize a plasma-based genomic biomarker of cell-free DNA (cfDNA) to guide therapy in metastatic breast and other cancers. In our approach, we use a cfDNA ‘ultra low pass whole genome sequencing’ (ULP-WGS) assay with computational pipeline (ichorCNA) to determine the amount of tumor DNA in circulation (‘tumor fraction’; TFx). Changes in TFx may serve as an early identifier for patients responding – or failing to respond – to therapy and cfDNA ULP-WGS provides a cost-effective, minimally-invasive approach to determine TFx. Our ULP-WGS cfDNA assay allows rapid, precise quantitation of TFx from a single blood sample without prior knowledge of tumor mutations. While most liquid biopsy approaches to date have focused on tracking known alterations or commonly mutated genes in cancer, our approach is mutation agnostic and broadly applicable across advanced cancers. This proposal developed through deep collaboration between three primary investigators working on concert on the development and application of a cell-free DNA assay to guide prognosis and therapy in advanced cancers. To date, we have performed the research version of this assay on over 3000 patients samples and, in three publications to date, we demonstrate clinical utility in metastatic breast and prostate cancer as well as multiple myeloma. We bring expertise in clinical breast cancer, sequencing assay development, and CLIA sequencing at scale, with a strong track record of collaboration with multiple shared publications. All three PIs are dedicated to the success of this proposal, with distinct yet complementary roles and responsibilities. In this proposal, we will analytically validate our cfDNA ULP-WGS assay (UH2 portion) then establish clinical validity and prospectively evaluate performance in therapeutic clinical trials (UH3 portion). In the UH2 portion, we will determine the sensitivity and specificity of ULP-WGS using serial dilutions of patient samples, then assess reproducibility, repeatability, and reportable range. We will then determine performance in the context of ‘real world’ pre-analytic variability including blood collection tube type, amount of plasma, and detection thresholds with respect to DNA input quantity. In the UH3 portion, we will establish clinical validity by evaluating TFx in 700 clinical plasma specimens from patients with metastatic breast cancer then advance our understanding of cfDNA by evaluating the association of TFx with patient response to therapy and survival outcomes. Finally, we will evaluate ULP-WGS in two prospective therapeutic clinical trials of metastatic triple- negative breast cancer, evaluating association with response to therapy.

项目摘要 这项研究的总体目标是利用基于等离子体的无细胞DNA基因组生物标志物（CFDNA） 指导转移性乳房和其他癌症的治疗。在我们的方法中，我们使用CFDNA的超低通 使用计算管道（Ichorcna）确定的整个基因组测序（ULP-WGS）测定 循环中的肿瘤DNA量（“肿瘤分数”； TFX）。 TFX的变化可以作为早期标识符 对治疗和CFDNA ULP-WGS做出反应（或无法做出反应）的患者提供了一种成本效益的， 确定TFX的最小侵入性方法。我们的ULP-WGS CFDNA分析可以快速，精确的定量 来自单个血液样本的TFX，没有事先了解肿瘤突变。虽然大多数流动活检 迄今 方法是突变不可知论，并且在高级癌症中广泛适用。 这项提案通过三名主要调查员之间的深入合作发展 关于无细胞DNA分析的开发和应用，以指导晚期的疾病和治疗 癌症。迄今为止，我们已经对3000多名患者样本进行了此评估的研究版本，并在 迄今为止的三个出版物，我们展示了转移性乳腺癌和前列腺癌以及 多发性骨髓瘤。我们为临床乳腺癌，测序分析开发和CLIA带来专业知识 大规模测序，具有与多个共享出版物的合作记录的良好记录。这三个PI 致力于该提案的成功，并具有独特而完整的角色和责任。 在此提案中，我们将分析验证我们的CFDNA ULP-WGS分析（UH2部分）然后建立了临床 有效性和前瞻性评估热临床试验（UH3部分）的性能。在UH2部分中， 我们将使用患者样品的系列稀释液确定ULP-WG的灵敏度和特异性，然后 评估可重复性，可重复性和可报告范围。然后，我们将在上下文中确定绩效 “现实世界”的预分析变异性，包括血管类型，血浆量和检测 关于DNA输入量的阈值。在UH3部分中，我们将通过 评估来自转移性乳腺癌患者的700个临床等离子体标本中的TFX，然后推进我们 通过评估TFX与患者对治疗和生存的反应的关联来了解CFDNA 结果。最后，我们将在两项转移性三重前瞻性治疗临床试验中评估ULP-WGS 乳腺癌阴性，评估与治疗反应的关联。