Development of a Universal Assay for Minimal Residual Disease in Acute Myeloid Leukemia using Duplex Sequencing

使用双重测序开发急性髓系白血病微小残留病的通用检测方法

• 批准号: 10678621
• 负责人: Jacob Emerson Higgins
• 金额: $ 113.91万
• 依托单位: TWINSTRAND BIOSCIENCES, INC.
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-16 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10678621
• 关键词: Acute Myelocytic Leukemia; Adoption; Allogenic; Biochemistry; Biological Assay; Biological Markers; Blood; Bone Transplantation; Cessation of life; Clinical; Clinical Trials; Collaborations; DNA; Data; Data Set; Detection; Development; Diagnosis; Diagnostic Procedure; Disease remission; Evaluation; Event; Face; Flow Cytometry; Frequencies; Funding; Genes; Goals; Guidelines; Hematopoietic Neoplasms; In complete remission; Informatics; Institution; Interview; Laboratories; Leadership; Leukemic Cell; Malignant Neoplasms; Marrow; Measurable; Methods; Microscope; Molecular; Monitor; Morphology; Mutation; Mutation Detection; Newly Diagnosed; Patients; Performance; Phase; Polymerase Chain Reaction; Polymerase Gene; Protocols documentation; Relapse; Reproducibility; Residual Neoplasm; Residual state; Sensitivity and Specificity; Small Business Innovation Research Grant; Standardization; Stem cell transplant; Technology; Testing; Transplantation; Transplantation Conditioning; United States; Variant; acute myeloid leukemia cell; aggressive therapy; chemotherapy; clinical decision-making; clinical remission; cohort; detection limit; detection method; drug development; evidence base; exome; gene panel; genetic variant; genome sequencing; genomic locus; hematopoietic cell transplantation; high risk; improved; leukemia; mortality; next generation sequencing; novel therapeutics; patient subsets; post-transplant; prognostic value; programs; prospective; relapse prediction; relapse risk; research study; standard of care; tool; tumor; whole genome

Problem: With a 5-year survival of ~30%, AML is the 6th deadliest cancer, and >20,000 new patients are diagnosed each year in the United States. Although most patients achieve Complete Remission (CR) with aggressive therapy, most will eventually relapse. The criteria for CR, however, is based on historical diagnostic methods, and patients in CR may carry up to 1010 residual leukemia blasts. Significant effort has gone into developing tools to detect Minimal amounts of Residual Disease (MRD), including multi-parametric flow cytometry (MFC) and polymerase chain reaction (PCR). MRD is the strongest predictor of relapse, and several AML trials have demonstrated that survival was significantly better when MRDpos patients were subjected to intensified therapy. Yet, lack of sensitivity is a clear problem with MFC and PCR. For example, relapses occur in ~40% of patients who are MRDneg by MFC after chemotherapy. Next Generation Sequencing (NGS) holds the promise to identify MRD by detecting mutations associated with residual AML cells. Yet, the sensitivity of conventional NGS is limited by a relatively high error rate, which makes it difficult to differentiate sequencing errors from true low-frequency mutations. Solution: Duplex Sequencing (DS) is an ultra-sensitive NGS technology which uses specialized biochemistry and informatics to improve the accuracy of standard DNA sequencers by more than ten-thousand-fold. In our prior Phase I SBIR study, we developed a broadly-applicable DS-based AML MRD assay that overcomes the above limitations. The DS assay targets many MRD-relevant genes simultaneously, with sensitivity and specificity rivaling or exceeding single-gene PCR assays. In Phase II, we demonstrated excellent reproducibility across labs, applied the optimized assay to retrospectively banked cohorts, and showed superior clinical performance vs. MFC. However, based on many customer interviews, the most substantial barrier to widespread commercial adoption we face is the lack of large-scale prospective clinical trial data. Specific Aims: In the present Phase 2b application we propose generating this comprehensive clinical utility data set through collaboration with the world-class US National Marrow Donor Program (NMDP) and other top AML MRD key opinion leaders. The primary goals of our proposed study include: Aim 1: Prospectively validate the prognostic value of pre-transplantation DS AML MRD testing for predicting post-transplant relapse and survival; Aim 2: Prospectively generate data supporting the ability of post-transplantation DS AML MRD testing to assess relapse risk for patients treated with different transplant conditioning intensities; and Aim 3: Demonstrate the potential of using tumor-informed DS AML MRD testing for patients without a driver gene variant targeted by our fixed gene panel. Impact: This combined approach may bring NGS MRD testing up to 100% patient applicability. Blood MRD comparison may present an equally sensitive but less invasive alternative to marrow. Our anticipated data will also support the use of the technology in assigning high-risk patients to intensified therapies and as an early marker of anti-leukemic efficacy for novel drug development efforts.

问题：AML 的 5 年生存率约为 30%，是第六大致命癌症，超过 20,000 名新患者正在接受治疗。 在美国每年都会确诊。尽管大多数患者达到完全缓解（CR） 积极治疗，大多数最终会复发。然而，CR 的标准是基于历史诊断 方法，CR患者可能携带多达1010个残留的白血病母细胞。已付出巨大努力 开发检测微量残留疾病 (MRD) 的工具，包括多参数流量 细胞计数（MFC）和聚合酶链式反应（PCR）。 MRD 是复发的最强预测因子，并且有几个 AML 试验表明，当 MRDpos 患者接受 MRDpos 治疗时，生存率显着提高 强化治疗。然而，缺乏敏感性是 MFC 和 PCR 的一个明显问题。例如，会出现复发的情况 约 40% 的化疗后 MFC 为 MRDneg 的患者。下一代测序 (NGS) 拥有 承诺通过检测与残留 AML 细胞相关的突变来识别 MRD。然而，敏感性 传统NGS受限于相对较高的错误率，导致测序难以区分 真正的低频突变产生的错误。解决方案：双重测序 (DS) 是一种超灵敏的 NGS 使用专门的生物化学和信息学来提高标准 DNA 准确性的技术 测序仪的数量增加了一万倍以上。在我们之前的 I 期 SBIR 研究中，我们开发了一种广泛适用的 基于 DS 的 AML MRD 检测克服了上述限制。 DS 检测针对许多与 MRD 相关的 同时检测多个基因，其灵敏度和特异性可与单基因 PCR 检测相媲美或超过。在第二阶段， 我们在实验室中展示了出色的重现性，将优化的测定应用于回顾性存储 队列，并显示出优于 MFC 的临床表现。然而，根据对许多客户的采访， 我们面临的广泛商业应用的最大障碍是缺乏大规模的前瞻性临床 试验数据。具体目标：在目前的 2b 期申请中，我们建议生成这个全面的临床 通过与世界级的美国国家骨髓捐赠计划 (NMDP) 和其他机构合作获得实用数据集 顶级 AML MRD 关键意见领袖。我们提议的研究的主要目标包括： 目标 1：前瞻性 验证移植前 DS AML MRD 检测对预测移植后复发的预后价值 和生存；目标 2：前瞻性生成支持移植后 DS AML MRD 能力的数据 进行测试以评估接受不同移植调理强度治疗的患者的复发风险；和目标 3： 展示对没有驱动基因变异的患者使用肿瘤相关 DS AML MRD 检测的潜力 由我们的固定基因组靶向。影响：这种组合方法可能使 NGS MRD 测试达到 100% 患者的适用性。血液 MRD 比较可能提供一种同样敏感但侵入性较小的替代方案 骨髓。我们预期的数据还将支持使用该技术将高风险患者分配给 强化治疗并作为新药开发工作抗白血病功效的早期标志。

项目成果

Quantification of measurable residual disease using duplex sequencing in adults with acute myeloid leukemia.

使用双链测序对成人急性髓系白血病的可测量残留疾病进行量化。

• DOI: 10.1101/2023.03.26.23287367
• 发表时间: 2023
• 期刊: medRxiv : the preprint server for health sciences
• 作者: Dillon,LauraW;Higgins,Jake;Nasif,Hassan;Othus,Megan;Beppu,Lan;Smith,ThomasH;Schmidt,Elizabeth;Valentine3rd,CharlesC;Salk,JesseJ;Wood,BrentL;Erba,HarryP;Radich,JeraldP;Hourigan,ChristopherS
• 通讯作者: Hourigan,ChristopherS