Measuring treatment response and residual disease in leukemia with personalized, sensitive, and quantitative genomic methods

项目摘要 为了改善癌症患者的预后，迫切需要更好的方法来衡量治疗反应。 并检测早期复发。在急性髓系白血病(AML)中，50%的缓解期患者会在2 好几年了。目前的方法缺乏检测微小残留病的灵敏度和通用性。 那些病人。多重准确灵敏定量(MASQ)，既灵敏又通用。它可以将目标锁定在 到50个特定于患者的突变，序列错误率降至百万分之一，并计算突变DNA 带有分子标签的分子。在对AML的一项试点研究中，MASQ检测到体细胞变异的水平从 每100人中有1人到近100万人中有1人，复发患者的突变频率更高。还有一个关键的问题 需要在白血病前期克隆性造血和进化的背景下解释微小残留病 白血病细胞。复发可能源于耐药白血病细胞、遗传分化的亚克隆或 白血病前期干细胞的储存库。在这项建议中，我应用和改进了创新的基因组工具来测量 治疗反应，预测临床结果，并调查AML中残留细胞的性质。 该项目利用对急性髓细胞白血病的大型观察性临床研究来追踪特定于患者的白血病相关疾病。 在疾病过程中采集的血液样本中的变种。AIM 1将分析亚克隆治疗反应 以及通过跟踪白血病相关变异等位基因频率随时间的变化来了解复发的动态。目标2将 建立个性化、高度敏感和定量的残留病检测的预后价值 AML。Aim 3建议将携带白血病相关变异的罕见残留细胞从缓解期分离出来 血液样本，以确定基因组和转录组特征，可能提供进一步的生物学和临床 对疾病的洞察。 我提出了一个量身定做的职业发展计划，为我向独立的过渡做好准备。 经过博士后培训后，我的目标是成为一名独立的终身教职教授。 研究型大学。冷泉港实验室(CSHL)的培训环境提供了 世界知名的会议和课程，以及大量具有癌症和定量研究专业知识的研究人员 生物学。我的职业发展活动围绕着指导、交流、教学、实验室 管理，并为学术求职做准备。我的培训还将包括临床课程 翻译和单细胞分析；在基因组信息学、癌症生物学和 液体活检；在我的导师Michael Wigler博士和我的合作伙伴的指导下指导研究目标 丹·利维博士导师。我已经组建了一个由其他科学顾问和合作者组成的团队，其中包括Dr。 CSHL的David Tuveson和Christopher Vakoc博士以及Northwell Health的Steven Allen博士。

Project Summary To improve patient outcome in cancer, better methods are urgently needed to measure therapeutic response and detect early relapse. In acute myeloid leukemia (AML), 50% of patients in remission will relapse within 2 years. Current methods lack the sensitivity and generality to detect minimal residual disease (MRD) in all of those patients. Multiplex Accurate Sensitive Quantitation (MASQ), is both sensitive and general. It can target up to 50 patient-specific mutations, with sequence error rates reduced to 1 in 1 million, and count mutant DNA molecules with molecular tags. In a pilot study of AML, MASQ detected somatic variants at levels ranging from 1 in 100 to nearly 1 in 1 million, with higher mutation frequencies in patients who relapsed. There is also a critical need to interpret minimal residual disease in the context of pre-leukemic clonal hematopoiesis and the evolution of leukemic cells. Relapse may arise from drug-resistant leukemic cells, a genetically diverged subclone, or a reservoir of pre-leukemic stem cells. In this proposal, I apply and improve innovative genomic tools for measuring treatment response, predicting clinical outcome, and investigating the nature of residual cells in AML. This project utilizes a large observational clinical study of AML to track patient-specific leukemia-associated variants in blood samples taken over the course of the disease. Aim 1 will analyze subclonal treatment response and the dynamics of relapse by tracking leukemia-associated variant allele frequencies across time. Aim 2 will establish the prognostic value of a personalized, highly sensitive, and quantitative test for residual disease in AML. Aim 3 proposes to isolate the rare residual cells harboring leukemia-associated variants from a remission blood sample to determine the genomic and transcriptomic profiles that may provide further biological and clinical insight into the disease. I have proposed a tailored career development plan that will prepare me for my transition to independence. Following my postdoctoral fellowship training, I aim to be an independent tenure-track professor at a major research university. The training environment at Cold Spring Harbor Laboratory (CSHL) provides access to world-renowned meetings and courses, and a plethora of investigators with expertise in cancer and quantitative biology. My professional development activities center around mentorship, communication, teaching, lab management, and preparing for the academic job search. My training will also include coursework in clinical translation and single cell analysis; presentations at conferences in genome informatics, cancer biology, and liquid biopsy; and mentored research goals under the guidance of my mentor Dr. Michael Wigler and my co- mentor Dr. Dan Levy. I have assembled a team of additional scientific advisors and collaborators including Dr. David Tuveson and Dr. Christopher Vakoc from CSHL and Dr. Steven Allen from Northwell Health.