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 及早发现复发在急性髓细胞白血病（AML）中，50%的缓解患者在2周内复发。 年目前的方法缺乏检测所有患者微小残留病（MRD）的敏感性和通用性。 这些病人。多重准确灵敏定量法（MASQ）是一种既灵敏又通用的方法。它可以向上瞄准 到50个患者特异性突变，序列错误率降低到百万分之一， 带有分子标签的分子。在一项AML的初步研究中，MASQ检测到体细胞变异体的水平范围为 1/100至近1/100万，复发患者的突变频率更高。还有一个关键的 需要在白血病前克隆性造血的背景下解释微小残留病， 白血病细胞。复发可能来自耐药白血病细胞、基因分化的亚克隆或 白血病前期干细胞的储存库。在这个建议中，我应用并改进了创新的基因组工具， 治疗反应、预测临床结果和研究AML中残留细胞的性质。 该项目利用AML的大型观察性临床研究来跟踪患者特异性白血病相关性 在疾病过程中采集的血液样本中的变异。目的1将分析亚克隆治疗反应 以及通过追踪白血病相关变异等位基因频率随时间变化的复发动力学。目标2将 建立一个个性化的，高灵敏度的，定量的残留疾病检测的预后价值， 急性髓细胞白血病目的3提出从缓解期分离携带白血病相关变异的罕见残留细胞 血液样本，以确定基因组和转录谱，可以提供进一步的生物学和临床 深入了解疾病。 我提出了一个量身定制的职业发展计划，为我向独立过渡做好准备。 在我的博士后奖学金培训之后，我的目标是成为一名独立的终身教授， 研究型大学。在冷泉港实验室（CSHL）的培训环境中， 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， 生物学我的专业发展活动围绕导师制，沟通，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 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;并在我的导师Michael Wigler博士和我的合作伙伴的指导下指导研究目标， 丹·利维博士的导师我已经召集了一个由其他科学顾问和合作者组成的团队，其中包括博士。 来自CSHL的大卫·图维森和克里斯托弗·瓦科克博士以及来自诺斯韦尔健康中心的史蒂文·艾伦博士。

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.