APPLYING ERROR-CORRECTED SEQUENCING TO DETECT MINIMAL RESIDUAL IN THE AAML 1031 STUDY

应用纠错测序来检测 AAML 1031 研究中的最小残留

• 批准号: 9216965
• 负责人: Todd E Druley
• 金额: $ 38.86万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-12-09 至 2021-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9216965
• 关键词: Acute Myelocytic Leukemia; Adult; Adult Acute Myeloblastic Leukemia; Algorithms; Alleles; BAY 54-9085; Biological Markers; Bone Marrow; Bortezomib; Categories; Cessation of life; Childhood; Childhood Acute Myeloid Leukemia; Childhood Leukemia; Clinical; Clinical Data; Collaborations; Complex; Cytogenetics; DNA; DNA Sequence Alteration; DNA sequencing; Data; Detection; Diagnosis; Diagnostic; Disease; Disease Marker; Disease-Free Survival; Enrollment; Epigenetic Process; Exons; FLT3 gene; Family; Flow Cytometry; Frequencies; Future; Gene Targeting; Genes; Genetic; Goals; Gold; Immunophenotyping; Individual; Investigation; Machine Learning; Measures; Methodology; Methods; Monitor; Mutate; Mutation; Normal Cell; North America; Oncogenes; Outcome; Participant; Patients; Pattern; Pediatric Oncology Group; Phase; Point Mutation; Population; Probability; Prospective Studies; Protein Tyrosine Kinase; Protein phosphatase; Protocols documentation; Reagent; Recurrent disease; Refractory Disease; Relapse; Residual Neoplasm; Residual Tumors; Residual state; Resolution; Risk; Risk Assessment; Risk stratification; Role; Sampling; Site; Spliceosomes; Surface; Testing; Time; Treatment Efficacy; Tumor Suppressor Proteins; United States National Institutes of Health; Variant; analytical method; base; chemotherapy; cohesion; design; digital; falls; functional group; gene function; improved; improved outcome; insertion/deletion mutation; insight; leukemia; leukemia treatment; next generation; next generation sequencing; novel; nucleocytoplasmic transport; outcome prediction; pediatric patients; personalized cancer care; personalized medicine; prognostic; prospective; randomized trial; relapse risk; response; specific biomarkers; subclonal heterogeneity; transcription factor

Abstract Acute myeloid leukemia (AML) accounts for half of all pediatric leukemia deaths and is the leading cause of leukemia-related death in adulthood. One reason for worse outcomes is the inability to properly assess for minimal residual disease (MRD) following therapy. Unlike ALL, AML presents with multiple subclonal populations without a singular clonal surface marker, and surface markers can change during therapy. The current gold standard for AML MRD is multi-parameter flow cytometry (MPFC), which is predictive of outcomes to frequencies of 0.001, yet 30% of MPFC-MRD-negative patients still relapse. Alternatively, every AML case harbors leukemia-specific mutations that could be markers of disease, except that next-generation sequencing has high error rate of ~1%. In this proposal, we will implement a novel, validated error-corrected sequencing (ECS) strategy, developed by the Druley lab in collaboration with Illumina, to improve MRD assessment of AML subclonal heterogeneity in 990 pediatric de novo AML cases from the Children's Oncology Group AAML1031 study. We hypothesize that using a highly sensitive sequencing method will improve identification of residual AML, provide important insights on subclonal heterogeneity in pediatric AML, improve understanding of the role of germline variability and gene function on relapses or refractory disease and facilitate personalized medicine. To interrogate this hypothesis, we propose the following aims: 1. Define subclonal heterogeneity at diagnosis and end of Induction 1 (EOI1) in 990 pediatric de novo AML patients (n=1890). By using the largest prospective study of pediatric AML that has ever been performed, we will perform ECS on 94 genes that are the most frequently mutated genes in pediatric and adult AML at diagnosis and EOI1 to identify patterns of mutation associated with relapsed disease, FAB subtypes or other cytogenetic features. 2. Correlate ECS-MRD with existing EOI1 MPFC-MRD for all participants in the COG AAML1031 study. A major question is whether the “different from normal” cell population identified as residual disease by MPFC is actually the same population(s) identified by ECS. We will define residual disease by ECS and compare results to MPFC status (positive/negative), actual MPFC percentages (<0.001) and the clinical outcomes (relapse risk, disease-free survival and overall survival) of study participants. 3. Integrate germline variation and all subclonal mutations into mechanistic groups that are frequently mutated in pediatric AML and correlate with outcomes using unbiased machine learning algorithms. Preliminary data tells us that every patient will have multiple subclones at diagnosis and EOI1 as well as germline variants in AML-associated genes, which may be important for outcome. In this aim, we will take these mutations into account as well as MPFC, clinical features and cytogenetics for probabilistic risk assessment using unsupervised machine learning algorithms for improved outcome prognostication.

抽象的 急性髓细胞白血病（AML）占所有儿科白血病的一半，是领先的 成年后与白血病有关的原因。结局更糟的原因之一是无法正确正确 评估治疗后最小残留疾病（MRD）。与所有人不同，AML呈现多个 没有单个克隆表面标记的亚克隆种群，表面标记可以改变 治疗。 AML MRD的当前金标准是多参数流式细胞仪（MPFC），这是预测的 频率为0.001的结果，但仍有30％的MPFC-MRD阴性患者仍然继承。另外，每个 AML病例具有可能是疾病标志的白血病特异性突变，除了下一代 测序的高错误率〜1％。在此提案中，我们将实施一个新颖的，经过验证的错误校正 由Druley Lab与Illumina合作开发的测序（ECS）策略，以改善MRD 从儿童肿瘤学中评估990个小儿AML病例中AML亚克隆异质性的评估 AAML1031组研究。我们假设使用高度敏感的测序方法将改善 残留AML的识别，提供有关小儿AML亚克隆异质性的重要见解，改进 了解种系变异性和基因功能在继电器或难治性疾病中的作用以及 促进个性化医学。为了审问这一假设，我们提出以下目的： 1。在诊断和诱导结束时定义下克隆异质性1（EOI1）。 AML患者（n = 1890）。通过使用有史以来最大的小儿AML的前瞻性研究 进行的，我们将对94个基因进行EC，这是小儿最常见的基因，并且 成人AML诊断和EOI1，以识别与中继疾病，FAB相关的突变模式 亚型或其他细胞遗传学特征。 2。对于COG AAML1031研究的所有参与者，将ECS-MR与现有的EOII1 MPFC-MRD相关联。 一个主要的问题是，是否“与正常”细胞群体被确定为残留疾病的“不同” MPFC实际上是ECS确定的同一人群。我们将通过ECS定义残留疾病， 将结果与MPFC状态（正/负），实际MPFC百分比（<0.001）和临床进行比较 研究参与者的结果（复发风险，无病生存和整体生存）。 3。将种系变异和所有亚克隆突变整合到经常是机械组中 在小儿AML中突变并使用公正的机器学习与结果相关 算法。初步数据告诉我们，每个患者在诊断和EOI1中都有多个子克隆 以及与AML相关基因中的种系变体，这对于结果可能很重要。在这个目标中，我们 将考虑这些突变以及MPFC，临床特征和概率的细胞遗传学 使用无监督的机器学习算法进行风险评估，以改善结果提示。