Genomics of AML Clonality

AML 克隆性的基因组学

• 批准号: 8829765
• 负责人: TIMOTHY J. LEY
• 金额: $ 33.06万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至 2016-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8829765
• 关键词: Acute Myelocytic Leukemia; Algorithms; Architecture; Biological Assay; Bone marrow biopsy; Cell Cycle; Cells; Chromosome abnormality; Clinical; Clonality; Correlative Study; Coupled; Cryopreserved Cell; Custom; Cytarabine; DNA; Data; Daunorubicin; Decitabine; Development; Disease; Disease remission; Drug resistance; Drug usage; Early Intervention; Gene Frequency; Gene Targeting; Genome; Genomic DNA; Genomics; Goals; Growth; Heterogeneity; Homologous Transplantation; Human; Immunodeficient Mouse; Immunophenotyping; In Vitro; Individual; Lead; Learning; Measures; Metabolic Clearance Rate; Methods; Morphology; Mus; Mutation; Outcome; Patients; Pattern; Pharmaceutical Preparations; Property; Reagent; Refractory Disease; Relapse; Resistance; Risk; Sampling; System; Techniques; Therapeutic Agents; Translating; Tyrosine Kinase Inhibitor; Variant; Xenograft procedure; adverse outcome; base; chemotherapy; clinically relevant; digital; drug sensitivity; genome sequencing; high risk; in vivo; novel; novel strategies; novel therapeutic intervention; novel therapeutics; outcome forecast; physical property; research clinical testing; response; targeted treatment

The long-term goal of this project is to determine whether the clonal architecture of AML samples is relevant for clinical outcomes, and whether that information can be translated into clinical testing to predict prognosis. Our group has recently discovered that the clonal architecture of AML samples can be deduced by whole genome sequencing (which defines ali mutations in every case), followed by deep digital sequencing of ail mutations to define their variant allele frequencies (VAFs). Groups of mutations with similar VAFs represent subclones, Ali AML samples have a founding clone, and most contain 1-3 additional subclones that are derived from the founding clone. The dominant clone at relapse, however, is often a subclone that has acquired addition mutations. These data suggest that specific subclones contain mutations that are relevant for altered grov/th properties and/or altered drug sensitivity, which may contribute to refractory disease or relapse. In this project, we will study the clonal architecture of AML genomes, and determine their relevance for ciinical outcomes, via the following specific Aims: Specific Aim 1: We will use custom capture reagents and deep digital sequencing to determine the rate of clearance of individual AML subclones after induction chemotherapy. We will utilize DNA derived from bone marrow biopsies of 89 AML samples that have already undergone whole genome sequencing. gDNA from bone marrow biopsies obtained 2-4 weeks after initiation of therapy will be subjected to custom capture for all known mutations in each genome, and deep digital sequencing will be performed to assess the rate of clearance of the founding clone and all subclones. Clearance patterns will be correlated with clinical parameters to define impact on outcomes. Specific Aim 2: We will use a stromal-based culture system and xenotransplantation to evaluate the clonal architecture of AML samples grown in vitro and in vivo. Our stromal-based culture system allows for the expansion of most primary AML samples for at least 7 days without significantly altered physical properties or clonal drift. We will treat cultured AML cells with a variety of drugs, and responses will be measured using cell cycle assays and deep digital sequencing to define the drug sensitivity of each sample and each subclone. We will also analyze AML cells that expand in immunodeficient mice to determine whether specific subclones have a growth advantage in mice. These data will be used to identify mutations in subclones that may negatively influence prognosis.

该项目的长期目标是确定AML样品的克隆结构是否为 与临床结果相关，以及该信息是否可以转化为临床测试 预测预后。我们的小组最近发现，AML样品的克隆建筑可以是 通过整个基因组测序推导（在每种情况下定义ALI突变），然后是深数字 AIL突变的测序以定义其变异等位基因频率（VAFS）。一组突变 类似的VAF代表亚克隆，ALI AML样品具有创建克隆 从创始克隆得出的子克隆。但是，复发时的主要克隆通常是 获得加法突变的亚克隆。这些数据表明特定的子克隆包含突变 与改变的grov/th属性和/或药物敏感性有关的，这可能有助于 难治性疾病或复发。在这个项目中，我们将研究AML基因组的克隆体系结构，并研究 通过以下特定目的确定它们与ciinical结果的相关性： 特定目的1：我们将使用自定义捕获试剂和深度数字测序来确定 诱导化疗后单个AML亚克隆的清除率。我们将使用DNA 来自已经经历了整个基因组的89个AML样品的骨髓活检 测序。启动治疗后2-4周获得的骨髓活检的GDNA将是 对每个基因组中的所有已知突变进行自定义捕获，并且深度数字测序将是 进行以评估创始克隆和所有子克隆的清除率。清除模式将是 与临床参数相关，以定义对结果的影响。 特定目的2：我们将使用基于基础的培养系统和异种移植来评估 AML样品的克隆结构在体外和体内生长。我们基于基础的培养系统允许 对于大多数主要AML样品的扩展至少7天，没有显着改变 特性或克隆漂移。我们将用多种药物处理培养的AML细胞，反应将是 使用细胞周期测定和深数字测序来定义每个样品的药物敏感性 和每个子克隆。我们还将分析在免疫缺陷小鼠中扩展的AML细胞以确定 特定的亚克隆是否在小鼠中具有增长优势。这些数据将用于识别突变 在可能对预后产生负面影响的子克隆中。