(PDQ5)Integrated Genetic and Epigenetic Prognostication for Acute Myeloid Leukemi

(PDQ5)急性髓性白血病的综合遗传和表观遗传预测

• 批准号: 8687082
• 负责人: MARTIN CARROLL
• 金额: $ 24.36万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-05-05 至 2016-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8687082
• 关键词: Acute; Acute Myelocytic Leukemia; Address; Age; Biological Assay; CEBPA gene; Cancer Center; Cancer Diagnostics; Clinical; Collection; Cytogenetics; DNA Methylation; DNA Mutational Analysis; DNA Sequence; Data; Data Set; Development; Discrimination; Disease; Doctor of Medicine; Eastern Cooperative Oncology Group; Epigenetic Process; Evaluation; FLT3 gene; Gene Mutation; Genes; Genetic; Genetic Markers; Goals; Health; Hereditary Disease; High Dose Chemotherapy; Karyotype; Laboratories; Lead; Ligation; Mediating; Methodology; Methylation; Microspheres; Molecular; Molecular Genetics; Mutate; Mutation; Mutation Analysis; Myelogenous; NPM1 gene; Outcome; Patients; Refractory; Relapse; Reproducibility; Research; Risk; Risk Assessment; Sampling; Stratification; Survival Rate; System; Technology; Testing; Therapeutic; Work; base; chemotherapy; clinical practice; cohort; epigenetic marker; genetic analysis; genome wide methylation; genome-wide; improved; leukemia; molecular pathology; next generation; novel; outcome forecast; prognostic; response

DESCRIPTION (provided by applicant): Current risk stratification in acute myeloid leukemia (AML) is based on clinical variables such as age and traditional cytogenetics. Recently, molecular genetic analysis has proven to be useful in risk stratification and therapeutic management of AML patients. For example, FLT3, NPM1, and CEBPA mutational analysis was found to improve risk stratification in patients without karyotypic abnormalities. However, all current prognostication schema fail to robustly separate patients who will be cured by chemotherapy from those who will relapse. To address this problem, we have performed studies to enhance molecular prognostication using both genetic and epigenetic markers and, importantly, to make these assays clinically feasible. The Levine Laboratory recently completed mutational analysis of 16 genes mutated in AML in a large cohort of patients with de novo AML and identified novel predictors of outcome, including TET2, PHF6, DNMT3A, and IDH2 R140Q mutations. Importantly, combinations of these genetic variables provide enhanced prognostic ability for many AML patients, leading to predictions of survival of greater than 80% in these sub-groups. In other cases, combinations of genetic variables provide only modest discrimination of prognosis. Additionally, the Melnick laboratory has recently demonstrated through genome-wide DNA methylation analysis that response to therapy for AML patients can be predicted with a fifteen-gene DNA methylation panel. This panel was identified using a genome-wide methylation profiling platform not currently amenable to use in the clinical setting. Taken together, these studies lead to the hypothesis that AML is a disease characterized by both genetic and epigenetic changes and that optimal prognostication schema will need to incorporate both types of markers. To make the prognostic use of DNA methylation profiling feasible in clinical practice, we have developed a microsphere-based methylation profiling (MELP) assay which uses technology widely available in molecular pathology laboratories (see below for details). Initial evaluation demonstrates that the assay robustly reproduces results generated with the original HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) research-based methylation platforms and predicts outcome in a previously described AML cohort (HOVON). In addition, we have implemented a next generation based DNA sequencing methodology to determine genetic mutations in AML and applied this methodology to a recently annotated UPENN AML group (described below). In this proposal, we will further develop a robust, clinically feasible, AML prognostication system combining genetic, epigenetic and clinical features. We will initially focus on confirming a robust DNA methylation based clinical assay and then integrate this assay into a multivariate risk assessment system being developed. The latter system should serve as a platform for ongoing development of a fully integrated prognostic system as we move towards realization of the goal of personalized cancer diagnostics.

描述（由申请人提供）：目前急性髓性白血病（AML）的风险分层是基于临床变量，如年龄和传统的细胞遗传学。最近，分子遗传学分析已被证明是有用的AML患者的危险分层和治疗管理。例如，发现FLT3、NPM1和CEBPA突变分析可改善无核型异常患者的风险分层。然而，所有目前的化疗方案都未能有力地将通过化疗治愈的患者与复发的患者分开。为了解决这个问题，我们已经进行了研究，以提高分子鉴定使用遗传和表观遗传标记，重要的是，使这些测定临床可行。Levine实验室最近完成了对一个大型初治AML患者队列中AML中16个突变基因的突变分析，并确定了新的预后预测因子，包括TET2、PHF6、DNMT3A和IDH2 R140Q突变。重要的是，这些遗传变量的组合为许多AML患者提供了更强的预后能力，从而预测这些亚组的生存率超过80%。在其他情况下，遗传变量的组合仅提供适度的预后区分。此外，Melnick实验室最近通过全基因组DNA甲基化分析证明，AML患者对治疗的反应可以用15个基因的DNA甲基化面板来预测。使用目前不适合在临床环境中使用的全基因组甲基化分析平台鉴定该组。综上所述，这些研究导致了这样的假设，即AML是一种以遗传和表观遗传变化为特征的疾病，并且最佳诊断方案将需要结合这两种类型的标志物。为了使DNA甲基化谱的预后用途在临床实践中可行，我们开发了一种基于微球的甲基化谱（MELP）测定法，该测定法使用分子病理学实验室中广泛使用的技术（详情见下文）。初步评价表明，该检测方法稳健地再现了原始HELP（通过连接介导的PCR进行HpaII微小片段富集）研究型甲基化平台生成的结果，并预测了先前描述的AML队列（HOVON）的结果。此外，我们已经实施了基于下一代DNA测序的方法来确定AML中的基因突变，并将该方法应用于最近注释的UPENN AML组（如下所述）。在这项提案中，我们将进一步开发一个强大的，临床上可行的，结合遗传，表观遗传和临床特征的AML诊断系统。我们将首先专注于确认一个强大的基于DNA甲基化的临床检测，然后将该检测整合到正在开发的多变量风险评估系统中。后一个系统应该作为一个平台，为正在进行的开发一个完全集成的预后系统，因为我们朝着实现个性化的癌症诊断的目标。