Genomics of Acute myelogenous leukemia (AML): Whole Genome Resequencing

急性髓性白血病 (AML) 的基因组学：全基因组重测序

• 批准号: 7465873
• 负责人: RICHARD K. WILSON
• 金额: $ 57.98万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-04-01 至 2013-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7465873
• 关键词: Acute; Acute Myelocytic Leukemia; Behavior; Bioinformatics; Biological Assay; Bone Marrow; Cells; Characteristics; Chromosome abnormality; Cluster Analysis; Custom; DNA; DNA Resequencing; Data; Disease; Ensure; Frequencies; Funding; Gene Expression Profiling; Genes; Genome; Genomics; Genotype; Goals; Human; Human Genome; Informatics; Leukemia, Myeloid, Acute, M1; Maps; Molecular Profiling; Mutate; Mutation; Mutation Detection; Myeloid Leukemia; Numbers; Oligonucleotides; Outcome; Pathogenesis; Patients; Polymerase Chain Reaction; Reading; Research; Running; Sampling; Skin; Software Tools; Somatic Mutation; Variant; base; cost; falls; genome sequencing; mouse model; myeloblast; tumor

The long-term goal of this project is to identify all of the somatic, non-synonymous mutations in the unique portion of at least 10 human AML genomes by performing genome-wide, comprehensive resequencing of a number of tumor samples from carefully selected AML patients; the frequency of these changes will be determined in an additional 187 cases of AML. Although the current high cost of whole genome resequencing is high, we anticipate that costs will continue to fall through the proposed research period. Hence, we will use the data and informatics platforms created by this study to analyze as many AML genomes as possible. We have chosen to initially study one of the most common subtypes of AML, FAB M1, which has no associated mutations that have been shown to be responsible for the initiation of this disease. Samples chosen for analysis have the following characteristics: 1. Adequate amounts of bone marrow and skin DMA are available to perform 10X whole genome sequencing coverage, if necessary (i.e. 5 ug of each sample, non-amplified). 2. > 70% myeloblasts in the bone marrow sample to assure enrichment of AML cells. 3. Two or fewer clonal cytogenetic abnormalities, and complete analysis of tumor and germline DMA samples on the 500K Affy SNP array and the 2.1 M long oligo CGH array platforms for copy number variants. 4. "Typical" expression signature of M1 AML samples after gene expression profiling analysis. 10 FAB M1 samples from our locally banked AML samples meet all criteria, and most have already had several genes resequenced in the initial funding period. Importantly, the detection of mutations in these samples by directed PCR and resequencing assures their quality for whole genome resequencing. Using material from these 10 cases, we propose the following Aims: Specific Aim 1: We will use the Solexa massively parallel sequencing platform to perform 30 sequencing runs (10X genomic coverage at 1Gb per run) on at least 10 FAB M1 AML samples, and matched skin DNA samples for the first two AML genomes. Additional AML samples will be analyzed as cost permits. Specific Aim 2: We will use the Solexa-based bioinformatics analysis pipeline and our own read mapping strategy to iteratively align the short Solexa reads onto the human reference genome sequence. Specific Aim 3: We will develop approaches to identify, validate (in Core D), and annotate all nonsynonymous somatic mutations in the AML genomes sequenced, following read mapping and identification of high quality discrepancies. The frequency of these mutations will be evaluated in 187 additional AML cases in Core D, and their relevance for pathogenesis and outcomes will be evaluated in other PPG projects.

这个项目的长期目标是确定所有的体细胞，非同义突变的独特的 至少10个人类AML基因组的一部分，通过对AML基因组进行全基因组全面重测序， 来自精心挑选的AML患者的肿瘤样本数量;这些变化的频率将是 在另外187例AML病例中确定。尽管目前全基因组的高成本 由于重新排序的成本很高，我们预计在拟议的研究期间成本将继续下降。 因此，我们将使用本研究创建的数据和信息学平台来分析尽可能多的AML 尽可能的基因组。我们选择最初研究AML最常见的亚型之一FAB， M1，它没有相关的突变，已被证明是负责启动这一点， 疾病选择用于分析的样本具有以下特征： 1.有足够数量的骨髓和皮肤DMA可用于执行10 X全基因组 测序覆盖率，如有必要（即每个样品5 μ g，未扩增）。 2.骨髓样品中> 70%的成髓细胞，以确保AML细胞的富集。 3.两个或更少的克隆细胞遗传学异常，以及肿瘤和生殖系DMA的完整分析 在500K Affy SNP阵列和2.1 M长寡核苷酸CGH阵列平台上对样品进行拷贝数变体分析。 4.基因表达谱分析后M1 AML样本的"典型"表达特征。 我们当地库存的AML样本中有10个FAB M1样本符合所有标准，其中大多数已经接受了 几个基因在最初的资助期间重新排序。重要的是，检测这些基因中的突变 通过定向PCR和重测序获得的样品保证了其用于全基因组重测序的质量。使用 从这10个案例中，我们提出了以下目标： 具体目标1：我们将使用Solexa大规模并行测序平台进行30 对至少10份FAB M1 AML样本进行测序运行（10X基因组覆盖率，每次运行1Gb），以及 与前两个AML基因组的皮肤DNA样本相匹配将分析额外的AML样本， 成本许可。 具体目标2：我们将使用基于Solexa的生物信息学分析管道和我们自己的读取 将短Solexa读数迭代比对到人参考基因组序列上的映射策略。 具体目标3：我们将开发方法来识别，验证（核心D），并注释所有非同义词 测序AML基因组中的体细胞突变，随后进行读段作图， 识别高质量的差异。这些突变的频率将在187年进行评估。 核心D中的其他AML病例及其与发病机制和结局的相关性将在 其他PPG项目。