WHOLE GENOME SEQUENCING OF MYELODYSPLASTIC SYNDROMES

骨髓增生异常综合征的全基因组测序

• 批准号: 7939902
• 负责人: TIMOTHY A GRAUBERT
• 金额: $ 123.2万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7939902
• 关键词: Acute Myelocytic Leukemia; Adult Acute Myeloblastic Leukemia; Algorithms; Am 80; Arts; Bioinformatics; Biopsy; Bone Marrow; Bone Marrow Cells; Bone Marrow Neoplasms; Clinical; Code; Collaborations; DNA; DNA Resequencing; DNA Sequence; Data; Development; Diagnosis; Diploidy; Disease; Dysmyelopoietic Syndromes; Early Diagnosis; FGF3 gene; Frequencies; Funding; Genes; Genetic; Genetic Polymorphism; Genetic Transcription; Genome; Genomics; Genotype; Hand; Haploidy; Hematological Disease; Hematopoietic; Incidence; Individual; Inherited; International; Intervention; Investments; Knowledge; Libraries; Life Expectancy; Malignant Neoplasms; Minority; Modeling; Molecular; Molecular Profiling; Morbidity - disease rate; Multivariate Analysis; Mutation; Mutation Detection; National Heart, Lung, and Blood Institute; Nucleotides; Outcome; Pathogenesis; Pathway interactions; Patient Care; Patients; Pattern; Phenotype; Prevalence; Quality of life; Reading; Reagent; Recurrence; Reporting; Research; Resources; Risk; Sampling; Single Nucleotide Polymorphism; Skin; Somatic Mutation; Sorting - Cell Movement; Stratification; Subgroup; System; Techniques; Technology; Time; Uniparental Disomy; Universities; Variant; Washington; adverse outcome; aging population; base; cancer genome; cancer genomics; chemotherapy; clinically relevant; cohort; cost; cytopenia; genome sequencing; insertion/deletion mutation; mortality; myeloblast; next generation; novel; outcome forecast; prognostic; public health relevance; research study; response; therapeutic target; tool; tumor

DESCRIPTION (provided by applicant): PROJECT SUMMARY: This application responds to the NHLBI "Grand Opportunities" RC2 topic, "Large-scale DNA Sequencing and Molecular Profiling of Well-Phenotyped NHLBI Cohorts." We will use whole genome resequencing to identify genetic changes relevant for the pathogenesis of Myelodysplastic Syndromes (MDS). MDS is an increasingly prevalent clonal hematopoietic disorder that causes significant morbidity and mortality. Understanding of the genetic basis of MDS lags behind the closely related disease, acute myeloid leukemia (AML). Our group has pioneered the use of whole genome sequencing as a discovery tool in cancer genomics. We recently reported the complete DNA sequence of a cytogenetically normal AML genome and have now completed the analysis of a second AML case. Remarkably, we found eight novel non-synonymous somatic mutations in each case. One of these mutations is recurrent in 8.5% of 188 unselected adult AML cases and is associated with an adverse outcome. These results demonstrate the feasibility and utility of this strategy for mutation discovery. We will now apply these tools to MDS in the following specific aims: in Specific Aim 1, we will sequence the genomes of at least 10 paired tumor/normal samples from patients with intermediate risk de novo MDS. We will use "Next generation" sequencing to obtain 99% diploid coverage of the tumor and matched normal genomes. Copy number alterations (amplifications, deletions, and uniparental disomies) and RNA expression profiles will be analyzed on microarray platforms. In Specific Aim 2, we will perform bioinformatic analysis to identify all somatic mutations in at least 10 MDS genomes and define their frequencies in 144 other cases of MDS. Somatic mutations (present in the tumor, but not in the normal genomes) will be confirmed by deep resequencing of amplicon-based libraries. The prevalence of validated mutations will be assessed in pooled DNA obtained from a cohort of 144 MDS patients and recurrent mutations will be genotyped in individual samples. These experiments are ready to be initiated immediately, they can be completed in a two year time period, and with this significant short-term investment of resources, we can generate results that will greatly accelerate research in this field and have a lasting impact on the diagnosis, risk stratification, and treatment of patients with MDS. PUBLIC HEALTH RELEVANCE: The Myelodysplastic Syndromes are a poorly understood group of disorders that impair quality of life and shorten life expectancy. We will use state of the art sequencing technology to define the genetic basis of this disease. This represents a "Grand Opportunity" to rapidly increase knowledge that will have long-term benefits for the care of these patients.

描述(由申请人提供)：项目概要：本申请响应NHLBI“重大机遇”RC2主题，“良好表型NHLBI队列的大规模DNA测序和分子图谱分析”。我们将使用全基因组重测序来识别与骨髓增生异常综合征(MDS)发病机制相关的基因变化。MDS是一种日益流行的克隆性造血疾病，会导致严重的发病率和死亡率。对MDS的遗传学基础的了解落后于与其密切相关的疾病--急性髓系白血病(AML)。我们小组率先使用全基因组测序作为癌症基因组学中的发现工具。我们最近报道了一个细胞遗传学正常的AML基因组的完整DNA序列，现在已经完成了第二个AML病例的分析。值得注意的是，我们在每个病例中都发现了八个新的非同义体细胞突变。其中一个突变在188例未经选择的成人AML病例中有8.5%复发，并与不良结局有关。这些结果证明了该策略用于突变发现的可行性和实用性。我们现在将在以下特定目标中将这些工具应用于MDS：在特定目标1中，我们将对来自中等风险新生MDS患者的至少10对肿瘤/正常样本的基因组进行测序。我们将使用“下一代”测序来获得99%的肿瘤和匹配的正常基因组的二倍体覆盖率。拷贝数改变(扩增、缺失和单亲二体)和RNA表达谱将在微阵列平台上进行分析。在具体目标2中，我们将进行生物信息学分析，以确定至少10个MDS基因组中的所有体细胞突变，并确定它们在144个其他MDS病例中的频率。体细胞突变(存在于肿瘤中，但不存在于正常基因组中)将通过对基于扩增子的文库进行深度重测序来确认。将在从144名MDS患者队列中获得的混合DNA中评估验证突变的流行率，并将在个别样本中对反复发生的突变进行基因分型。这些实验可以立即启动，它们可以在两年的时间内完成，通过这种重大的短期资源投资，我们可以产生结果，这些结果将极大地加速该领域的研究，并对MDS患者的诊断、风险分层和治疗产生持久的影响。 与公共卫生相关：骨髓增生异常综合征是一组知之甚少的疾病，会损害生活质量并缩短预期寿命。我们将使用最先进的测序技术来确定这种疾病的遗传基础。这代表着一个快速增长知识的“大好机会”，这些知识将对这些患者的护理产生长期好处。