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：此应用程序响应NHLBI“大机会”RC 2主题，“大规模DNA测序和分子分析良好的表型NHLBI队列。“我们将使用全基因组重测序来鉴定与骨髓增生异常综合征（MDS）发病机制相关的遗传变化。MDS是一种日益流行的克隆性造血疾病，可导致显著的发病率和死亡率。对MDS遗传基础的理解落后于密切相关的疾病急性髓细胞白血病（AML）。我们的团队率先使用全基因组测序作为癌症基因组学的发现工具。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，我们在每种情况下都发现了8种新的非同义体细胞突变。其中一种突变在188例成人AML病例中的8.5%复发，并与不良结局相关。这些结果证明了该策略用于突变发现的可行性和实用性。我们现在将这些工具应用于MDS，具体目标如下：在具体目标1中，我们将对来自中等风险新发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%的肿瘤二倍体覆盖率和匹配的正常基因组。将在微阵列平台上分析拷贝数改变（扩增、缺失和单亲二体）和RNA表达谱。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，并确定其在144例其他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）将通过基于扩增子的文库的深度重测序来确认。将在从144例MDS患者队列中获得的合并DNA中评估经验证突变的患病率，并将在个体样本中对复发突变进行基因分型。这些实验可以立即启动，它们可以在两年的时间内完成，通过这种显著的短期资源投资，我们可以产生结果，这将大大加速该领域的研究，并对MDS患者的诊断，风险分层和治疗产生持久的影响。 公共卫生相关性： 骨髓增生异常综合征是一组知之甚少的疾病，损害生活质量和缩短预期寿命。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。这代表了一个“大机会”，以迅速增加知识，将有长期利益的照顾这些病人。