A Novel sequencing-based approach to discovering rare genetic factors for ALL.

一种基于测序的新方法，用于发现 ALL 的罕见遗传因素。

基本信息

批准号：
7893449
负责人：
Todd E Druley
金额：
$ 14.6万
依托单位：
WASHINGTON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-09-10 至 2015-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7893449
关键词：
Accounting Acute Lymphocytic Leukemia Address Affect Age Alleles Architecture B-Lymphocytes Base Sequence Biochemical Pathway Biological Assay Candidate Disease Gene Cell Cycle Cell Lineage Cells Child Childhood Childhood Acute Lymphocytic Leukemia Children&apos s Oncology Group Chromosome abnormality Complex Critical Pathways Cytogenetics DNA DNA Resequencing DNA Sequence Data Disease Disease Progression Future Gene Rearrangement Gene Targeting General Population Genes Genetic Genetic Code Genetic Models Genetic Polymorphism Genetic Predisposition to Disease Genomics Genotype Goals Hematopoietic stem cells Heterogeneity In Vitro Incidence Individual Knowledge MLL gene Malignant - descriptor Malignant Childhood Neoplasm Malignant Neoplasms Methods Mutation Outcome Pathogenesis Pathway interactions Patients Phenotype Population Pre-B Acute Lymphoblastic Leukemia Predisposition Protocols documentation Reading Relative (related person)Reporting Research Resolution Risk Assessment Sampling Sequence Analysis Signal Transduction Specimen Target Populations Techniques Therapeutic Therapeutic Agents Time Validation Variant base case control cohort combinatorial cost design disease phenotype gene interaction genetic variant genome sequencing genome wide association study high risk leukemia leukemogenesis mutant next generation novel patient population population based prospective public health relevance response stem cell differentiation therapy design treatment response tumor

项目摘要

DESCRIPTION (provided by applicant): Acute lymphoblastic leukemia (ALL) is the most common cancer of childhood, and despite much research, the genetic etiology of this complex, deadly, and widely variable disease remains unknown. This lack of knowledge is a critical obstacle to advances in predicting individual outcomes and designing more targeted, less toxic therapeutic agents. There is mounting evidence suggesting that a large degree of the variability observed in complex disease is due to inter-individual rare genetic variants. Identifying rare causal genetic variants requires deep resequencing of multiple genetic loci from a population of affected individuals, and is most informative when compared to similar sequencing from an unaffected cohort. Traditional dideoxy sequencing methods are too cost and time prohibitive for such large scale analyses. However, by applying a targeted, population-based pooled DNA sequencing method that we have designed to leverage the massively parallel, high-throughput capacity of next-generation sequencing, we propose to deeply resequence 56 genes implicated in pediatric high-risk leukemogenesis from the germline DNA of 96 unaffected children and 96 matched non-tumor and tumor DNA from pediatric high-risk ALL patients. While a specific causal rare variant is individually rare, a disease-associated genetic locus, when interrogated on a population-based scale, might demonstrate a variety of different rare variants all resulting in a similar phenotype. We expect to identify such loci in our pediatric ALL cohort. We will confirm these results in a validation cohort of 250 pediatric high-risk ALL patients followed by individual genotyping of validated loci to identify potential inter-individual gene-gene interactions. We expect these results to identify a variety of genes and biochemical pathways involved in pediatric leukemogenesis which would then form the basis for long-term cell based functional study, with the ultimate goal of providing additional data that could be used for prospective individual patient genotyping for risk assessment, individualized therapy, and design of new targeted therapeutic agents. PUBLIC HEALTH RELEVANCE: There is increasing evidence that unique individual combinations of rare genetic changes may account for a significant degree of variability in the susceptibility and treatment response of complex disease, particularly pediatric leukemia. We have designed a new high-throughput, targeted, cost-effective method for DNA sequencing. By applying this method and sequencing dozens of genes important in pediatric leukemia, I expect to rapidly identify a variety of new genetic changes and biochemical pathways that, when altered, may predispose a child to developing leukemia at such a young age.

描述（由申请人提供）：急性淋巴细胞白血病（ALL）是儿童最常见的癌症，尽管进行了大量研究，但这种复杂、致命且变化广泛的疾病的遗传病因学仍然未知。这种知识的缺乏是预测个体结果和设计更有针对性、毒性较小的治疗药物取得进展的关键障碍。越来越多的证据表明，复杂疾病中观察到的变异很大程度上是由于个体间罕见的遗传变异造成的。识别罕见的因果遗传变异需要对受影响个体群体的多个遗传位点进行深度重测序，并且与未受影响群体的类似测序相比，信息最丰富。传统的双脱氧测序方法对于如此大规模的分析来说成本和时间都太高。然而，通过应用我们设计的有针对性的、基于人群的混合 DNA 测序方法，以利用下一代测序的大规模并行、高通量能力，我们建议对来自儿童高危白血病发生的 56 个基因进行深度重测序。 96 名未受影响儿童的种系 DNA 和 96 名来自儿科高危 ALL 患者的匹配非肿瘤和肿瘤 DNA。虽然特定的因果罕见变异在个体上是罕见的，但当在基于人群的规模上进行询问时，与疾病相关的遗传位点可能会表现出多种不同的罕见变异，所有这些变异都会导致相似的表型。我们希望在儿科 ALL 队列中识别出此类基因座。我们将在由 250 名儿科高危 ALL 患者组成的验证队列中确认这些结果，然后对经过验证的位点进行个体基因分型，以确定潜在的个体间基因间相互作用。我们期望这些结果能够鉴定出与儿科白血病发生有关的多种基因和生化途径，从而为长期细胞功能研究奠定基础，最终目标是提供可用于前瞻性个体患者基因分型的额外数据。风险评估、个体化治疗以及新靶向治疗药物的设计。公共卫生相关性：越来越多的证据表明，罕见基因变化的独特个体组合可能导致复杂疾病（尤其是儿童白血病）的易感性和治疗反应存在显着差异。我们设计了一种新的高通量、有针对性、经济高效的 DNA 测序方法。通过应用这种方法并对儿童白血病中的数十个重要基因进行测序，我希望能够快速识别出各种新的基因变化和生化途径，这些变化和生化途径一旦发生改变，可能会使儿童在这么小的年纪就容易患上白血病。