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

描述（由申请人提供）：急性淋巴细胞白血病（ALL）是儿童期最常见的癌症，尽管进行了大量研究，但这种复杂、致命且变异广泛的疾病的遗传病因仍不清楚。这种知识的缺乏是预测个体结局和设计更具针对性、毒性更低的治疗药物的关键障碍。越来越多的证据表明，在复杂疾病中观察到的很大程度的变异性是由于个体间罕见的遗传变异。鉴定罕见的致病性遗传变异需要对受影响个体群体的多个遗传基因座进行深度重测序，并且与来自未受影响群体的类似测序相比信息量最大。传统的双脱氧测序方法对于这样的大规模分析来说成本太高，时间太长。然而，通过应用一种靶向的、基于人群的合并DNA测序方法，我们设计了这种方法来利用下一代测序的大规模并行、高通量能力，我们建议对涉及儿科高危白血病发生的56个基因进行深度重测序，这些基因来自96名未受影响儿童的生殖系DNA和96名来自儿科高危ALL患者的匹配非肿瘤和肿瘤DNA。虽然一个特定的致病罕见变异是个别罕见的，疾病相关的遗传基因座，当在基于人群的规模上询问，可能会显示出各种不同的罕见变异，所有导致相似的表型。我们希望在我们的儿童ALL队列中确定这样的基因座。我们将在250例儿童高危ALL患者的验证队列中确认这些结果，然后对验证位点进行个体基因分型，以确定潜在的个体间基因-基因相互作用。我们希望这些结果能够识别出参与儿童白血病发生的各种基因和生化途径，从而为长期基于细胞的功能研究奠定基础，最终目标是提供额外的数据，用于前瞻性个体患者基因分型，以进行风险评估，个体化治疗和设计新的靶向治疗药物。 公共卫生相关性：越来越多的证据表明，罕见遗传变化的独特个体组合可能导致复杂疾病（特别是儿科白血病）的易感性和治疗反应的显著差异。我们设计了一种新的高通量、靶向、经济有效的DNA测序方法。通过应用这种方法并对儿科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遗传变化和生化途径，当这些变化发生时，可能会使儿童在如此年轻的时候患上白血病。

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.