Genetic Susceptibility to Pediatric Glioma inIndividuals and Diverse populations

 描述（由申请人提供）：脑肿瘤是儿童中最常见的实体瘤和第二常见的恶性肿瘤。在美国，每年有近2,000例15岁以下儿童被诊断出患有小儿神经胶质瘤（PG），其中只有一半能活到成年。80%的幸存者经历与治疗相关的危及生命的疾病，包括中风和第二种恶性肿瘤。尽管有明确的证据表明PG风险的遗传成分，但对影响这种致命脑瘤的遗传因素知之甚少。如先前对成人胶质瘤所证明的，鉴定稳健且经验证的遗传风险因素可导致改善的风险分层，并揭示疾病发病机制的基本生物学途径。以前试图确定PG遗传风险因素的研究受到样本量小的限制。这一障碍使得研究不足以以高通量的方式鉴定真实的遗传关联。此外，技术限制迫使先前的研究集中在共同的遗传变异，这可能只是潜在的PG风险的遗传起源的一个组成部分。罕见和常见的遗传变异都有助于PG风险和特定亚型风险的假设，将在本提案中得到正式验证。为了实现这一目标，一项基于人群的病例对照研究，嵌套在加州出生队列（CBC），已经开发。对常见和罕见遗传变异的全基因组分析将使用1988年至2013年期间诊断为PG的2，920名加利福尼亚儿童的现有存档新生儿血斑和1：1匹配的对照进行。首先，来自300名患有恶性星形细胞瘤的儿童和100名对照的DNA将进行全外显子组测序（WES），以确定导致疾病风险的罕见变异（次要等位基因频率<1%）。与CBC和公共对照外显子组相比，受影响儿童中显示出罕见变异显著富集的基因将通过靶向测序在来自CBC的另外675名恶性星形细胞瘤病例儿童和875名对照儿童中进行验证。接下来，从WES中识别出的20，000个有希望的低频变异（MAF 1-5%）将作为定制内容添加到全基因组基因分型阵列中，该阵列已经包含818，000个常见变异。来自所有2，920名CBC病例儿童和2，920名CBC对照儿童的DNA样本将进行全基因组基因分型，以进行药物富集的全基因组关联研究（eeGWAS）。eeGWAS分析可以识别潜在PG风险的低频和常见变异，并且对于汇总和亚型分层分析具有统计学效力。eeGWAS确定的大约1,500种变异将在来自三个合作机构的1,210名病例和1,850名对照儿童中进行尝试复制。通过利用加州公共卫生部遗传病分支内独特和成熟的资源，这种基于登记的方法将产生前所未有的大样本量。鉴定罕见和常见的PG风险变异可以揭示新的知识，从而改善对面临这种诊断的儿童，青少年和年轻人的护理。

 DESCRIPTION (provided by applicant): Brain tumors are the most common solid tumor and the second most common malignancy in children. Nearly 2,000 pediatric gliomas (PG) are diagnosed annually in U.S. children under the age of 15, only half of whom survive into adulthood. 80% of survivors experience life-threatening conditions related to treatment, including stroke and second malignancies. Despite clear evidence of a genetic component underlying PG risk, little is known about heritable factors affecting this deadly brain tumor. As previously demonstrated for adult glioma, identification of robust and validated genetic risk factors can lead to improved risk stratification and reveal the biologic pathways fundamental to the disease pathogenesis. Previous studies seeking to identify genetic risk factors for PG were limited by small sample size. This obstacle rendered studies inadequate for the identification of authentic genetic associations in high-throughput fashion. Furthermore, technological limitations have forced prior studies to focus on common genetic variation, which may be only one component of the genetic origins underlying PG risk. The hypothesis that both rare and common genetic variation contribute to PG risk, and risk of specific subtypes, will be formally tested in this proposal. To achieve this, a population-based case-control study, nested within the California Birth Cohort (CBC), has been developed. Genome-wide analysis of common and rare genetic variants will be conducted using existing archived neonatal bloodspots from 2,920 Californian children diagnosed with PG between 1988 and 2013, and 1:1 matched controls. First, DNA from 300 children with malignant astrocytoma and 100 controls will undergo whole-exome sequencing (WES) to identify rare variants contributing to disease risk (Minor Allele Frequency<1%). Genes displaying significant enrichment of rare variants in affected children compared to CBC and public control exomes will be validated by targeted sequencing in an additional 675 malignant astrocytoma case children and 875 control children from the CBC. Next, 20,000 promising low-frequency variants (MAF 1-5%) identified from the WES will be added as custom content to a genome-wide genotyping array, already containing 818,000 common variants. DNA samples from all 2,920 CBC case children and 2,920 CBC control children will undergo genome-wide genotyping to perform an empirically-enriched genome-wide association study (eeGWAS). The eeGWAS analysis can identify both low-frequency and common variants underlying PG risk, and is statistically powered for both pooled and subtype-stratified analyses. Approximately 1,500 variants identified by the eeGWAS will undergo attempted replication in 1,210 case and 1,850 control children from three collaborating institutions. By leveraging the unique and mature resources within the Genetic Diseases Branch of the California Department of Public Health, this registry-based approach will yield an unprecedentedly large sample size. The identification of both rare and common variants underlying PG risk can expose new knowledge leading to improved care of children, adolescents, and young adults facing this diagnosis.