Genetics and epigenetics of pediatric germ cell tumors

科学摘要儿童和成人的恶性生殖细胞肿瘤(GCTS)被认为是一种 子宫内事件的结果。成人睾丸GCT(TGCT)的高遗传率提示有遗传病因，并且 最近的全基因组关联研究通过发现多个易感基因来支持这一点。我们 最近证实这些基因座的一个子集是儿童GCT的易感变异。而5年的相对存活率 总体来说，GCTS的发生率非常高，主要是由于顺铂化疗的有效性，大约 20%的患者会出现化疗耐药或在治疗后复发。临床风险分层 识别预后不良的患者仍然非常粗略，进一步的分子分析，包括分析 肿瘤表观遗传学，可能有助于量身定做治疗。我们最近完成的儿童肿瘤学小组(COG)病例- GCT的父母三联体研究是第一个从儿童和青少年中收集生殖系DNA样本的大型研究 GCT病例、肿瘤标本和预后数据。这项申请中提出的研究将使我们能够 通过评估肿瘤DNA甲基化作为GCT和GCT预后因素，扩大我们正在进行的研究的范围 通过扩大我们对生殖系遗传变异的分析，将性染色体包括在内。我们的首要目标 旨在评估遗传学和表观遗传学在儿童GCT风险和 结果。我们的假设是，DNA甲基化模式将预测可能患有贫困的GCT病例 结果。此外，我们假设性染色体上常见的和中等罕见的变异 增加GCT的风险。为了评估这些假设，我们将结合正在进行的COG案例-家长的数据 获得GCT病例和对照的儿童GCT(N=867例和1,517例父母对照)的三联体研究 来自加利福尼亚州、密歇根州和华盛顿州的州生物库项目(N=1,601例和1,601例对照)。 我们的主要目标将是：1)识别预测不良结果的甲基化模式，包括疾病复发 和死亡，以及2)在基因上发现单核苷酸多态(SNP)和拷贝数变异(CNV) 导致儿童和青少年GCT风险的性染色体。我们还将评估贡献 在一个探索性的目的中，通过使用综合负荷测试来研究GCT中罕见的遗传变异。甲基化将 在500个GCT肿瘤样本中使用Illumina EPIC甲基化阵列进行评估。种系遗传分析 将利用在Illumina Human CoreExome阵列上生成的现有全球核安全数据进行研究。这个 稀有变异的贡献将通过分析产生的整个外显子组测序数据来评估 通过加布里埃拉·米勒儿童第一儿科研究计划(N=250三人组)和Exome内容提供 整个数据集(N=2,468例)。对儿童GCT的病因知之甚少；生殖系分析 基因变异将揭示疾病生物学。识别与不良相关的甲基化模式 预后可以改善现有的临床风险分层，并为治疗提供新的途径。最后， 这将是首次在包括非欧洲血统的个人的任何年龄组中对GCT易感性进行研究。

Scientific Abstract Malignant germ cell tumors (GCTs) in children and adults are hypothesized to occur as a result of events in utero. The high heritability of adult testicular GCT (TGCT) suggests a genetic etiology, and recent genomewide association studies support this through the discovery of multiple susceptibility loci. We recently confirmed a subset of these loci as susceptibility variants for pediatric GCT. While 5-year relative survival rates are very high overall for GCTs, mainly due to the effectiveness of cisplatin chemotherapy, approximately 20% of patients will display resistance to chemotherapy or relapse following treatment. Clinical risk stratification to identify patients with poor prognosis is still very crude and further molecular analysis, including analysis of tumor epigenetics, may help to tailor treatment. Our recently completed Children’s Oncology Group (COG) case- parent triad study of GCT was the first large study to collect germline DNA samples from pediatric and adolescent GCT cases, tumor specimens and outcomes data. The research proposed in this application will allow us to extend the scope of our ongoing study by evaluating tumor DNA methylation as a prognostic factor for GCT and by expanding our analyses of germline genetic variation to include the sex chromosomes. Our overarching goal for the proposed study is to evaluate the contribution of genetics and epigenetics in pediatric GCT risk and outcomes. Our hypothesis is that DNA methylation patterns will predict GCT cases who are likely to have poor outcomes. Further, we hypothesize that common and moderately rare variants on the sex chromosomes increase risk for GCT. To evaluate these hypotheses, we will combine data from our ongoing COG case-parent triad study of pediatric GCT (N=867 cases and 1,517 parent controls) with GCT cases and controls obtained from the state biobank programs in California, Michigan and Washington (N=1,601 cases and 1,601 controls). Our primary aims will be to: 1) Identify methylation patterns that predict poor outcomes, including disease relapse and death, and 2) Discover single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) on the sex chromosomes that contribute to GCT risk in children and adolescents. We will also evaluate the contribution of rare genetic variants in GCT through the use of aggregate burden tests in an exploratory aim. Methylation will be evaluated using the Illumina EPIC methylation array in 500 GCT tumor samples. Germline genetic analyses will be conducted using existing GWAS data generated on the Illumina Human CoreExome array. The contribution of rare variants will be assessed through analysis of whole exome sequencing data generated through the Gabriella Miller Kids First Pediatric Research Program (N=250 trios) and Exome content available for the entire dataset (N=2,468 cases). Little is known about the etiology of pediatric GCT; analysis of germline genetic variation will shed light on disease biology. Identification of methylation patterns associated with poor prognosis could improve the existing clinical risk stratification and suggest new avenues for treatment. Finally, this will be the first study of GCT susceptibility in any age group to include individuals of non-European ancestry.