Post genome wide association studies in testicular germ cell tumors

睾丸癌联盟（TECAC）是唯一的国际合作组织，其目标是 了解睾丸生殖细胞肿瘤（TGCT）的遗传易感性。TGCT的发病率最高 在欧洲血统的男性中，是影响15-45岁男性的最常见癌症。TECAC及其 成员进行了成功的TGCT全基因组关联研究（GWAS）;我们的最新分析 已鉴定出22个新的易感等位基因，使总验证的风险标志物达到68个，占43%， 遗传性。我们的研究已经揭示了影响雄性生殖的重要途径的变异的关键作用 细胞发育和成熟，性别决定，染色体分离和DNA维持， TGCT敏感性。我们提出了三个互补的目标，以加深我们的发现遗传变异的 对TGCT的易感性，其结果将完善我们对TGCT和男性生殖细胞生物学的理解 发展，提供深入了解遗传变异诱发基因组不稳定性，并提高我们的 识别疾病风险最高的患者的能力。在目标1中，我们将识别罕见和常见的变体 （个体和基因负荷）使用全外显子组（WES）方法，随后进行独立验证。我们 将对来自1000名和1000名有和没有TGCT的男性的现存生物样本进行重新WES， 分别收集来自TECAC成员的2066名TGCT男性的现有WES数据， 与来自Penn Medicine和UK Biobank的基因组匹配（1：4）的未受影响的男性进行比较。到 为了解决数据异构性问题，来自所有来源的WES数据将使用一个公共管道一起调用。五十 将从5000个基因和500个SNP中选择一组独立的现存生物样品进行验证， 5000名男性，分别与和没有TGCT，所有现有的全基因组基因分型。在目标2中，我们将 进行全转录组关联研究（TWAS），之前是迄今为止最大的GWAS研究， 15，847名男性患有TGCT，27，178名（230，610名患有deCODE）男性未患有TGCT。我们将使用定制的 用于执行TWAS的FUSION版本，注释了来自TGCT细胞系的表达数据，胎儿 以及成体生殖细胞、GTEx和生殖细胞的单细胞测序。在目标3中，计算机模拟评估后， 根据优先顺序，将使用siRNA和CRISPR在TGCT体外模型中评估20个顶级基因座/基因，以评估 对形态学、增殖、染色体异常的过表达和敲低效应，以及 顺铂敏感性我们将从我们过去的遗传关联工作中选择候选基因（初步为11个 优先级），并从我们的WES（目标1），GWAS和TWAS（目标2）中发现的新基因座/基因。我们 更新建立在我们的成就和铺平了道路，以确定新的易感基因座通过三个 具有高度凝聚力的目标。我们的发现将导致对生物学和遗传学的进一步突破性见解 TGCT的病因，并将提供所需的数据，以确定男性在最需要的监测，最佳的 降低严重TGCT治疗相关发病率的方法。

The Testicular Cancer Consortium (TECAC) is the only international collaborative group whose goal is to understand the genetic susceptibility to testicular germ cell tumors (TGCT). The incidence of TGCT is highest among men of European ancestry, and the most common cancer affecting men aged 15-45. TECAC and its members have conducted successful genome-wide association studies (GWAS) of TGCT; our latest analysis has identified 22 novel susceptibility alleles bringing the total validated risk markers to 68, accounting for 43% of heritability. Our studies have revealed the critical role of variation affecting essential pathways of male germ cell development and maturation, sex determination, chromosomal segregation, and DNA maintenance in TGCT susceptibility. We propose three complementary aims to deepen our discovery of inherited variation of susceptibility to TGCT, results of which will refine our understanding of the biology of TGCT and male germ cell development, provide insights into inherited variation predisposing to genomic instability, and improve our ability to identify patients at highest risk of disease. In Aim 1, we will identify rare and common variants (individual and gene burden) using whole exome (WES) approaches followed by independent validation. We will conduct de novo WES on extant biosamples from 1000 and 1000 men with and without TGCT, respectively, and assemble existing WES data from 2066 men with TGCT from TECAC members for comparison to genomically matched (1:4) unaffected men from the Penn Medicine and UK Biobanks. To address data heterogeneity, WES data from all sources will be called together using a common pipeline. Fifty genes and 500 SNPs will be selected for validation in an independent set of extant biosamples from 5000 and 5000 men with and without TGCT, respectively, all with existing genome-wide genotyping. In Aim 2, we will conduct a transcriptome-wide association study (TWAS), preceded by the largest GWAS study to date in 15,847 men with TGCT and 27,178 (230,610 with deCODE) men without TGCT. We will use a customized version of FUSION to perform the TWAS, annotated with expression data derived from TGCT cell lines, fetal and adult germ cells, GTEx, and single cell sequencing of germ cells. In Aim 3, after in silico assessment and prioritization, 20 top loci/genes will be evaluated in TGCT in vitro models using siRNA and CRISPR to assess over-expression and knockdown effects on morphology, proliferation, chromosomal abnormalities, and cisplatin sensitivity. We will select candidate genes from our past genetic association efforts (11 preliminarily prioritized) and from novel loci/genes found in our WES (Aim 1), GWAS and TWAS (Aim 2) efforts. Our renewal builds upon our accomplishments and paves the way to identify novel susceptibility loci through three highly cohesive aims. Our findings will lead to further ground-breaking insights into the biology and genetic etiology of TGCT and will provide data needed to identify men at greatest need for surveillance, the optimal way to decrease serious TGCT treatment-related morbidity.