Exome sequencing for head and neck cancer susceptibility genes

描述(申请人提供)：在美国，每年有54,640例头颈部癌(HNC)病例和11,520例因HNC而死亡。HNC是一种发生在口腔、咽部和喉部的恶性肿瘤。烟草和酒精是口咽癌的两大危险因素，而人类乳头瘤病毒(HPV)感染是口咽癌的重要危险因素。我们进行了HNC全基因组关联研究，但命中率最高的是酒精代谢基因家族，我们已经在候选基因项目中报告了这一家族。虽然进一步的GWAS将发现其他影响较小的常见遗传变异，毫无疑问，一些家庭风险将归因于非遗传因素，如烟草和酒精暴露，但这些额外因素不太可能将家庭风险的已解释组成部分增加到50%以上。有必要采取超越GWAS的新方法，针对低频遗传变异(MAF=1.0-4.9%)或含有许多罕见变异的易感基因(单个MAF&lt；1%)。我们的假设是，有相当一部分 未解释的HNC家族性风险是由于多个基因中的低频率或罕见的遗传变异带来的相对风险，范围从大约两倍到五倍以上，而全基因组SNP关联方法(即使使用数百万个SNP)也无法检测到这些风险。我们的方法将在两阶段设计中应用大规模并行测序，首先对家族性HNC病例资源应用完整外显子组测序，然后对精心策划的HNC病例对照系列进行有针对性的候选基因重测序。因此，我们提出了以下具体目标：1)准备和管理200个家族性HNC病例的强大资源，然后对这些病例进行基于整个外显子组测序的候选HNC易感基因的搜索；2)对目标1中确定的候选HNC易感基因进行病例对照突变筛查；3)评估HNC易感基因所赋予的风险是否因亚点和流行病学危险组而异。在具体目标1中，我们将把我们的结果与1000个基因组计划中约500个个体的对照外显子进行比较。我们预计将定义大约500个候选基因，这些基因将在特定的目标2中进行测序，并建立一个针对蛋白质编码外显子、启动子和已知转录调控元件的外显子捕获小组。对于那些具有与乳腺癌ATM和CHEK2相似的优势比和致病序列变异频谱的基因，AIMS 1和AIMS 2的组合将有80%的力量达到全基因组意义(p&lt；2.5x10-6)。针对具体目标3，我们将按HNC分站点、吸烟、饮酒和HPV16/18感染状况进行分层分析。我们还将评估基因和流行病学风险因素之间对HNC风险的潜在交互作用。总体而言，这项研究很有可能找到与HNC易感性有关的临床相关“缺失遗传性”的很大一部分，并提供将这些发现直接转化为临床实践所需的关键数据。

DESCRIPTION (provided by applicant): In the US, 54,640 head and neck cancer (HNC) cases and 11,520 deaths due to HNC occur each year. HNCs are malignancies that arise in the oral cavity, pharynx and larynx. Tobacco and alcohol are the two major risk factors for HNC, while human papillomavirus (HPV) infection is an important risk factor for oropharyngeal cancer. We conducted a HNC genome wide association study (GWAS), but the top hits were in the alcohol metabolism gene families, which we had already reported in our candidate gene projects. While further GWAS will identify additional common genetic variants with small effects, and undoubtedly some of the familial risk will be attributed to non-genetic factors such as tobacco and alcohol exposure, it is unlikely that these additional factors will increase the explained component of familial risk to over 50%. New approaches beyond GWAS, targeting either low frequency genetic variants (MAF=1.0-4.9%), or susceptibility genes harboring many rare variants (individual MAFs <1%), are necessary. It is our hypothesis that a significant portion of the unexplained familial risk of HNC is due to low frequency or rare genetic variants in multiple genes conferring relative risks ranging from approximately two-fold to greater than five-fold that cannot be detected by genome-wide SNP association approaches (even using several million SNPs). Our approach will apply massively parallel sequencing in a two-stage design, first applying whole-exome sequencing to a familial HNC case resource and then targeted candidate gene resequencing to a well curated HNC case- control series. Thus we propose the following Specific Aims: 1) to prepare and curate a powerful resource of 200 familial HNC cases and then to subject those cases to a whole exome sequencing based search for candidate HNC susceptibility genes, 2) to apply case-control mutation screening to the candidate HNC predisposition genes identified in Aim 1 in a series of 2,000 HNC cases and 2,000 cancer-free controls, and 3) to assess whether the risks conferred by the HNC susceptibility genes differ by sub-site and epidemiologic risk groups. In specific aim 1, we will compare our results with control exomes from ~500 individuals from the 1,000 Genomes project. We expect to define approximately 500 candidate genes, which will be sequenced in specific aim 2 with a targeted exon capture panel directed at the protein coding exons, promoters, and known transcriptional regulatory elements. The combination of Aims 1 and 2 will have >80% power to reach genome- wide significance (p<2.5x10-6) for genes that have odds ratio and pathogenic sequence variant frequency spectra similar to those of ATM and CHEK2 in breast cancer. For specific aim 3, we will conduct stratified analyses by HNC sub-site, tobacco smoking, alcohol drinking and HPV 16/18 infection status. We will also assess potential interactions between genes and epidemiologic risk factors on HNC risk. Overall, the study has a strong probability of finding a substantial fraction of the clinically relevant "missing heritability" that contributes to HNC predisposition and of providing key data required to translate these findings directly to clinical practice.