Exome sequencing for head and neck cancer susceptibility genes

描述（由申请人提供）：在美国，每年发生54，640例头颈癌（HNC）病例和11，520例HNC死亡。HNC是发生在口腔、咽和喉的恶性肿瘤。吸烟和饮酒是HNC的两个主要危险因素，而人乳头瘤病毒（HPV）感染是口咽癌的重要危险因素。我们进行了一项HNC全基因组关联研究（GWAS），但最热门的是酒精代谢基因家族，我们已经在候选基因项目中报道过了。虽然进一步的GWAS将确定其他影响较小的常见遗传变异，毫无疑问，一些家族风险将归因于非遗传因素，如烟草和酒精暴露，但这些额外的因素不太可能将家族风险的解释成分增加到50%以上。除了GWAS之外，针对低频率遗传变异（MAF=1.0-4.9%）或携带许多罕见变异（单个MAF <1%）的易感基因的新方法是必要的。我们的假设是 HNC的不明原因的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，其相对风险范围为约2倍至大于5倍，无法通过全基因组SNP关联方法（即使使用数百万个SNP）检测到。我们的方法将在两阶段设计中应用大规模平行测序，首先将全外显子组测序应用于家族性HNC病例资源，然后将靶向候选基因重测序应用于精心策划的HNC病例对照系列。因此，我们提出以下具体目标：1）制备和管理200个家族性HNC病例的强大资源，然后对这些病例进行基于全外显子组测序的候选HNC易感基因的搜索，2）在一系列2，000个HNC病例和2，000个无癌症对照中对目标1中鉴定的候选HNC易感基因应用病例对照突变筛选，以及3）评估HNC易感基因所赋予的风险是否因亚位点和流行病学风险组而不同。在具体目标1中，我们将比较我们的结果与来自1,000个基因组项目的约500个个体的对照外显子组。我们预计将确定约500个候选基因，这些基因将在特定目标2中使用针对蛋白质编码外显子、启动子和已知转录调控元件的靶向外显子捕获面板进行测序。目的1和2的组合将具有>80%的功效以达到乳腺癌中具有与ATM和CHEK 2相似的优势比和致病性序列变体频谱的基因的全基因组显著性（p<2.5x10-6）。对于特定目标3，我们将按照HNC子中心、吸烟、饮酒和HPV 16/18感染状态进行分层分析。我们还将评估基因和流行病学危险因素对HNC风险的潜在相互作用。总体而言，该研究很有可能发现导致HNC易感性的临床相关“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.