Detection of Colorectal Cancer Susceptibility Loci Using Genome-Wide Sequencing

描述(申请人提供)：结直肠癌(CRC)是美国癌症死亡的第二大原因。连锁研究和全基因组关联研究已经成功地发现了高外显性突变，如发生在APC或DNA错配修复基因中的突变，以及低外显性变异，如8q24和Smad7。然而，这些变异只解释了CRC遗传性的一小部分。这并不令人惊讶， 作为一大类遗传变异的贡献者，尤其是等位基因频率为0.1-5%的频率较低和罕见的单核苷酸变异(SNV)、插入/缺失(INDELs)和拷贝数变异(CNV)，在整个基因组中尚未得到系统的研究。据预测，这些遗传变异比常见的低外显性变异具有更强的效应大小，并被认为可以解释相当大比例的结直肠癌遗传性。为了全面识别基因组中的这些变异，我们建议使用下一代技术对全基因组进行测序，在2,123例高危结直肠癌病例和2,123例对照病例中覆盖12倍(目标1.1)。这些病例和对照将选自我们现有的结直肠癌遗传学和流行病学联合会(GECCO；U01CA137088，PI：彼得斯)，其中包括15个特征良好的前瞻性队列和病例对照研究。我们证明，在大型病例对照研究中，将全基因组序列数据与使用现有Gwas数据的归因相结合，可以有效地筛查CRC易感基因座。这种方法特别适合于识别不常见和罕见的SNV、INDELs和CNV。因此，在AIM 1.2中，我们使用来自AIM 1.1的测序数据，将另外8,958例结直肠癌病例和10,212例对照中的~2,000万个变异与现有的Gwas数据联系起来。我们将在总共11,081个病例和12,335个对照中测试CRC风险和变异(测序和归因于)之间的关联。在目标1.3中，我们将通过对8,827例独立CRC病例和8,595名对照的3,000个变异进行基因分型来复制最有希望的基因座。在目标2中，我们将利用GECCO研究来调查直接测序和归因于变异的基因-环境相互作用，这些研究具有详细的临床和流行病学数据，这些数据已经在不同的研究中得到协调。为了提高目标1和目标2的能力，我们将应用新的统计方法。该项目汇集了一支高素质、多学科的研究团队，他们拥有CRC研究、生物统计学、人口和统计遗传学、流行病学和下一代测序方面的专业知识。我们希望发现几个新的CRC易感变异，其影响大小大于先前GWAS的发现。这些结果将提高我们对哪些基因影响CRC的理解。这些关于潜在生物学的知识可能会对筛查、治疗和疾病预防产生长期影响。 公共卫生相关性：这项多学科的努力将调查不同类型的基因变异，包括罕见的变异和结构变异，是否会影响结直肠 人类罹患癌症的风险。具体地说，我们将检查结直肠癌病例和对照的整个基因组中的基因变异，以确定结直肠癌新的遗传风险因素。 这项研究的发现将提高我们对影响这种严重疾病风险的全谱基因的了解。

DESCRIPTION (provided by applicant): Colorectal cancer (CRC) is the second leading cause of cancer death in the US. Linkage studies and genome-wide association studies (GWAS) have successfully identified high-penetrance mutations such as those that occur in APC or DNA mismatch-repair genes, as well as low-penetrance variants such as 8q24 and SMAD7. However, these variants explain only a fraction of the heritability of CRC. This is not surprising, as contributions from large classes of genetic variation, specifically less frequent and rare singl nucleotide variants (SNV) with allele frequency of 0.1-5%, insertion/deletions (indels), and copy number variants (CNVs), have not been systematically investigated across the genome. These genetic variants are predicted to have stronger effect sizes than common low-penetrance variants and are postulated to explain a substantial proportion of the heritability of CRC. To comprehensively identify these variants across the genome, we propose to use next generation technology to sequence the whole genome with 12x coverage in 2,123 high-risk CRC cases and 2,123 controls (Aim 1.1). These cases and controls will be selected from our existing Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO; U01CA137088, PI: Peters) of 15 well-characterized prospective cohorts and case-control studies. We demonstrate that combining whole genome sequence data with imputation using existing GWAS data in large sets of case-control studies allows a powerful and efficient screen for CRC susceptibility loci. This method is particularly well suited to identifying less frequent and rare SNVs, indels, and CNVs. Accordingly, in Aim 1.2 we use the sequencing data from Aim 1.1 to impute ~20M variants in an additional 8,958 CRC cases and 10,212 controls with existing GWAS data. We will test the associations between CRC risk and variants (sequenced and imputed) in a total of 11,081 cases and 12,335 controls. In Aim 1.3, we will replicate the most promising loci by genotyping 3,000 variants in 8,827 independent CRC cases and 8,595 controls. In Aim 2, we will investigate gene-environment interactions for directly sequenced and imputed variants, utilizing GECCO studies, which have detailed clinical and epidemiologic data that have already been harmonized across studies. To improve the power for Aim 1 and 2, we will apply novel statistical methods. This project brings together a highly qualified, multidisciplinary team of investigators with expertise in CRC research, biostatistics, population and statistical genetics, epidemiology, and next generation sequencing. We expect to identify several novel CRC susceptibility variants with effect sizes larger than previous GWAS findings. These results will improve our understanding of which genes are impacting CRC. Such knowledge about the underlying biology could have long term impacts on screening, treatment and disease prevention. PUBLIC HEALTH RELEVANCE: This multidisciplinary effort will investigate whether different types of genetic variations, including rare variants and structural variation, influence colorectal cancer risk in humans. Specifically, we will examine genetic variants across the entire genomes of colorectal cancer cases and controls to identify new genetic risk factors for colorectal cancer. Findings from this study will improve our knowledge of the full spectrum of genes that affect the risk of this severe disease.