Detection of Colorectal Cancer Susceptibility Loci Using Genome-Wide Sequencing

描述（由申请人提供）：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（GWAS）已经成功地鉴定了高突变率突变，如APC或DNA错配修复基因中发生的突变，以及低突变率突变，如8 q24和SMAD 7。然而，这些变异只能解释CRC遗传性的一小部分。这并不奇怪， 因为来自大类遗传变异的贡献，特别是等位基因频率为0.1- 5%的较不频繁和罕见的单核苷酸变异（SNV）、插入/缺失（indels）和拷贝数变异（CNV），尚未在整个基因组中进行系统研究。这些遗传变异被预测比常见的低突变率变异具有更强的效应量，并被假定解释了CRC遗传性的很大一部分。为了在基因组中全面识别这些变异，我们建议使用下一代技术对2，123例高风险CRC病例和2，123例对照的全基因组进行12倍覆盖率的测序（目标1.1）。这些病例和对照将从我们现有的结直肠癌遗传学和流行病学联盟（GECCO; U 01 CA 137088，PI：Peters）的15项充分表征的前瞻性队列和病例对照研究中选择。我们证明，在大量病例对照研究中，将全基因组序列数据与使用现有GWAS数据的插补相结合，可以有效筛选CRC易感基因座。该方法特别适合于鉴定不太频繁和罕见的SNV、插入缺失和CNV。因此，在Aim 1.2中，我们使用Aim 1.1的测序数据，用现有的GWAS数据在另外8，958例CRC病例和10，212例对照中插补~ 20 M变异。我们将在总共11，081例病例和12，335例对照中测试CRC风险与变体（测序和插补）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例对照中的3，000个变体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研究调查直接测序和插补变异的基因-环境相互作用，这些研究具有详细的临床和流行病学数据，这些数据已经在研究中得到协调。为了提高目标1和目标2的功效，我们将应用新的统计方法。该项目汇集了一支高素质的多学科研究人员团队，他们在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具有专业知识。我们期望识别出几种新的CRC易感性变异，其效应量大于先前的GWAS发现。这些结果将提高我们对哪些基因影响CRC的理解。这种关于潜在生物学的知识可能对筛查、治疗和疾病预防产生长期影响。

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.