Genomic Wide Association Study of Colorectal Cancer

描述(由申请人提供)：利用NCI支持的结直肠癌研究合作家庭登记(Colon CFR)的既定资源，提出一项关于结直肠癌的两阶段全基因组关联研究。具体地说，我们提出了以下目标。目的1：采用基于人群的病例对照研究设计，对结直肠癌进行全基因组相关性研究。这一目标将通过对992例基于人群的病例和通过科隆CFR招募的1,020多名按年龄和家族病史分层的人群对照进行基因分型来实现，基因组中平均每5kb有1个500,000个SNPs相隔。只包括微卫星稳定(MSS)或微卫星不稳定低(MSI-L)表型和错配修复(MMR)突变阴性的病例。初步分析包括单SNP关联测试和基于单倍型的分析，这些分析代表了与人类基因组中发现的所有约400万种常见变异的关联。SNP和单倍型将使用一种基于统计显著性的新选择策略进行排序，并将先前的基因组数据合并到分层建模程序中，以产生更可能代表“真正积极的”和“重要的”关联的SNP子集。目的2：在同一病例对照的结直肠癌人群中，将使用额外的单核苷酸多态来证实正相关性。利用AIM 1产生的信息，我们将利用每个地区平均另外4个SNP，在同一研究样本中确认1,000个最重要地区的SNP与结直肠癌风险之间的任何关联。SNP(htSNPs或tSNPs)的选择将基于来自国际HapMap项目和其他类似项目(例如PerLegen)的信息，以及选择具有已知或预测功能效应的变体(例如，先前分别涉及CRC或非同义SNPs)。将对额外的SNPs进行基因分型，并使用目标1中分析的所有病例和对照来确定关联。目标3：将在第二个独立的以家庭为基础的病例对照CRC人群中验证积极关联。利用AIMS 1和AIMS 2中的信息，将确定每个区域和关联中信息量最大的SNPs，在612例额外的家族性多发性硬化或微卫星综合征-L病例和950名同代亲属对照(未受影响的兄弟姐妹、同父异母的兄弟姐妹和堂兄弟姐妹)中得到验证。将利用目标1、2和3中分析的所有病例和对照来确定相关性。为了确定与结直肠癌风险最相关的变异，将联合进行单变量分析和单倍型特定测试，考虑到两个阶段的关联证据，以及与环境暴露的相互作用。目的4：将在AIM 3中所有可用的家系成员中验证正相关性。最终分析将包括对所有可用家系成员(总共约3,000名受试者，包括病例和对照)进行额外的基因分型，以获得有意义的基因组区域/SNP子集，包括测试家庭内和家庭之间受影响对之间的单倍型共享。

DESCRIPTION (provided by applicant): pose a two-stage genome-wide association study of colorectal cancer using the established resources of the NCI-supported Cooperative Family Registry for Colorectal Cancer Studies (Colon CFR). Specifically, we propose the following Aims. Aim 1: Perform a genome-wide association study for CRC using a population-based case-control study design. This aim will be accomplished by genotyping 992 population-based cases and over 1,020 age - and family history- stratified population-based controls recruited through the Colon CFR with >500,000 SNPs spaced on average 1 every 5 kb in the genome. Only microsatellite stable (MSS) or microsatellite instability low (MSI-L) phenotype and mismatch repair (MMR) mutation negative cases will be included. The primary analysis includes single-SNP association tests and haplotype-based analyses that represent associations with all ~4 million common variants found in the human genome. SNPs and haplotypes will be rank-ordered using a novel selection strategy based on statistical significance and the incorporation of prior genomic data into a hierarchical modeling procedure to yield a subset of SNPs that is more likely to represent "true positive" and "important" associations. Aim 2: Positive associations will be confirmed in the same case-control CRC population using additional SNPs. Using the information generated through Aim 1, we will confirm any association between SNPs in the 1,000 most significant regions and CRC risk in this same study sample using on average 4 additional SNPs from each region. Selection of SNPs (either htSNPs or tSNPs), will be based on information from the International HapMap Project and other similar projects (e.g., Perlegen), as well as selecting variants with known or predicted functional effects (e.g., previously implicated in CRC or non-synonymous SNPs, respectively). The additional SNPs will be genotyped and associations determined using all cases and controls analyzed in Aim 1. Aim 3: Positive associations will be validated in a second independent family-based case-control CRC population. Using information from Aims 1 and 2, the most informative SNPs will be identified for each region and association validated in 612 additional familial MSS or MSI-L cases and 950 same-generation relative controls (unaffected siblings, half-siblings, and cousins). Association will be determined using all cases and controls analyzed in Aims 1, 2 and 3. To identify variants that are most strongly associated with CRC risk, single-variant analyses and haplotype-specific tests will be performed jointly considering evidence of association from both stages, and interactions with environmental exposures. Aim 4: Positive associations will be validated among all available pedigree members in families from Aim 3. A final analysis will incorporate additional genotyping on all available pedigree members (~3,000 total subjects, including cases and controls) for the subset of genomic regions/SNPs attaining significance, including tests of haplotype sharing amongst affected pairs within and between families.