Genomic Wide Association Study of Colorectal Cancer

描述（由申请人提供）：使用NCI-supported Cooperative Family Registry for Colorectal Cancer Studies（Colon CFR）的现有资源，提出一项两阶段的结直肠癌全基因组关联研究。具体而言，我们提出以下目标。目的1：使用基于人群的病例对照研究设计进行CRC的全基因组关联研究。这一目标将通过对992例基于人群的病例和超过1，020例年龄和家族史分层的基于人群的对照进行基因分型来实现，这些病例和对照通过Colon CFR招募，其中基因组中平均每5 kb间隔> 500，000个SNP。仅纳入微卫星稳定（MSS）或微卫星不稳定性低（MSI-L）表型和错配修复（MMR）突变阴性病例。主要分析包括单SNP关联测试和基于单体型的分析，这些分析代表了与人类基因组中发现的所有~ 400万种常见变异的关联。SNP和单倍型将使用基于统计学显著性的新选择策略进行排序，并将先前的基因组数据并入分层建模程序中，以产生更可能代表“真阳性”和“重要”关联的SNP子集。目的2：使用额外的SNP在相同的病例对照CRC人群中证实正相关性。使用通过目标1生成的信息，我们将使用来自每个区域的平均4个额外SNP来确认1，000个最重要区域中的SNP与同一研究样本中的CRC风险之间的任何关联。SNPs（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），以及选择具有已知或预测的功能效应的变体（例如，先前分别涉及CRC或非同义SNP）。将对额外的SNP进行基因分型，并使用目标1中分析的所有病例和对照确定相关性。目的3：在第二个独立的基于家庭的病例对照CRC人群中验证阳性相关性。使用目标1和2的信息，将为每个区域确定最具信息性的SNP，并在612个额外的家族性MSS或MSI-L病例和950个同代亲属对照（未受影响的兄弟姐妹，半同胞和堂兄弟姐妹）中验证关联。将使用目标1、2和3中分析的所有病例和对照确定相关性。为了确定与CRC风险最密切相关的变异，将联合进行单变异分析和单倍型特异性检测，考虑来自两个阶段的关联证据以及与环境暴露的相互作用。目标4：将在目标3的家族中所有可用的谱系成员中验证正相关性。最终分析将纳入所有可用谱系成员（约3，000名受试者，包括病例和对照）的额外基因分型，以获得显著性的基因组区域/SNP子集，包括家庭内和家庭之间受影响对之间的单倍型共享测试。

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.