Probing The Dark Matter of the Genome in the NHLBI Family Heart Study

描述(由申请人提供)：最近的大规模GWAS，包括我们在NHLBI家族心脏研究(FamHS)中的研究，已经确定并验证了许多具有GW水平的心脏病表型基因。然而，这些基因座的重要性仍然不确定，因为几乎所有这些基因座似乎都解释了所研究性状的最小方差。一些大规模的外显子组测序项目现在正在病例对照队列中进行，以突出这种“缺失遗传性”背后是否可能是罕见的编码变异。但到目前为止，信号很难与噪声区分开来，部分原因是在人类群体中发现了大量进化上最新的变异(例如，Coventry等人，2010年)。对于这种近乎私人的、特定于谱系的突变，无关的病例对照研究导致了大量个体威力较低的单态变异，这些变异共同对负担测试构成了挑战。最近开发的外显子芯片解决了这个问题的一部分，它专注于“不那么罕见”的外显子变体(出现在多个无关的受试者中)，但忽略了最近进化的特定谱系的外显子变体，费舍尔-赖特模型预测这些外显子变体将具有最大的外显效应。更重要的是，在病例对照测序和外显子芯片研究中，只关注外显子变异，而忽略了调控变异，这可能对许多心血管疾病的定量内表型(例如，血清脂类、细胞因子、肥胖、CAC)最重要。为了弥补这些研究空白，我们建议使用大型的、具有良好特征的家系研究FamHS作为整个外显子组测序(WES)的平台，以及与心血管疾病、动脉粥样硬化和相关的内表型相关的变异体的靶向调控测序(TRS)。FAMHS代表了建议研究的理想资源，具有其他NHLBI队列所不具备的独特特征组合。GAW 17的结果显示(Wilson和Ziegler，2011)，以及我们自己的模拟证实，家庭研究比无关对象的研究具有更大的能力来检测近私人的、特定于谱系的罕见变异，使我们能够比目前的病例对照WES和外显子芯片研究更好地检测新的相关外显子变异。此外，我们的FAMHS家系继续显示出具有挑衅性的强有力的、独立复制的各种心血管性状的连锁证据，GWASSNPs无法解释，这表明这些特定区域可能包含罕见的编码和/或调节变异。我们建议对来自广泛表型的FamHS队列中的所有N=5,763个欧洲裔美国人(在1,253个家庭中)进行两阶段WES TRS实验。在第一阶段，我们将获得3,389个家系EAs的WES信息，包括最大的491个家系(平均家系人数=6.9)，以扫描冠心病、动脉粥样硬化及其危险因素表型(如肥胖、高血压、血脂异常、糖尿病、胰岛素抵抗和炎症)的新的罕见编码/调节变异。在第二阶段，我们将通过对其余独立家系受试者(N=660个家系中的2,374个EA)中所有相关基因座的测序来验证这些区域。我们还将通过进行平行的WES TRS，在N=622(F=221个家庭)的家庭中验证这些发现。

DESCRIPTION (provided by applicant): Recent large scale GWAS, including ours in the NHLBI Family Heart Study (FamHS), have identified and validated many loci for heart disease phenotypes at GW levels of significance. Yet the importance of these loci remains uncertain as nearly all appear to explain minimal amounts of the variance for the traits studied. A number of large scale exome sequencing projects are now being conducted on case-control cohorts to ad- dress whether rare coding variants may be behind this "missing heritability". But so far, signals have been difficult to distinguish from noise, partly due to large number of evolutionarily recent variants found in human populations (e.g. Coventry et al., 2010). For such nearly private, lineage-specific mutations, unrelated case- control studies result in a large number of singleton variants with low individual power, and which collectively pose a challenge to burden testing. The recently developed exome-chip addresses part of this problem by focusing on the "not so rare" exonic variants (seen in multiple unrelated subjects), but neglects the evolutionary recent lineage-specific exonic variants which the Fisher-Wright model predicts would have the greatest penetrance effects. More importantly, the exclusive focus on exonic variation in both case-control sequencing and exome chip studies ignores regulatory variants, which may be most important to many of the quantitative endophenotypes of cardiovascular disease (e.g. serum lipids, cytokines, obesity, CAC). To address these research gaps, we propose using the large, well characterized family study, FamHS, as a platform for Whole Exome Sequencing (WES), plus Targeted Regulatory Sequencing (TRS) for variants associated with cardiovascular disease, atherosclerosis and associated endophenotypes. The FamHS represents the ideal resource for the proposed studies, having a unique combination of features which no other NHLBI cohort possesses. Results from GAW 17 show (Wilson and Ziegler, 2011), and our own simulations confirm, that family studies have greater power to detect near-private, lineage-specific rare variants than studies of unrelated subjects, allowing us greater ability to detect novel associated exonic variants than the current case- control WES and exome chip studies. Further, our FamHS pedigrees continue to show provocatively strong, independently replicated linkage evidence for a variety of cardiovascular traits, unexplained by GWAS SNPs, suggesting that these particular regions may contain rare coding and/or regulatory variants. We propose a two-stage, WES+TRS experiment on all N=5,763 European-Americans (EAs) (in 1,253 families) from the extensively phenotyped FamHS cohort. In Stage 1, we will obtain WES information for 3,389 FamHS EAs comprising the largest 491 pedigrees (mean family size=6.9), to scan for novel rare coding/regulatory variants for CHD, atherosclerosis, and their risk factor phenotypes, such as obesity, hypertension, dyslipidemia, diabetes, insulin resistance, and inflammation. In Stage 2, we will validate these regions by sequencing all implicated loci in the remaining independent FamHS subjects (N=2,374 EAs in 660 families). We will also validate these findings in the N=622 (F=221 families) African-Americans in FamHS by conducting parallel WES+TRS.