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，已经在GW显著性水平上鉴定和验证了许多心脏病表型的基因座。然而，这些基因座的重要性仍然不确定，因为几乎所有的基因座似乎都能解释所研究性状的最小方差。目前正在对病例对照组进行一些大规模外显子组测序项目，以确定罕见的编码变异是否可能是这种“缺失的遗传性”的原因。但到目前为止，信号一直难以与噪声区分开，部分原因是在人类群体中发现了大量进化上最近的变体（例如，Coventry等人，2010年）。对于这种几乎私密的谱系特异性突变，不相关的病例对照研究导致大量个体功效低的单例变异，并且这些变异共同对负荷测试构成挑战。最近开发的外显子组芯片通过关注“不那么罕见”的外显子变体（在多个不相关的受试者中可见）解决了这个问题的一部分，但忽略了Fisher-Wright模型预测的进化最近的谱系特异性外显子变体将具有最大的突变效应。更重要的是，在病例对照测序和外显子组芯片研究中对外显子变异的专门关注忽略了调节变体，这可能对心血管疾病的许多定量内表型（例如，血脂、细胞因子、肥胖、CAC）最重要。 为了解决这些研究空白，我们建议使用大型的，充分表征的家族研究，FamHS，作为全外显子组测序（WES）的平台，加上靶向调控测序（TRS）与心血管疾病，动脉粥样硬化和相关内在表型相关的变异。FamHS代表了拟议研究的理想资源，具有其他NHLBI队列所不具备的独特功能组合。来自GAW 17的结果显示（Wilson和齐格勒，2011），并且我们自己的模拟证实，家族研究比无关受试者的研究具有更大的能力来检测近私有的、谱系特异性的罕见变体，从而使我们比当前病例对照WES和外显子组芯片研究更有能力检测新的相关外显子变体。此外，我们的FamHS家系继续显示出对各种心血管性状的强有力的、独立复制的连锁证据，这是GWAS SNP无法解释的，表明这些特定区域可能含有罕见的编码和/或调控变体。我们提出了一个两阶段，WES+TRS实验的所有N=5,763欧洲裔美国人（EA）（在1,253个家庭）从广泛的表型FamHS队列。在第1阶段，我们将获得3，389个FamHS EA的WES信息，包括最大的491个家系（平均家族规模=6.9），以扫描CHD、动脉粥样硬化及其风险因素表型（如肥胖、高血压、血脂异常、糖尿病、胰岛素抵抗和炎症）的新型罕见编码/调控变体。在第2阶段，我们将通过对剩余的独立FamHS受试者（660个家庭中的N= 2，374个EA）中的所有相关基因座进行测序来验证这些区域。我们还将通过进行平行WES+TRS，在FamHS中的N=622（F=221个家庭）非裔美国人中验证这些发现。

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.