Building on GWAS for NHLBI-Diseases: The U.S. CHARGE Consortium - Sequencing (CHARGE-S): CHS

**Note: This substudy phs000667 CHARGE-S Cardiovascular Health Study contains harmonized phenotype data, whole genome, exome, targeted sequencing and exome chip data of a subset of the CHS cohort selected for NHLBI's CHARGE-S CONSORTIUM Project. Summary level phenotypes of the Cardiovascular Health Cohort study participants may be viewed at the top-level study page, phs000287 Cardiovascular Health Study (CHS) Cohort. Individual level phenotype data and molecular data for the top-level Cardiovascular Health Study and its substudies are available by requesting Authorized Access to the Cardiovascular Health Study (CHS) Cohort study [phs000287](./study.cgi?study_id=phs000287). **

Genome-wide association studies (GWAS) have successfully localized multiple loci containing common variations influencing coronary heart disease and its risk factors, but in most cases neither the gene underlying disease susceptibility nor the spectrum of candidate functional variants has been identified. Building on GWAS for NHLBI-diseases: the U.S. CHARGE consortium (the CHARGE sequencing (CHARGE-S) consortium) is a collaborative effort to leverage existing population, laboratory and computational resources to identify susceptibility genes underlying genome-wide significant and well-replicated GWAS findings for heart, lung and blood diseases and their risk factors. The sequencing approach was funded by NHLBI with funds provided by the American Recovery and Reinvestment Act of 2009 (ARRA). The U.S. CHARGE consortium consists of multiple large population-based longitudinal cohort studies, including the Atherosclerosis Risk in Communities (ARIC) Study (N=15,792), the Cardiovascular Health Study (CHS) (N=5,888), and the Framingham Heart Study (FHS) (N=14,428).

The study has taken a two pronged approach to following-up GWAS. First, regional capture targeted sequencing was performed in genomic regions influencing 15 phenotypes to localize causal variants that are responsible for the GWAS signal. The phenotypes examined were atrial fibrillation, blood pressure, body mass index (BMI), bone mineral density, C-reactive protein (CRP), carotid intima-media thickness (IMT), echocardiography, electrocardiogram PR and QRS interval, fasting insulin, hematocrit, pleiotropy, pulmonary function, retinal venule diameter, and stroke. A case-cohort study design was used in which a common reference sample was selected from all three cohorts at baseline. The cohort random sample included 2,000 individuals composed of 1,000 participants from the ARIC study, 500 participants from FHS, and 500 participants from CHS in a 1:1 gender ratio. The comparison groups were either selected cases for discrete phenotypes, or participants drawn from the top and/or bottom tail of the distribution for quantitative phenotypes. The size of each comparison group was 200 individuals. Approximately 2 Mb of the genome was sequenced for the targeted loci.

Second, whole exome capture sequencing and low-pass whole genome sequencing was completed for the cohort random sample and 7 phenotypes for which there were more than 3 GWAS signals in coding regions to detect novel rare and common variants. The phenotypes investigated by whole exome sequencing were age at menopause, electrocardiogram QT interval, fasting blood glucose, fibrinogen level, renal function, Stamler-Kannel-like extremes of risk factors, and waist-to-hip ratio.

Follow-up genotyping using the Illumina HumanExome BeadChip has also been completed. Additional information including variant annotation is available at: [http://www.chargeconsortium.com/main/exomechip](http://www.chargeconsortium.com/main/exomechip).

All sequencing was performed at the Human Genome Sequencing Center at the Baylor College of Medicine, and all genotyping with the HumanExome BeadChip was performed at Cedars-Sinai Medical Center. This study contains the Cardiovascular Health Study (CHS) study subset of CHARGE-S. Additional data from CHARGE-S is also available via dbGaP.

**注意：本亚研究phs000667 CHARGE-S心血管健康研究包含为美国国家心肺血液研究所（National Heart, Lung, and Blood Institute, NHLBI）CHARGE-S联盟项目遴选的心血管健康研究（Cardiovascular Health Study, CHS）队列子集的标准化表型数据、全基因组测序数据、外显子组测序数据、靶向测序数据及外显子芯片数据。心血管健康队列研究参与者的汇总级表型可在顶层研究页面phs000287 心血管健康研究（Cardiovascular Health Study, CHS）队列查看。顶层心血管健康研究及其亚研究的个体级表型数据与分子数据，需通过申请获得心血管健康研究（CHS）队列研究[phs000287](./study.cgi?study_id=phs000287)的授权访问权限方可获取。
全基因组关联研究（Genome-Wide Association Studies, GWAS）已成功定位多个包含影响冠心病及其危险因素的常见变异的基因座，但在多数情况下，既未明确疾病易感相关的功能基因，也未鉴定出候选功能变异的谱系。依托美国国家心肺血液研究所疾病相关全基因组关联研究的美国CHARGE联盟（即CHARGE测序（CHARGE-S）联盟）是一项协作研究项目，旨在整合现有人群、实验室与计算资源，识别心脏、肺及血液疾病及其危险因素的全基因组显著且已被重复验证的全基因组关联研究发现背后的易感基因。本测序项目由美国国家心肺血液研究所通过2009年《美国复苏与再投资法案》（American Recovery and Reinvestment Act of 2009, ARRA）提供资金支持。美国CHARGE联盟包含多项大型基于人群的纵向队列研究，包括社区动脉粥样硬化风险（Atherosclerosis Risk in Communities, ARIC）研究（样本量N=15792）、心血管健康研究（Cardiovascular Health Study, CHS）（样本量N=5888）及弗雷明汉心脏研究（Framingham Heart Study, FHS）（样本量N=14428）。
本研究采用双路径策略跟进全基因组关联研究发现。其一，针对影响15种表型的基因组区域开展区域捕获靶向测序，以定位介导全基因组关联研究信号的因果变异。本次分析的表型包括心房颤动、血压、体重指数（Body Mass Index, BMI）、骨密度、C反应蛋白（C-reactive Protein, CRP）、颈动脉内膜中层厚度（Carotid Intima-Media Thickness, IMT）、超声心动图、心电图PR间期与QRS间期、空腹胰岛素、血细胞比容、多效性、肺功能、视网膜静脉直径及脑卒中。本研究采用病例队列研究设计，基线时从全部3个队列中选取共同参考样本。队列随机样本共包含2000名个体，其中1000名来自ARIC研究、500名来自弗雷明汉心脏研究、500名来自心血管健康研究，性别比例为1:1。对照组要么为离散表型的确诊病例，要么为定量表型分布上下极端尾端的参与者，每组对照组样本量均为200名。本研究对靶向基因座所在的约2Mb基因组区域进行了测序。
其二，针对队列随机样本及编码区存在超过3个全基因组关联研究信号的7种表型，完成了全外显子组捕获测序与低覆盖度全基因组测序，以检测新型罕见变异与常见变异。通过全外显子组测序分析的表型包括绝经年龄、心电图QT间期、空腹血糖、纤维蛋白原水平、肾功能、Stamler-Kannel样危险因素极端值及腰臀比。
此外，本研究还完成了基于Illumina人类外显子组芯片（Illumina HumanExome BeadChip）的跟进基因分型工作。包括变异注释在内的更多信息可访问：[http://www.chargeconsortium.com/main/exomechip](http://www.chargeconsortium.com/main/exomechip)。
所有测序工作均由贝勒医学院人类基因组测序中心完成，而Illumina人类外显子组芯片的基因分型工作则由西达赛奈医疗中心完成。本研究包含CHARGE-S项目中的心血管健康研究（CHS）队列子集。CHARGE-S项目的其他数据也可通过dbGaP获取。