High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributions to Human Disease: Genotyping of the ZOE 2.0 Pediatric Oral Health Cohort Study (Divaris)

儿童早期龋病(ECC)是儿童最常见的慢性疾病，是一个长期存在的临床和公共卫生问题。在美国，ECC的患病率在过去20年里增加了15%，根据最新的国家数据，2-5岁的儿童中有28%受到影响。幼儿保育可对儿童的总体健康和福祉产生严重的后遗症，并对其家庭、社区和卫生系统产生重要的社会和经济影响。龋病是一种多因素疾病，有很大的遗传成分，估计在40%-60%之间(使用我们自己的试点数据为43%)，但对特定的遗传因素知之甚少。到目前为止，还没有对ECC的传统定义(包括72个月以下儿童因龋齿而受影响、修复或丢失的牙面)进行全面评估。对1300名3-12岁的欧洲血统儿童进行了儿童龋齿的第一次GWA研究--这项研究没有发现任何显著的信号，但提名了7个基因，其中2个在儿童和成人的后续研究中显示出关联的证据。最近的一项GWAS荟萃分析在17,033名欧洲血统的儿童中发现了一个儿童龋齿的重要基因座。在这里，我们建议进行一次大规模的幼儿保育中心的GWAS，涉及6,000名3至5岁儿童的多种族社区样本。根据NIH/NIDCR U01-DE025046，我们对北卡罗来纳州Head Start计划注册的6,000多名儿童的社区样本进行了全面的临床牙科特征分析。我们使用最新的国际龋病诊断系统(ICDAS)视觉诊断标准来定义ECC特征，获得了龋齿的牙面水平数据。我们已经从几乎所有接受检查的参与者那里获得了唾液样本，并一直在从他们身上提取超过足够的DNA产量。收集了大量其他行为风险因素和感兴趣的社会人口学信息。还收集并储存了牙龈上菌斑样本，以用于未来的微生物组分析，该分析将单独提供资金。为了确定与ECC相关的遗传变异，我们建议对ECC及其相关性状进行跨种族GWA，利用高密度基因分型并随后归因于最新的参考小组。我们将使用先进的统计方法来利用种族/民族群体之间的基因结构差异。随后，我们将利用可公开获得的儿童早期和成人龋齿的GWAS数据，来确定我们研究中确定的基因座、基因和基因集/途径的种族/民族和年龄组泛化/可转移性。我们团队在进行遗传流行病学研究方面的经验、研究人员团队之间的持续合作以及已经收集的信息的广度和质量，创造了开展这项重要调查的独特机会，并推进了龋齿基因组学的知识基础。这项研究将提高我们对ECC基因组病因学的理解，这是减少幼儿人群中疾病负担的关键知识，包括那些在研究中代表性不足的人群。

Early childhood caries (ECC) is the most common chronic disease of childhood and a persistent clinical and public health problem. The prevalence of ECC in the US increased by 15% during the last 2 decades, and according to the most recent national data 28% of children ages 2-5 are affected. ECC can have severe sequelae for children's general health and well-being and confers important social and economic impacts on their families, communities, and the health system. Caries is a multifactorial disease with a substantial genetic component, which is estimated between 40-60% (43% using our own pilot data), but little is known regarding specific genetic factors. To-date, a GWAS of the traditional definition of ECC (including tooth surfaces affected, restored or missing due to dental caries in children younger than 72 months) has not been done. The first GWAS of childhood caries was conducted among 1,300 3-12-year-old European-ancestry children—that study did not identify any significant signals but nominated 7 genes, 2 of which showed evidence of association in follow-up studies among children and adults. A recent GWAS meta-analysis identified one significant locus for childhood caries, among 17,033 children of European ancestry. Here, we propose to conduct a large-scale GWAS of ECC involving a multi-ethnic community-based sample of 6,000 children ages 3 to 5. Under NIH/NIDCR U01-DE025046, we have undertaken comprehensive clinical dental characterization of a community-based sample of over 6,000 children enrolled in Head Start programs in North Carolina. We have obtained tooth-surface level data of dental caries experience using the latest International Caries Diagnosis System (ICDAS) visual diagnostic criteria to define ECC traits. We have obtained saliva samples from virtually all examined participants and have been extracting more-than-adequate DNA yields from them. A wealth of additional behavioral risk factor and socio-demographic information of interest has been collected. Supragingival plaque samples have also been collected and stored to be used in future microbiome analyses that will be funded separately. To identify genetic variants that are associated with ECC, we propose to conduct a trans-ethnic GWAS of ECC and related traits, utilizing high- density genotyping and subsequent imputation to the most current reference panels. We will use advanced statistical approaches to leverage differences in genetic structure between racial/ethnic groups. Subsequently, we will utilize publicly available GWAS data of early childhood and adult caries, to determine the racial/ethnic and age-group generalization/transferability of loci, genes, and gene sets/pathways identified in our study. Our group's experience in conducting genetic epidemiologic studies, ongoing collaboration among the investigators' team and the breadth and quality of the already-collected information, create a unique opportunity to carry out this important investigation and advance the knowledge base of genomics of dental caries. The study will improve our understanding of ECC's genomic etiology, key knowledge to reduce the burden of disease in populations of young children, including those underrepresented in research.