Finding Genomic Profiles of COVID-19 Phenotypes from the EHR

摘要：在全世界寻找新冠肺炎疫情的有效治疗方法和潜在疗法的同时， 能够整合来自多个不同来源的数据、洞察力和专业知识将是完全 了解感染的患者结局。促进这类研究的关键是有凝聚力和 安全的研究环境，使临床医生、研究人员、数据科学家和技术专家能够 多个组织携手合作，实现更好地了解新冠肺炎症状的共同目标， 相关的风险因素和成功的治疗方法。在已有的教职员工和基础设施的基础上建设 通过麻省总医院的Emerge IV临床中心，我们提议建立一个COVID- 19 Biobank门户，为构建符合以下标准的真正协作环境奠定基础 患者隐私，并提供一套通用的生物信息工具和标准化的IT方法来进行分期 数据和分析。我们将通过实现以下三个具体目标来实现这一点，这些目标是对 Parent Grant的目标I是：“多基因风险评分将使我们能够根据以下因素对新兴参与者进行分层 常见复杂性状的遗传风险“，在本补充资料中将重点介绍与疾病严重程度有关的风险因素 新冠肺炎病在我们的生物库参与者中。我们建议利用我们的专业知识来完成具体的 目标：目标1：我们将创建一个以新冠肺炎为中心的生物库门户，允许机构通过以下方式通用 制定了适当的研究协议，其中患者队列可以使用易于评估和 转化的数据，并通过这些数据可以获得基因组样本。目标二：对新冠肺炎进行补充 生物库门户网站，包含新冠肺炎的测试结果、表型风险因素、症状和结果 使用自然语言处理从电子健康记录(EHR)中的数据派生而来 计算表型，并通过执行图表审查来验证严重性指数和临床结果 在新冠肺炎感染患者中发现。目标3：遗传数据(阵列和序列数据)将有助于 Emerge IV网络和国际L新冠肺炎宿主遗传学倡议(https://covid19hg.org)这样的 该数据可用于计算全基因组风险关联研究的多基因风险分数(PR 在我们的数据集和数据集中，新冠肺炎预后的表型和患者预后以及多基因风险分数(PR) 在与他人的合作中。

Abstract: As the world searches for effective treatments and potential cures for the COVID-19 pandemic, the ability to consolidate data, insights, and expertise from many disparate sources will be key to fully understanding the patient outcomes of the infection. Key to facilitating this type of research is a cohesive and secure research environment that enables clinicians, researchers, data scientists, and technologists from multiple organizations to work together with a common goal of better understanding COVID-19 symptoms, associated risk factors, and successful therapies. Building upon faculty, staff and infrastructure already in place through the eMERGE IV Clinical Center at Mass General Brigham, we are proposing the creation of a COVID- 19 Biobank Portal to provide a foundation for building a truly collaborative environment that is compliant with patient privacy and offers a common set of bioinformatic tools and a standardized IT approach for the staging of data and analyses. We will do this by accomplishing the following three Specific Aims which supplement the parent grant’s Aim I which is: “Polygenic risks scores will allow us to stratify eMERGE participants based on genetic risk for common complex traits” which will focus in this supplement on risk factors for severity of COVID-19 illness in our biobank participants. We propose to build on our expertise to accomplish the specific aims: Aim 1: We will create a COVID-19 Centric Biobank Portal that allows general institutional use with proper research agreements in place where patient cohorts can be studied using easily assessable and transformed data and through which genomic samples can be obtained. Aim 2: Supplement the COVID-19 Biobank Portal with test results, phenotype risk factors, symptoms, and outcomes for COVID-19 which are derived from data in the electronic health record (EHR) by using natural language processing and computational phenotypes and by performing chart reviews to validate severity indices and clinical outcomes found in COVID-19 infected patients. Aim 3: Genetic data (array and sequence data) will be contributed to the eMERGE IV network and to the International l COVID-19 Host Genetics Initiative (https://covid19hg.org) such that data can be used to calculate polygenic risk scores (PRS) for genome-wide association studies of risk phenotypes and patient outcomes and polygenic risk scores (PRS) for COVID-19 outcomes in our dataset and in collaborations with others.