UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER
UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER
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DOI：
10.1093/jamia/ocz105
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发表时间：
2019-12-01
影响因子：
6.4
通讯作者：
Hemingway, Harry
中科院分区：
文献类型：
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作者：
Denaxas, Spiros;Gonzalez-Izquierdo, Arturo;Hemingway, Harry
目的：电子健康记录(EHR)是人类疾病信息的丰富来源，但这些信息结构多样、零碎，使用不同的编码系统进行整理，并用于医学研究以外的目的。我们描述了一种方法，用于开发、验证和共享英国国家结构化EHR的可重复表型，并应用于翻译研究。材料和方法：我们实现了一个基于规则的表型框架，具有多达6种验证方法。我们将我们的框架应用于国家EHR数据源(基于人口的初级保健，所有年龄段)中与英格兰住院和死亡记录相关的1500万人的样本。数据包括连续测量(例如，血压；药物信息；编码的诊断、症状、程序和转诊)，使用5个受控临床术语记录：(1)READ(初级保健，SNOMED-CT[医学临床术语系统化术语]的子集)，(2)国际疾病分类-第九次修订和第十次修订(二级保健诊断和死亡原因)，(3)人口普查和调查外科手术和程序分类，第四次修订(医院外科手术)，以及(4)DM+D处方编码。结果：使用口径表型框架，我们为51种疾病、综合征、生物标志物和生活方式风险因素创建了算法，并提供了多达6种验证方法。电子病历表型在开放获取口径门户网站(https://www.caliberresearch.org/portal))中进行管理，并已被40个国家和国际研究小组在60个同行评议的出版物中使用。结论：我们描述了一种英国电子病历表型组学方法，该方法具有初步的有效性和实用性，是迈向英国电子病历数据在国际上用于健康研究的重要一步。
Objective: Electronic health records (EHRs) are a rich source of information on human diseases, but the information is variably structured, fragmented, curated using different coding systems, and collected for purposes other than medical research. We describe an approach for developing, validating, and sharing reproducible phenotypes from national structured EHR in the United Kingdom with applications for translational research.Materials and Methods: We implemented a rule-based phenotyping framework, with up to 6 approaches of validation. We applied our framework to a sample of 15 million individuals in a national EHR data source (population-based primary care, all ages) linked to hospitalization and death records in England. Data comprised continuous measurements (for example, blood pressure; medication information; coded diagnoses, symptoms, procedures, and referrals), recorded using 5 controlled clinical terminologies: (1) read (primary care, subset of SNOMED-CT [Systematized Nomenclature of Medicine Clinical Terms]), (2) International Classification of Diseases-Ninth Revision and Tenth Revision (secondary care diagnoses and cause of mortality), (3) Office of Population Censuses and Surveys Classification of Surgical Operations and Procedures, Fourth Revision (hospital surgical procedures), and (4) DM+D prescription codes.Results: Using the CALIBER phenotyping framework, we created algorithms for 51 diseases, syndromes, bio-markers, and lifestyle risk factors and provide up to 6 validation approaches. The EHR phenotypes are curated in the open-access CALIBER Portal (https://www.caliberresearch.org/portal) and have been used by 40 national and international research groups in 60 peer-reviewed publications.Conclusions: We describe a UK EHR phenomics approach within the CALIBER EHR data platform with initial evidence of validity and use, as an important step toward international use of UK EHR data for health research.