ConceptWAS: a high-throughput method for early identification of COVID-19 presenting symptoms.
ConceptWAS: a high-throughput method for early identification of COVID-19 presenting symptoms.
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ConceptWAS：一种用于早期识别出现症状的 COVID-19 的高通量方法。
DOI：
10.1101/2020.11.06.20227165
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发表时间：
2020
期刊：
影响因子：
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通讯作者：
Wei,Wei-Qi
中科院分区：
文献类型：
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作者：
Zhao,Juan;Grabowska,MonikaE;Kerchberger,VernEric;Smith,JoshuaC;Eken,HNur;Feng,QiPing;Peterson,JoshF;Rosenbloom,STrent;Johnson,KevinB;Wei,Wei-Qi
识别对COVID-19具有高度特异性的症状将改善对传染病爆发的临床和公共卫生反应。在这里，我们描述了一种高通量的方法-概念范围的关联研究（ConceptWAS），系统地扫描疾病的临床表现，从临床笔记。我们使用这种方法在大流行早期识别COVID-19特有的症状。方法使用范德比尔特大学医学中心（VUMC）的EHR，我们通过自然语言处理管道解析临床笔记以提取临床概念。我们检查了从PCR检测日期的COVID-19阳性和COVID-19阴性患者的注释中得出的概念差异。我们每两周使用累积数据进行ConceptWAS，以早期识别特定的COVID-19症状。结果我们处理了87，753份记录，19，692名患者（1，483名COVID-19阳性）在2020年3月8日至2020年5月27日期间接受了COVID-19 PCR检测。我们发现68个临床概念与COVID-19显著相关。我们发现了与COVID-19风险增加相关的症状，包括“嗅觉缺失”（比值比[OR] = 4.97，95%置信区间[CI] = 3.21-7.50），“发热”（OR = 1.43，95% CI = 1.28-1.59）、“伴咳嗽发热”（OR = 2.29，95% CI = 1.75-2.96）和“味觉丧失”（OR = 5.18，95% CI = 3.02-8.58）。使用ConceptWAS，我们能够检测嗅觉或味觉丧失三周前，他们被疾病控制和预防中心（CDC）列为疾病的症状。ConclusionConceptWAS是一种高通量的方法，用于探索COVID-19等疾病的特定症状，并有望实现EHR驱动的早期疾病表现识别。
ObjectiveIdentifying symptoms highly specific to COVID-19 would improve the clinical and public health response to infectious outbreaks. Here, we describe a high-throughput approach – Concept-Wide Association Study (ConceptWAS) that systematically scans a disease’s clinical manifestations from clinical notes. We used this method to identify symptoms specific to COVID-19 early in the course of the pandemic.MethodsUsing the Vanderbilt University Medical Center (VUMC) EHR, we parsed clinical notes through a natural language processing pipeline to extract clinical concepts. We examined the difference in concepts derived from the notes of COVID-19-positive and COVID-19-negative patients on the PCR testing date. We performed ConceptWAS using the cumulative data every two weeks for early identifying specific COVID-19 symptoms.ResultsWe processed 87,753 notes 19,692 patients (1,483 COVID-19-positive) subjected to COVID-19 PCR testing between March 8, 2020, and May 27, 2020. We found 68 clinical concepts significantly associated with COVID-19. We identified symptoms associated with increasing risk of COVID-19, including “absent sense of smell” (odds ratio [OR] = 4.97, 95% confidence interval [CI] = 3.21–7.50), “fever” (OR = 1.43, 95% CI = 1.28–1.59), “with cough fever” (OR = 2.29, 95% CI = 1.75–2.96), and “ageusia” (OR = 5.18, 95% CI = 3.02–8.58). Using ConceptWAS, we were able to detect loss sense of smell or taste three weeks prior to their inclusion as symptoms of the disease by the Centers for Disease Control and Prevention (CDC).ConclusionConceptWAS is a high-throughput approach for exploring specific symptoms of a disease like COVID-19, with a promise for enabling EHR-powered early disease manifestations identification.