Kehl Kenneth L, Elmarakeby Haitham, Nishino Mizuki, Van Allen Eliezer M, Lepisto Eva M, Hassett Michael J, Johnson Bruce E, Schrag Deborah
Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.
Thoracic Oncology Program, Dana-Farber Cancer Institute, Boston, Massachusetts.
JAMA Oncol. 2019 Oct 1;5(10):1421-1429. doi: 10.1001/jamaoncol.2019.1800.
IMPORTANCE: A rapid learning health care system for oncology will require scalable methods for extracting clinical end points from electronic health records (EHRs). Outside of clinical trials, end points such as cancer progression and response are not routinely encoded into structured data. OBJECTIVE: To determine whether deep natural language processing can extract relevant cancer outcomes from radiologic reports, a ubiquitous but unstructured EHR data source. DESIGN, SETTING, AND PARTICIPANTS: A retrospective cohort study evaluated 1112 patients who underwent tumor genotyping for a diagnosis of lung cancer and participated in the Dana-Farber Cancer Institute PROFILE study from June 26, 2013, to July 2, 2018. EXPOSURES: Patients were divided into curation and reserve sets. Human abstractors applied a structured framework to radiologic reports for the curation set to ascertain the presence of cancer and changes in cancer status over time (ie, worsening/progressing vs improving/responding). Deep learning models were then trained to capture these outcomes from report text and subsequently evaluated in a 10% held-out test subset of curation patients. Cox proportional hazards regression models compared human and machine curations of disease-free survival, progression-free survival, and time to improvement/response in the curation set, and measured associations between report classification and overall survival in the curation and reserve sets. MAIN OUTCOMES AND MEASURES: The primary outcome was area under the receiver operating characteristic curve (AUC) for deep learning models; secondary outcomes were time to improvement/response, disease-free survival, progression-free survival, and overall survival. RESULTS: A total of 2406 patients were included (mean [SD] age, 66.5 [10.8] years; 1428 female [59.7%]; 2170 [90.2%] white). Radiologic reports (n = 14 230) were manually reviewed for 1112 patients in the curation set. In the test subset (n = 109), deep learning models identified the presence of cancer, improvement/response, and worsening/progression with accurate discrimination (AUC >0.90). Machine and human curation yielded similar measurements of disease-free survival (hazard ratio [HR] for machine vs human curation, 1.18; 95% CI, 0.71-1.95); progression-free survival (HR, 1.11; 95% CI, 0.71-1.71); and time to improvement/response (HR, 1.03; 95% CI, 0.65-1.64). Among 15 000 additional reports for 1294 reserve set patients, algorithm-detected cancer worsening/progression was associated with decreased overall survival (HR for mortality, 4.04; 95% CI, 2.78-5.85), and improvement/response was associated with increased overall survival (HR, 0.41; 95% CI, 0.22-0.77). CONCLUSIONS AND RELEVANCE: Deep natural language processing appears to speed curation of relevant cancer outcomes and facilitate rapid learning from EHR data.
重要性:肿瘤学的快速学习型医疗保健系统将需要可扩展的方法来从电子健康记录(EHR)中提取临床终点。在临床试验之外,诸如癌症进展和反应等终点并未常规编码到结构化数据中。 目的:确定深度自然语言处理是否可以从放射学报告中提取相关癌症结局,放射学报告是一种普遍存在但非结构化的EHR数据源。 设计、设置和参与者:一项回顾性队列研究评估了1112例接受肿瘤基因分型以诊断肺癌并于2013年6月26日至2018年7月2日参加丹娜法伯癌症研究所PROFILE研究的患者。 暴露:患者被分为精选集和保留集。人工摘要撰写人员对精选集中的放射学报告应用结构化框架,以确定癌症的存在以及癌症状态随时间的变化(即恶化/进展与改善/反应)。然后训练深度学习模型从报告文本中捕获这些结局,并随后在精选患者的10%留出测试子集中进行评估。Cox比例风险回归模型比较了精选集中无病生存期、无进展生存期和改善/反应时间的人工和机器整理结果,并测量了报告分类与精选集和保留集中总生存期之间的关联。 主要结局和指标:主要结局是深度学习模型的受试者工作特征曲线下面积(AUC);次要结局是改善/反应时间、无病生存期、无进展生存期和总生存期。 结果:共纳入2406例患者(平均[标准差]年龄,66.5[10.8]岁;1428例女性[59.7%];2170例[90.2%]为白人)。对精选集中1112例患者的放射学报告(n = 14230份)进行了人工审核。在测试子集中(n = 109),深度学习模型能够准确识别癌症的存在、改善/反应以及恶化/进展(AUC>0.90)。机器和人工整理得出的无病生存期(机器与人工整理的风险比[HR],1.18;95%CI,0.71 - 1.95)、无进展生存期(HR,1.11;95%CI,0.71 - 1.71)和改善/反应时间(HR,1.03;95%CI,0.65 - 1.64)的测量结果相似。在另外1294例保留集患者的15000份报告中,算法检测到的癌症恶化/进展与总生存期降低相关(死亡HR,4.04;95%CI,2.78 - 5.85),而改善/反应与总生存期增加相关(HR,0.41;95%CI,0.22 - 0.77)。 结论及意义:深度自然语言处理似乎能加快相关癌症结局的整理,并有助于从EHR数据中快速学习。
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