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一种用于估计转移性乳腺癌患者真实世界无进展生存期的深度学习工作流程:使用去识别化电子健康记录的研究

A Deep Learning-Enabled Workflow to Estimate Real-World Progression-Free Survival in Patients With Metastatic Breast Cancer: Study Using Deidentified Electronic Health Records.

作者信息

Varma Gowtham, Yenukoti Rohit Kumar, Kumar M Praveen, Ashrit Bandlamudi Sai, Purushotham K, Subash C, Ravi Sunil Kumar, Kurien Verghese, Aman Avinash, Manoharan Mithun, Jaiswal Shashank, Anand Akash, Barve Rakesh, Thiagarajan Viswanathan, Lenehan Patrick, Soefje Scott A, Soundararajan Venky

机构信息

Department of Clinical Sciences, Nference, 4th Floor, Indiqube, Golf View Campus Tower-2, 22, 3rd Cross Rd, Murugeshpalya, S R Layout, Bangalore, 560017, India, 91 8728831787.

Department of Data Science and Engineering, Nference, Bangalore, India.

出版信息

JMIR Cancer. 2025 May 15;11:e64697. doi: 10.2196/64697.


DOI:10.2196/64697
PMID:40372953
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12097284/
Abstract

BACKGROUND: Progression-free survival (PFS) is a crucial endpoint in cancer drug research. Clinician-confirmed cancer progression, namely real-world PFS (rwPFS) in unstructured text (ie, clinical notes), serves as a reasonable surrogate for real-world indicators in ascertaining progression endpoints. Response evaluation criteria in solid tumors (RECIST) is traditionally used in clinical trials using serial imaging evaluations but is impractical when working with real-world data. Manual abstraction of clinical progression from unstructured notes remains the gold standard. However, this process is a resource-intensive, time-consuming process. Natural language processing (NLP), a subdomain of machine learning, has shown promise in accelerating the extraction of tumor progression from real-world data in recent years. OBJECTIVES: We aim to configure a pretrained, general-purpose health care NLP framework to transform free-text clinical notes and radiology reports into structured progression events for studying rwPFS on metastatic breast cancer (mBC) cohorts. METHODS: This study developed and validated a novel semiautomated workflow to estimate rwPFS in patients with mBC using deidentified electronic health record data from the Nference nSights platform. The developed workflow was validated in a cohort of 316 patients with hormone receptor-positive, human epidermal growth factor receptor-2 (HER-2) 2-negative mBC, who were started on palbociclib and letrozole combination therapy between January 2015 and December 2021. Ground-truth datasets were curated to evaluate the workflow's performance at both the sentence and patient levels. NLP-captured progression or a change in therapy line were considered outcome events, while death, loss to follow-up, and end of the study period were considered censoring events for rwPFS computation. Peak reduction and cumulative decline in Patient Health Questionnaire-8 (PHQ-8) scores were analyzed in the progressed and nonprogressed patient subgroups. RESULTS: The configured clinical NLP engine achieved a sentence-level progression capture accuracy of 98.2%. At the patient level, initial progression was captured within ±30 days with 88% accuracy. The median rwPFS for the study cohort (N=316) was 20 (95% CI 18-25) months. In a validation subset (n=100), rwPFS determined by manual curation was 25 (95% CI 15-35) months, closely aligning with the computational workflow's 22 (95% CI 15-35) months. A subanalysis revealed rwPFS estimates of 30 (95% CI 24-39) months from radiology reports and 23 (95% CI 19-28) months from clinical notes, highlighting the importance of integrating multiple note sources. External validation also demonstrated high accuracy (92.5% sentence level; 90.2% patient level). Sensitivity analysis revealed stable rwPFS estimates across varying levels of missing source data and event definitions. Peak reduction in PHQ-8 scores during the study period highlighted significant associations between patient-reported outcomes and disease progression. CONCLUSIONS: This workflow enables rapid and reliable determination of rwPFS in patients with mBC receiving combination therapy. Further validation across more diverse external datasets and other cancer types is needed to ensure broader applicability and generalizability.

摘要

背景:无进展生存期(PFS)是癌症药物研究中的关键终点。临床医生确认的癌症进展,即在非结构化文本(即临床记录)中的真实世界PFS(rwPFS),在确定进展终点时可作为真实世界指标的合理替代指标。实体瘤疗效评价标准(RECIST)传统上用于使用系列影像评估的临床试验,但在处理真实世界数据时不切实际。从非结构化记录中人工提取临床进展仍然是金标准。然而,这个过程资源密集、耗时。自然语言处理(NLP)作为机器学习的一个子领域,近年来在加速从真实世界数据中提取肿瘤进展方面显示出前景。 目的:我们旨在配置一个预训练的通用医疗保健NLP框架,将自由文本临床记录和放射学报告转化为结构化进展事件,以研究转移性乳腺癌(mBC)队列中的rwPFS。 方法:本研究开发并验证了一种新颖的半自动化工作流程,使用来自Nference nSights平台的去识别化电子健康记录数据估计mBC患者的rwPFS。所开发的工作流程在316例激素受体阳性、人表皮生长因子受体2(HER-2)阴性的mBC患者队列中进行了验证,这些患者在2015年1月至2021年12月期间开始接受哌柏西利和来曲唑联合治疗。精心整理了真实数据集,以在句子和患者层面评估工作流程的性能。NLP捕获的进展或治疗线的变化被视为结局事件,而死亡、失访和研究期结束被视为rwPFS计算的删失事件。在进展和未进展的患者亚组中分析了患者健康问卷-8(PHQ-8)评分的峰值降低和累积下降情况。 结果:配置的临床NLP引擎在句子层面的进展捕获准确率达到98.2%。在患者层面,初始进展在±30天内被捕获,准确率为88%。研究队列(N = 316)的中位rwPFS为20(95%CI 18 - 25)个月。在一个验证亚组(n = 100)中,通过人工整理确定的rwPFS为25(95%CI 15 - 3

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/2128fa7b0b58/cancer-v11-e64697-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/19595206ccf3/cancer-v11-e64697-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/7b30e14c218f/cancer-v11-e64697-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/6c92e0fd377c/cancer-v11-e64697-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/efd2510c4890/cancer-v11-e64697-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/2128fa7b0b58/cancer-v11-e64697-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/19595206ccf3/cancer-v11-e64697-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/7b30e14c218f/cancer-v11-e64697-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/6c92e0fd377c/cancer-v11-e64697-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/efd2510c4890/cancer-v11-e64697-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d255/12097284/2128fa7b0b58/cancer-v11-e64697-g005.jpg

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本文引用的文献

[1]
Patient-Reported Outcome Measures in Cancer Care: An Updated Systematic Review and Meta-Analysis.

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[2]
Overview of approaches to estimate real-world disease progression in lung cancer.

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Analysis of a Real-World Progression Variable and Related Endpoints for Patients with Five Different Cancer Types.

Adv Ther. 2022-6

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Building a best-in-class automated de-identification tool for electronic health records through ensemble learning.

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Oncologist. 2021-7

[8]
Comparative effectiveness of first-line palbociclib plus letrozole versus letrozole alone for HR+/HER2- metastatic breast cancer in US real-world clinical practice.

Breast Cancer Res. 2021-3-24

[9]
Use of Real-World Evidence to Support FDA Approval of Oncology Drugs.

Value Health. 2020-10

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Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis.

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