JCO Clinical Cancer Informatics最新文献

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Value of Real-World Evidence for Treatment Selection: A Case Study in Colon Cancer. 真实世界证据对治疗选择的价值:结肠癌案例研究。
IF 4.2
JCO Clinical Cancer Informatics Pub Date : 2024-05-01 DOI: 10.1200/CCI.23.00186
Lingjie Shen, Anja van Gestel, Peter Prinsen, Geraldine Vink, Felice N van Erning, Gijs Geleijnse, Maurits Kaptein
{"title":"Value of Real-World Evidence for Treatment Selection: A Case Study in Colon Cancer.","authors":"Lingjie Shen, Anja van Gestel, Peter Prinsen, Geraldine Vink, Felice N van Erning, Gijs Geleijnse, Maurits Kaptein","doi":"10.1200/CCI.23.00186","DOIUrl":"https://doi.org/10.1200/CCI.23.00186","url":null,"abstract":"<p><strong>Purpose: </strong>Real-world evidence (RWE)-derived from analysis of real-world data (RWD)-has the potential to guide personalized treatment decisions. However, because of potential confounding, generating valid RWE is challenging. This study demonstrates how to responsibly generate RWE for treatment decisions. We validate our approach by demonstrating that we can uncover an existing adjuvant chemotherapy (ACT) guideline for stage II and III colon cancer (CC)-which came about using both data from randomized controlled trials and expert consensus-solely using RWD.</p><p><strong>Methods: </strong>Data from the population-based Netherlands Cancer Registry from a total of 27,056 patients with stage II and III CC who underwent curative surgery were analyzed to estimate the overall survival (OS) benefit of ACT. Focusing on 5-year OS, the benefit of ACT was estimated for each patient using G-computation methods by adjusting for patient and tumor characteristics and estimated propensity score. Subsequently, on the basis of these estimates, an ACT decision tree was constructed.</p><p><strong>Results: </strong>The constructed decision tree corresponds to the current Dutch guideline: patients with stage III or stage II with T stage 4 should receive surgery and ACT, whereas patients with stage II with T stage 3 should only receive surgery. Interestingly, we do not find sufficient RWE to conclude against ACT for stage II with T stage 4 and microsatellite instability-high (MSI-H), a recent addition to the current guideline.</p><p><strong>Conclusion: </strong>RWE, if used carefully, can provide a valuable addition to our construction of evidence on clinical decision making and therefore ultimately affect treatment guidelines. Next to validating the ACT decisions advised in the current Dutch guideline, this paper suggests additional attention should be paid to MSI-H in future iterations of the guideline.</p>","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Use of Natural Language Understanding to Facilitate Surgical De-Escalation of Axillary Staging in Patients With Breast Cancer. 利用自然语言理解促进乳腺癌患者腋窝分期的手术切除。
IF 4.2
JCO Clinical Cancer Informatics Pub Date : 2024-05-01 DOI: 10.1200/CCI.23.00177
Neil Carleton, Gilan Saadawi, Priscilla F McAuliffe, Atilla Soran, Steffi Oesterreich, Adrian V Lee, Emilia J Diego
{"title":"Use of Natural Language Understanding to Facilitate Surgical De-Escalation of Axillary Staging in Patients With Breast Cancer.","authors":"Neil Carleton, Gilan Saadawi, Priscilla F McAuliffe, Atilla Soran, Steffi Oesterreich, Adrian V Lee, Emilia J Diego","doi":"10.1200/CCI.23.00177","DOIUrl":"10.1200/CCI.23.00177","url":null,"abstract":"<p><strong>Purpose: </strong>Natural language understanding (NLU) may be particularly well equipped for enhanced data capture from the electronic health record given its examination of both content-driven and context-driven extraction.</p><p><strong>Methods: </strong>We developed and applied a NLU model to examine rates of pathological node positivity (pN+) and rates of lymphedema to determine whether omission of routine axillary staging could be extended to younger patients with estrogen receptor-positive (ER+)/cN0 disease.</p><p><strong>Results: </strong>We found that rates of pN+ and arm lymphedema were similar between patients age 55-69 years and ≥70 years, with rates of lymphedema exceeding rates of pN+ for clinical stage T1c and smaller disease.</p><p><strong>Conclusion: </strong>Data from our NLU model suggest that omission of sentinel lymph node biopsy might be extended beyond Choosing Wisely recommendations, limited to those older than 70 years and to all postmenopausal women with early-stage ER+/cN0 disease. These data support the recently reported SOUND trial results and provide additional granularity to facilitate surgical de-escalation.</p>","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11180980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141082837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Extraction and Imputation of Eastern Cooperative Oncology Group Performance Status From Unstructured Oncology Notes Using Language Models. 使用语言模型从非结构化肿瘤学笔记中提取和推算东部合作肿瘤学组的表现状态。
IF 3.3
JCO Clinical Cancer Informatics Pub Date : 2024-05-01 DOI: 10.1200/CCI.23.00269
Wenxin Xu, Bowen Gu, William E Lotter, Kenneth L Kehl
{"title":"Extraction and Imputation of Eastern Cooperative Oncology Group Performance Status From Unstructured Oncology Notes Using Language Models.","authors":"Wenxin Xu, Bowen Gu, William E Lotter, Kenneth L Kehl","doi":"10.1200/CCI.23.00269","DOIUrl":"10.1200/CCI.23.00269","url":null,"abstract":"<p><strong>Purpose: </strong>Eastern Cooperative Oncology Group (ECOG) performance status (PS) is a key clinical variable for cancer treatment and research, but it is usually only recorded in unstructured form in the electronic health record. We investigated whether natural language processing (NLP) models can impute ECOG PS using unstructured note text.</p><p><strong>Materials and methods: </strong>Medical oncology notes were identified from all patients with cancer at our center from 1997 to 2023 and divided at the patient level into training (approximately 80%), tuning/validation (approximately 10%), and test (approximately 10%) sets. Regular expressions were used to extract explicitly documented PS. Extracted PS labels were used to train NLP models to impute ECOG PS (0-1 <i>v</i> 2-4) from the remainder of the notes (with regular expression-extracted PS documentation removed). We assessed associations between imputed PS and overall survival (OS).</p><p><strong>Results: </strong>ECOG PS was extracted using regular expressions from 495,862 notes, corresponding to 79,698 patients. A Transformer-based Longformer model imputed PS with high discrimination (test set area under the receiver operating characteristic curve 0.95, area under the precision-recall curve 0.73). Imputed poor PS was associated with worse OS, including among notes with no explicit documentation of PS detected (OS hazard ratio, 11.9; 95% CI, 11.1 to 12.8).</p><p><strong>Conclusion: </strong>NLP models can be used to impute performance status from unstructured oncologist notes at scale. This may aid the annotation of oncology data sets for clinical outcomes research and cancer care delivery.</p>","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11492207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phenotyping Hepatic Immune-Related Adverse Events in the Setting of Immune Checkpoint Inhibitor Therapy. 免疫检查点抑制剂治疗过程中肝脏免疫相关不良事件的表型分析
IF 3.3
JCO Clinical Cancer Informatics Pub Date : 2024-05-01 DOI: 10.1200/CCI.23.00159
Theodore C Feldman, David E Kaplan, Albert Lin, Jennifer La, Jerry S H Lee, Mayada Aljehani, David P Tuck, Mary T Brophy, Nathanael R Fillmore, Nhan V Do
{"title":"Phenotyping Hepatic Immune-Related Adverse Events in the Setting of Immune Checkpoint Inhibitor Therapy.","authors":"Theodore C Feldman, David E Kaplan, Albert Lin, Jennifer La, Jerry S H Lee, Mayada Aljehani, David P Tuck, Mary T Brophy, Nathanael R Fillmore, Nhan V Do","doi":"10.1200/CCI.23.00159","DOIUrl":"10.1200/CCI.23.00159","url":null,"abstract":"<p><strong>Purpose: </strong>We present and validate a rule-based algorithm for the detection of moderate to severe liver-related immune-related adverse events (irAEs) in a real-world patient cohort. The algorithm can be applied to studies of irAEs in large data sets.</p><p><strong>Methods: </strong>We developed a set of criteria to define hepatic irAEs. The criteria include: the temporality of elevated laboratory measurements in the first 2-14 weeks of immune checkpoint inhibitor (ICI) treatment, steroid intervention within 2 weeks of the onset of elevated laboratory measurements, and intervention with a duration of at least 2 weeks. These criteria are based on the kinetics of patients who experienced moderate to severe hepatotoxicity (Common Terminology Criteria for Adverse Events grades 2-4). We applied these criteria to a retrospective cohort of 682 patients diagnosed with hepatocellular carcinoma and treated with ICI. All patients were required to have baseline laboratory measurements before and after the initiation of ICI.</p><p><strong>Results: </strong>A set of 63 equally sampled patients were reviewed by two blinded, clinical adjudicators. Disagreements were reviewed and consensus was taken to be the ground truth. Of these, 25 patients with irAEs were identified, 16 were determined to be hepatic irAEs, 36 patients were nonadverse events, and two patients were of indeterminant status. Reviewers agreed in 44 of 63 patients, including 19 patients with irAEs (0.70 concordance, Fleiss' kappa: 0.43). By comparison, the algorithm achieved a sensitivity and specificity of identifying hepatic irAEs of 0.63 and 0.81, respectively, with a test efficiency (percent correctly classified) of 0.78 and outcome-weighted F1 score of 0.74.</p><p><strong>Conclusion: </strong>The algorithm achieves greater concordance with the ground truth than either individual clinical adjudicator for the detection of irAEs.</p>","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11161238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140905166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assessment of BRCA1 and BRCA2 Germline Variant Data From Patients With Breast Cancer in a Real-World Data Registry. 评估真实世界数据登记册中乳腺癌患者的 BRCA1 和 BRCA2 基因变异数据。
IF 4.2
JCO Clinical Cancer Informatics Pub Date : 2024-05-01 DOI: 10.1200/CCI.23.00251
Thales C Nepomuceno, Paulo Lyra, Jianbin Zhu, Fanchao Yi, Rachael H Martin, Daniel Lupu, Luke Peterson, Lauren C Peres, Anna Berry, Edwin S Iversen, Fergus J Couch, Qianxing Mo, Alvaro N Monteiro
{"title":"Assessment of <i>BRCA1</i> and <i>BRCA2</i> Germline Variant Data From Patients With Breast Cancer in a Real-World Data Registry.","authors":"Thales C Nepomuceno, Paulo Lyra, Jianbin Zhu, Fanchao Yi, Rachael H Martin, Daniel Lupu, Luke Peterson, Lauren C Peres, Anna Berry, Edwin S Iversen, Fergus J Couch, Qianxing Mo, Alvaro N Monteiro","doi":"10.1200/CCI.23.00251","DOIUrl":"10.1200/CCI.23.00251","url":null,"abstract":"<p><strong>Purpose: </strong>The emergence of large real-world clinical databases and tools to mine electronic medical records has allowed for an unprecedented look at large data sets with clinical and epidemiologic correlates. In clinical cancer genetics, real-world databases allow for the investigation of prevalence and effectiveness of prevention strategies and targeted treatments and for the identification of barriers to better outcomes. However, real-world data sets have inherent biases and problems (eg, selection bias, incomplete data, measurement error) that may hamper adequate analysis and affect statistical power.</p><p><strong>Methods: </strong>Here, we leverage a real-world clinical data set from a large health network for patients with breast cancer tested for variants in <i>BRCA1</i> and <i>BRCA2</i> (N = 12,423). We conducted data cleaning and harmonization, cross-referenced with publicly available databases, performed variant reassessment and functional assays, and used functional data to inform a variant's clinical significance applying American College of Medical Geneticists and the Association of Molecular Pathology guidelines.</p><p><strong>Results: </strong>In the cohort, White and Black patients were over-represented, whereas non-White Hispanic and Asian patients were under-represented. Incorrect or missing variant designations were the most significant contributor to data loss. While manual curation corrected many incorrect designations, a sizable fraction of patient carriers remained with incorrect or missing variant designations. Despite the large number of patients with clinical significance not reported, original reported clinical significance assessments were accurate. Reassessment of variants in which clinical significance was not reported led to a marked improvement in data quality.</p><p><strong>Conclusion: </strong>We identify the most common issues with <i>BRCA1</i> and <i>BRCA2</i> testing data entry and suggest approaches to minimize data loss and keep interpretation of clinical significance of variants up to date.</p>","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11161245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Use of Natural Language Processing to Infer Sites of Metastatic Disease From Radiology Reports at Scale. 利用自然语言处理技术从放射学报告中推断转移性疾病的部位。
IF 3.3
JCO Clinical Cancer Informatics Pub Date : 2024-05-01 DOI: 10.1200/CCI.23.00122
See Boon Tay, Guat Hwa Low, Gillian Jing En Wong, Han Jieh Tey, Fun Loon Leong, Constance Li, Melvin Lee Kiang Chua, Daniel Shao Weng Tan, Choon Hua Thng, Iain Bee Huat Tan, Ryan Shea Ying Cong Tan
{"title":"Use of Natural Language Processing to Infer Sites of Metastatic Disease From Radiology Reports at Scale.","authors":"See Boon Tay, Guat Hwa Low, Gillian Jing En Wong, Han Jieh Tey, Fun Loon Leong, Constance Li, Melvin Lee Kiang Chua, Daniel Shao Weng Tan, Choon Hua Thng, Iain Bee Huat Tan, Ryan Shea Ying Cong Tan","doi":"10.1200/CCI.23.00122","DOIUrl":"10.1200/CCI.23.00122","url":null,"abstract":"<p><strong>Purpose: </strong>To evaluate natural language processing (NLP) methods to infer metastatic sites from radiology reports.</p><p><strong>Methods: </strong>A set of 4,522 computed tomography (CT) reports of 550 patients with 14 types of cancer was used to fine-tune four clinical large language models (LLMs) for multilabel classification of metastatic sites. We also developed an NLP information extraction (IE) system (on the basis of named entity recognition, assertion status detection, and relation extraction) for comparison. Model performances were measured by F1 scores on test and three external validation sets. The best model was used to facilitate analysis of metastatic frequencies in a cohort study of 6,555 patients with 53,838 CT reports.</p><p><strong>Results: </strong>The RadBERT, BioBERT, GatorTron-base, and GatorTron-medium LLMs achieved F1 scores of 0.84, 0.87, 0.89, and 0.91, respectively, on the test set. The IE system performed best, achieving an F1 score of 0.93. F1 scores of the IE system by individual cancer type ranged from 0.89 to 0.96. The IE system attained F1 scores of 0.89, 0.83, and 0.81, respectively, on external validation sets including additional cancer types, positron emission tomography-CT ,and magnetic resonance imaging scans, respectively. In our cohort study, we found that for colorectal cancer, liver-only metastases were higher in de novo stage IV versus recurrent patients (29.7% <i>v</i> 12.2%; <i>P</i> < .001). Conversely, lung-only metastases were more frequent in recurrent versus de novo stage IV patients (17.2% <i>v</i> 7.3%; <i>P</i> < .001).</p><p><strong>Conclusion: </strong>We developed an IE system that accurately infers metastatic sites in multiple primary cancers from radiology reports. It has explainable methods and performs better than some clinical LLMs. The inferred metastatic phenotypes could enhance cancer research databases and clinical trial matching, and identify potential patients for oligometastatic interventions.</p>","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141094670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Erratum: Development of an Automatic Rule-Based Algorithm for the Detection of Ovarian Cancer Recurrence From Electronic Health Records. 勘误:开发基于规则的自动算法,从电子健康记录中检测卵巢癌复发。
IF 4.2
JCO Clinical Cancer Informatics Pub Date : 2024-04-01 DOI: 10.1200/CCI.24.00062
{"title":"Erratum: Development of an Automatic Rule-Based Algorithm for the Detection of Ovarian Cancer Recurrence From Electronic Health Records.","authors":"","doi":"10.1200/CCI.24.00062","DOIUrl":"https://doi.org/10.1200/CCI.24.00062","url":null,"abstract":"","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140768639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Explainable Machine Learning Model to Preoperatively Predict Postoperative Complications in Inpatients With Cancer Undergoing Major Operations. 可解释的机器学习模型,用于术前预测接受大手术的癌症住院患者的术后并发症。
IF 4.2
JCO Clinical Cancer Informatics Pub Date : 2024-04-01 DOI: 10.1200/cci.23.00247
Matthew C Hernandez, Chen Chen, Andrew Nguyen, Kevin Choong, Cameron Carlin, Rebecca A. Nelson, Lorenzo A. Rossi, Naini S. Seth, Kathy McNeese, Bertram Yuh, Z. Eftekhari, Lily L. Lai
{"title":"Explainable Machine Learning Model to Preoperatively Predict Postoperative Complications in Inpatients With Cancer Undergoing Major Operations.","authors":"Matthew C Hernandez, Chen Chen, Andrew Nguyen, Kevin Choong, Cameron Carlin, Rebecca A. Nelson, Lorenzo A. Rossi, Naini S. Seth, Kathy McNeese, Bertram Yuh, Z. Eftekhari, Lily L. Lai","doi":"10.1200/cci.23.00247","DOIUrl":"https://doi.org/10.1200/cci.23.00247","url":null,"abstract":"PURPOSE\u0000Preoperative prediction of postoperative complications (PCs) in inpatients with cancer is challenging. We developed an explainable machine learning (ML) model to predict PCs in a heterogenous population of inpatients with cancer undergoing same-hospitalization major operations.\u0000\u0000\u0000METHODS\u0000Consecutive inpatients who underwent same-hospitalization operations from December 2017 to June 2021 at a single institution were retrospectively reviewed. The ML model was developed and tested using electronic health record (EHR) data to predict 30-day PCs for patients with Clavien-Dindo grade 3 or higher (CD 3+) per the CD classification system. Model performance was assessed using area under the receiver operating characteristic curve (AUROC), area under the precision recall curve (AUPRC), and calibration plots. Model explanation was performed using the Shapley additive explanations (SHAP) method at cohort and individual operation levels.\u0000\u0000\u0000RESULTS\u0000A total of 988 operations in 827 inpatients were included. The ML model was trained using 788 operations and tested using a holdout set of 200 operations. The CD 3+ complication rates were 28.6% and 27.5% in the training and holdout test sets, respectively. Training and holdout test sets' model performance in predicting CD 3+ complications yielded an AUROC of 0.77 and 0.73 and an AUPRC of 0.56 and 0.52, respectively. Calibration plots demonstrated good reliability. The SHAP method identified features and the contributions of the features to the risk of PCs.\u0000\u0000\u0000CONCLUSION\u0000We trained and tested an explainable ML model to predict the risk of developing PCs in patients with cancer. Using patient-specific EHR data, the ML model accurately discriminated the risk of developing CD 3+ complications and displayed top features at the individual operation and cohort level.","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140774755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Organizational Breast Cancer Data Mart: A Solution for Assessing Outcomes of Imaging and Treatment. 组织乳腺癌数据集市:评估成像和治疗结果的解决方案。
IF 4.2
JCO Clinical Cancer Informatics Pub Date : 2024-04-01 DOI: 10.1200/CCI.23.00193
Margarita L Zuley, Jonathan Silverstein, Durwin Logue, Richard S Morgan, Rohit Bhargava, Priscilla F. McAuliffe, A. Brufsky, Andriy I Bandos, Robert M. Nishikawa
{"title":"Organizational Breast Cancer Data Mart: A Solution for Assessing Outcomes of Imaging and Treatment.","authors":"Margarita L Zuley, Jonathan Silverstein, Durwin Logue, Richard S Morgan, Rohit Bhargava, Priscilla F. McAuliffe, A. Brufsky, Andriy I Bandos, Robert M. Nishikawa","doi":"10.1200/CCI.23.00193","DOIUrl":"https://doi.org/10.1200/CCI.23.00193","url":null,"abstract":"PURPOSE\u0000In the United States, a comprehensive national breast cancer registry (CR) does not exist. Thus, care and coverage decisions are based on data from population subsets, other countries, or models. We report a prototype real-world research data mart to assess mortality, morbidity, and costs for breast cancer diagnosis and treatment.\u0000\u0000\u0000METHODS\u0000With institutional review board approval and Health Insurance Portability and Accountability Act (HIPPA) compliance, a multidisciplinary clinical and research data warehouse (RDW) expert group curated demographic, risk, imaging, pathology, treatment, and outcome data from the electronic health records (EHR), radiology (RIS), and CR for patients having breast imaging and/or a diagnosis of breast cancer in our institution from January 1, 2004, to December 31, 2020. Domains were defined by prebuilt views to extract data denormalized according to requirements from the existing RDW using an export, transform, load pattern. Data dictionaries were included. Structured query language was used for data cleaning.\u0000\u0000\u0000RESULTS\u0000Five-hundred eighty-nine elements (EHR 311, RIS 211, and CR 67) were mapped to 27 domains; all, except one containing CR elements, had cancer and noncancer cohort views, resulting in a total of 53 views (average 12 elements/view; range, 4-67). EHR and RIS queries returned 497,218 patients with 2,967,364 imaging examinations and associated visit details. Cancer biology, treatment, and outcome details for 15,619 breast cancer cases were imported from the CR of our primary breast care facility for this prototype mart.\u0000\u0000\u0000CONCLUSION\u0000Institutional real-world data marts enable comprehensive understanding of care outcomes within an organization. As clinical data sources become increasingly structured, such marts may be an important source for future interinstitution analysis and potentially an opportunity to create robust real-world results that could be used to support evidence-based national policy and care decisions for breast cancer.","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140788135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Machine Learning-Based Survival Prediction Models for Progression-Free and Overall Survival in Advanced-Stage Hodgkin Lymphoma. 基于机器学习的晚期霍奇金淋巴瘤无进展生存期和总生存期预测模型
IF 4.2
JCO Clinical Cancer Informatics Pub Date : 2024-04-01 DOI: 10.1200/CCI.23.00255
R. Rask Kragh Jørgensen, Fanny Bergström, S. Eloranta, M. Tang Severinsen, K. Bjøro Smeland, Alexander Fosså, J. Haaber Christensen, Martin Hutchings, Rasmus Bo Dahl-Sørensen, P. Kamper, I. Glimelius, Karin E Smedby, Susan K Parsons, Angie Mae Rodday, Matthew J Maurer, Andrew M Evens, Tarec C El-Galaly, L. Hjort Jakobsen
{"title":"Machine Learning-Based Survival Prediction Models for Progression-Free and Overall Survival in Advanced-Stage Hodgkin Lymphoma.","authors":"R. Rask Kragh Jørgensen, Fanny Bergström, S. Eloranta, M. Tang Severinsen, K. Bjøro Smeland, Alexander Fosså, J. Haaber Christensen, Martin Hutchings, Rasmus Bo Dahl-Sørensen, P. Kamper, I. Glimelius, Karin E Smedby, Susan K Parsons, Angie Mae Rodday, Matthew J Maurer, Andrew M Evens, Tarec C El-Galaly, L. Hjort Jakobsen","doi":"10.1200/CCI.23.00255","DOIUrl":"https://doi.org/10.1200/CCI.23.00255","url":null,"abstract":"PURPOSE\u0000Patients diagnosed with advanced-stage Hodgkin lymphoma (aHL) have historically been risk-stratified using the International Prognostic Score (IPS). This study investigated if a machine learning (ML) approach could outperform existing models when it comes to predicting overall survival (OS) and progression-free survival (PFS).\u0000\u0000\u0000PATIENTS AND METHODS\u0000This study used patient data from the Danish National Lymphoma Register for model development (development cohort). The ML model was developed using stacking, which combines several predictive survival models (Cox proportional hazard, flexible parametric model, IPS, principal component, penalized regression) into a single model, and was compared with two versions of IPS (IPS-3 and IPS-7) and the newly developed aHL international prognostic index (A-HIPI). Internal model validation was performed using nested cross-validation, and external validation was performed using patient data from the Swedish Lymphoma Register and Cancer Registry of Norway (validation cohort).\u0000\u0000\u0000RESULTS\u0000In total, 707 and 760 patients with aHL were included in the development and validation cohorts, respectively. Examining model performance for OS in the development cohort, the concordance index (C-index) for the ML model, IPS-7, IPS-3, and A-HIPI was found to be 0.789, 0.608, 0.650, and 0.768, respectively. The corresponding estimates in the validation cohort were 0.749, 0.700, 0.663, and 0.741. For PFS, the ML model achieved the highest C-index in both cohorts (0.665 in the development cohort and 0.691 in the validation cohort). The time-varying AUCs for both the ML model and the A-HIPI were consistently higher in both cohorts compared with the IPS models within the first 5 years after diagnosis.\u0000\u0000\u0000CONCLUSION\u0000The new prognostic model for aHL on the basis of ML techniques demonstrated a substantial improvement compared with the IPS models, but yielded a limited improvement in predictive performance compared with the A-HIPI.","PeriodicalId":51626,"journal":{"name":"JCO Clinical Cancer Informatics","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140785070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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