Dataset Information

Validation of a coding algorithm to identify bladder cancer and distinguish stage in an electronic medical records database.

ABSTRACT: Studies on outcomes in bladder cancer rely on accurate methods to identify patients with bladder cancer and differentiate bladder cancer stage. Medical record and administrative databases are increasingly used to study cancer incidence, but few have distinguished cancer stage, and none have focused on bladder cancer. In this study, we used data from The UK Health Improvement Network (THIN) to identify patients with bladder cancer using at least one diagnostic code for bladder cancer, and distinguish muscle-invasive from non-invasive disease using a subsequent code for cystectomy. Algorithms were validated against a gold standard of physician-completed questionnaires, pathology reports, and consultant letters. Algorithm performance was evaluated by measuring positive predictive value (PPV) and corresponding 95% confidence interval (CI). Among all patients coded with bladder cancer (n = 194), PPV for any bladder cancer was 99.5% (95% CI, 97.2-99.9). PPV for incident bladder cancer was 93.8% (95% CI, 89.4-96.7). PPV for muscle-invasive bladder cancer was 70.1% (95% CI, 59.4-79.5) in patients with cystectomy (n = 95) and 83.9% (95% CI, 66.3-94.5) in those with cystectomy plus additional codes for metastases and death (n = 31). Using our codes for bladder cancer, the age- and sex-standardized incidence rate (SIR) of bladder cancer in THIN approximated that measured by cancer registries (SIR within 20%), suggesting that sensitivity was high as well. THIN is a valid and novel database for the study of bladder cancer. Our algorithm can be used to examine the epidemiology of muscle-invasive bladder cancer or outcomes following cystectomy for patients with muscle invasion.

SUBMITTER: Mamtani R

PROVIDER: S-EPMC4294969 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Validation of a coding algorithm to identify bladder cancer and distinguish stage in an electronic medical records database.

Mamtani Ronac R Haynes Kevin K Boursi Ben B Scott Frank I FI Goldberg David S DS Keefe Stephen M SM Vaughn David J DJ Malkowicz S Bruce SB Lewis James D JD

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 20141111 1

Studies on outcomes in bladder cancer rely on accurate methods to identify patients with bladder cancer and differentiate bladder cancer stage. Medical record and administrative databases are increasingly used to study cancer incidence, but few have distinguished cancer stage, and none have focused on bladder cancer. In this study, we used data from The UK Health Improvement Network (THIN) to identify patients with bladder cancer using at least one diagnostic code for bladder cancer, and disting ...[more]

PMID: 25389114

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Project description:ContextEnhanced recovery after surgery (ERAS) aims to improve surgical outcomes by integrating evidence-based practices across preoperative, intraoperative, and postoperative care. Data in electronic medical records (EMRs) provide insight on how ERAS is implemented and its impact on surgical outcomes. Because ERAS is a multimodal pathway provided by multiple physicians and health care providers over time, identifying ERAS cases in EMRs is not a trivial task. To better understand how EMRs can be used to study ERAS, we describe our experience with using current methodologies and the development and rationale of a new method for retrospectively identifying ERAS cases in EMRs.Case descriptionUsing EMR data from surgical departments at the University of North Carolina at Chapel Hill, we first identified ERAS cases using a protocol-based method, using basic information including the date of ERAS implementation, surgical procedure and date, and primary surgeon. We further examined two operational flags in the EMRs, a nursing order and a case request for OR order. Wide variation between the methods compelled us to consult with ERAS surgical staff and explore the EMRs to develop a more refined method for identifying ERAS cases.MethodWe developed a two-step method, with the first step based on the protocol definition and the second step based on an ERAS-specific medication definition. To test our method, we randomly sampled 150 general, gynecological, and urologic surgeries performed between January 1, 2016 and March 30, 2017. Surgical cases were classified as ERAS or not using the protocol definition, nursing order, case request for OR order, and our two-step method. To assess the accuracy of each method, two independent reviewers assessed the charts to determine whether cases were ERAS.FindingsOf the 150 charts reviewed, 74 were ERAS cases. The protocol only method and nursing order flag performed similarly, correctly identifying 74 percent and 73 percent of true ERAS cases, respectively. The case request for OR order flag performed less well, correctly identifying only 44 percent of the true ERAS cases. Our two-step method performed well, correctly identifying 98 percent of true ERAS cases.ConclusionERAS pathways are complex, making study of them from EMRs difficult. Current strategies for doing so are relatively easy to implement, but unreliable. We have developed a reproducible and observable ERAS computational phenotype that identifies ERAS cases reliably. This is a step forward in using the richness of EMR data to study ERAS implementation, efficacy, and how they can contribute to surgical care improvement.

Project description:Post-market medical device surveillance is a challenge facing manufacturers, regulatory agencies, and health care providers. Electronic health records are valuable sources of real-world evidence for assessing device safety and tracking device-related patient outcomes over time. However, distilling this evidence remains challenging, as information is fractured across clinical notes and structured records. Modern machine learning methods for machine reading promise to unlock increasingly complex information from text, but face barriers due to their reliance on large and expensive hand-labeled training sets. To address these challenges, we developed and validated state-of-the-art deep learning methods that identify patient outcomes from clinical notes without requiring hand-labeled training data. Using hip replacements-one of the most common implantable devices-as a test case, our methods accurately extracted implant details and reports of complications and pain from electronic health records with up to 96.3% precision, 98.5% recall, and 97.4% F1, improved classification performance by 12.8-53.9% over rule-based methods, and detected over six times as many complication events compared to using structured data alone. Using these additional events to assess complication-free survivorship of different implant systems, we found significant variation between implants, including for risk of revision surgery, which could not be detected using coded data alone. Patients with revision surgeries had more hip pain mentions in the post-hip replacement, pre-revision period compared to patients with no evidence of revision surgery (mean hip pain mentions 4.97 vs. 3.23; t?=?5.14; p?<?0.001). Some implant models were associated with higher or lower rates of hip pain mentions. Our methods complement existing surveillance mechanisms by requiring orders of magnitude less hand-labeled training data, offering a scalable solution for national medical device surveillance using electronic health records.

Dataset Information

Validation of a coding algorithm to identify bladder cancer and distinguish stage in an electronic medical records database.

Publications

Validation of a coding algorithm to identify bladder cancer and distinguish stage in an electronic medical records database.

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