Medical records based analysis and making model of long-term outcome of mini-laparotomy colorectal cancer in structured clinical data
Ontology highlight
ABSTRACT:
DISEASE(S): Colorectal Cancer
PROVIDER: 2689050 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
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Project description:BackgroundCommon data models (CDMs) enable data to be standardized, and facilitate data exchange, sharing, and storage, particularly when the data have been collected via distinct, heterogeneous systems. Moreover, CDMs provide tools for data quality assessment, integration into models, visualization, and analysis. The observational medical outcome partnership (OMOP) provides a CDM for organizing and standardizing databases. Common data models not only facilitate data integration but also (and especially for the OMOP model) extends the range of available statistical analyses.ObjectiveThis study aimed to evaluate the feasibility of implementing French national electronic health records in the OMOP CDM.MethodsThe OMOP's specifications were used to audit the source data, specify the transformation into the OMOP CDM, implement an extract-transform-load process to feed data from the French health care system into the OMOP CDM, and evaluate the final database.ResultsSeventeen vocabularies corresponding to the French context were added to the OMOP CDM's concepts. Three French terminologies were automatically mapped to standardized vocabularies. We loaded nine tables from the OMOP CDM's "standardized clinical data" section, and three tables from the "standardized health system data" section. Outpatient and inpatient data from 38,730 individuals were integrated. The median (interquartile range) number of outpatient and inpatient stays per patient was 160 (19-364).ConclusionOur results demonstrated that data from the French national health care system can be integrated into the OMOP CDM. One of the main challenges was the use of international OMOP concepts to annotate data recorded in a French context. The use of local terminologies was an obstacle to conceptual mapping; with the exception of an adaptation of the International Classification of Diseases 10th Revision, the French health care system does not use international terminologies. It would be interesting to extend our present findings to the 65 million people registered in the French health care system.
| S-EPMC6949163 | biostudies-literature
Project description:electronic Medical Records & Genomics (eMERGE)
| PRJNA158491 | ENA
Project description:BACKGROUND:The development and adoption of health care common data models (CDMs) has addressed some of the logistical challenges of performing research on data generated from disparate health care systems by standardizing data representations and leveraging standardized terminology to express clinical information consistently. However, transforming a data system into a CDM is not a trivial task, and maintaining an operational, enterprise capable CDM that is incrementally updated within a data warehouse is challenging. OBJECTIVES:To develop a quality assurance (QA) process and code base to accompany our incremental transformation of the Department of Veterans Affairs Corporate Data Warehouse health care database into the Observational Medical Outcomes Partnership (OMOP) CDM to prevent incremental load errors. METHODS:We designed and implemented a multistage QA) approach centered on completeness, value conformance, and relational conformance data-quality elements. For each element we describe key incremental load challenges, our extract, transform, and load (ETL) solution of data to overcome those challenges, and potential impacts of incremental load failure. RESULTS:Completeness and value conformance data-quality elements are most affected by incremental changes to the CDW, while updates to source identifiers impact relational conformance. ETL failures surrounding these elements lead to incomplete and inaccurate capture of clinical concepts as well as data fragmentation across patients, providers, and locations. CONCLUSION:Development of robust QA processes supporting accurate transformation of OMOP and other CDMs from source data is still in evolution, and opportunities exist to extend the existing QA framework and tools used for incremental ETL QA processes.
| S-EPMC6811349 | biostudies-literature
Project description:BackgroundDual processing theory of human cognition postulates that reasoning and decision-making can be described as a function of both an intuitive, experiential, affective system (system I) and/or an analytical, deliberative (system II) processing system. To date no formal descriptive model of medical decision-making based on dual processing theory has been developed. Here we postulate such a model and apply it to a common clinical situation: whether treatment should be administered to the patient who may or may not have a disease.MethodsWe developed a mathematical model in which we linked a recently proposed descriptive psychological model of cognition with the threshold model of medical decision-making and show how this approach can be used to better understand decision-making at the bedside and explain the widespread variation in treatments observed in clinical practice.ResultsWe show that physician's beliefs about whether to treat at higher (lower) probability levels compared to the prescriptive therapeutic thresholds obtained via system II processing is moderated by system I and the ratio of benefit and harms as evaluated by both system I and II. Under some conditions, the system I decision maker's threshold may dramatically drop below the expected utility threshold derived by system II. This can explain the overtreatment often seen in the contemporary practice. The opposite can also occur as in the situations where empirical evidence is considered unreliable, or when cognitive processes of decision-makers are biased through recent experience: the threshold will increase relative to the normative threshold value derived via system II using expected utility threshold. This inclination for the higher diagnostic certainty may, in turn, explain undertreatment that is also documented in the current medical practice.ConclusionsWe have developed the first dual processing model of medical decision-making that has potential to enrich the current medical decision-making field, which is still to the large extent dominated by expected utility theory. The model also provides a platform for reconciling two groups of competing dual processing theories (parallel competitive with default-interventionalist theories).
| S-EPMC3471048 | biostudies-literature
Project description:Medical record abstraction (MRA) is often cited as a significant source of error in research data, yet MRA methodology has rarely been the subject of investigation. Lack of a common framework has hindered application of the extant literature in practice, and, until now, there were no evidence-based guidelines for ensuring data quality in MRA. We aimed to identify the factors affecting the accuracy of data abstracted from medical records and to generate a framework for data quality assurance and control in MRA.Candidate factors were identified from published reports of MRA. Content validity of the top candidate factors was assessed via a four-round two-group Delphi process with expert abstractors with experience in clinical research, registries, and quality improvement. The resulting coded factors were categorized into a control theory-based framework of MRA. Coverage of the framework was evaluated using the recent published literature.Analysis of the identified articles yielded 292 unique factors that affect the accuracy of abstracted data. Delphi processes overall refuted three of the top factors identified from the literature based on importance and five based on reliability (six total factors refuted). Four new factors were identified by the Delphi. The generated framework demonstrated comprehensive coverage. Significant underreporting of MRA methodology in recent studies was discovered.The framework generated from this research provides a guide for planning data quality assurance and control for studies using MRA. The large number and variability of factors indicate that while prospective quality assurance likely increases the accuracy of abstracted data, monitoring the accuracy during the abstraction process is also required. Recent studies reporting research results based on MRA rarely reported data quality assurance or control measures, and even less frequently reported data quality metrics with research results. Given the demonstrated variability, these methods and measures should be reported with research results.
| S-EPMC4615628 | biostudies-literature
Project description:Modern medical research relies on multi-institutional collaborations which enhance the knowledge discovery and data reuse. While these collaborations allow researchers to perform analytics otherwise impossible on individual datasets, they often pose significant challenges in the data integration process. Due to the lack of a unique identifier, data integration solutions often have to rely on patient's protected health information (PHI). In many situations, such information cannot leave the institutions or must be strictly protected. Furthermore, the presence of noisy values for these attributes may result in poor overall utility. While much research has been done to address these challenges, most of the current solutions are designed for a static setting without considering the temporal information of the data (e.g. EHR). In this work, we propose a novel approach that uses non-PHI for linking patient longitudinal data. Specifically, our technique captures the diagnosis dependencies using patterns which are shown to provide important indications for linking patient records. Our solution can be used as a standalone technique to perform temporal record linkage using non-protected health information data or it can be combined with Privacy Preserving Record Linkage solutions (PPRL) when protected health information is available. In this case, our approach can solve ambiguities in results. Experimental evaluations on real datasets demonstrate the effectiveness of our technique.
| S-EPMC5758434 | biostudies-other
Project description:BackgroundImprovements in the quality of health care services are often measured using data present in medical records. Electronic Medical Records (EMRs) contain potentially valuable new sources of health data. However, data quality in EMRs may not be optimal and should be assessed. Data reliability (are the same data elements being measured over time?) is a prerequisite for data validity (are the data accurate?). Our objective was to measure the reliability of data for preventive services in primary care EMRs during the transition to EMR.MethodsOur data sources were randomly selected eligible patients' medical records and data obtained from provincial administrative datasets. Eighteen community-based family physicians in Toronto, Ontario that implemented EMRs starting in 2006 participated in this study. We measured the proportion of patients eligible for a service (Pap smear, screening mammogram or influenza vaccination) that received the service. We compared the change in rates of selected preventive services calculated from the medical record audits with the change in administrative datasets.ResultsIn the first year of EMR use (2006) services decreased by 8.7% more (95% CI -11.0%- - 6.4%, p < 0.0001) when measured through medical record audits as compared with administrative datasets. Services increased by 2.4% more (95% CI 0%-4.9%, p = 0.05) in the medical record audits during the second year of EMR use (2007).ConclusionThere were differences between the change measured through medical record audits and administrative datasets. Problems could include difficulties with organizing new data entry processes as well as continued use of both paper and EMRs. Data extracted from EMRs had limited reliability during the initial phase of EMR implementation. Unreliable data interferes with the ability to measure and improve health care quality.
| S-EPMC3442990 | biostudies-literature
Project description:Increasing numbers of older patients are undergoing emergency laparotomy (EL). They are at increased risk of adverse outcomes, making the shared decision on whether to operate challenging. This retrospective cohort study aimed to assess the role of age and life-expectancy predictions on short- and long-term survival in patients undergoing EL. All patients who underwent EL at one hospital in the West of Scotland between March 2014 to December 2016 were included. Clinical parameters were collected, and patients were followed up to allow reporting of 30-, 60- and 90-day and 1-year mortality rates. Period life expectancy was used to stratify patients into below life expectancy (bLEP) and at-or-above life expectancy (aLEP) groups at presentation. Remaining life expectancy was used to calculate the net years of life gained (NYLG). Some 462 patients underwent EL: 20 per cent in the aLEP group. These patients were older (P < 0.001), had more co-morbidities (P < 0.001) and were high risk on P-POSSUM scoring (P = 0.008). The 30-, 60- and 90-day and 1-year mortality rates were 11, 14, 16 and 23 per cent respectively. Advanced age (P = 0.011) and high ASA score (P = 0.004) and P-POSSUM score (P < 0.001) were independent predictors of death at 1 year on multivariable analysis. The cohort NYLG were 19.2 years. Comparing patients aged less than 70 with those aged 70 years or older, the NYLG were 25.9 versus 5.5 years. Comparing bLEP and aLEP, the NYLG were 22.2 versus 4.4 years. In patients aged 70 years and older, NYLG decreased by more than half in patients with co-morbidities (ASA score 3,4,5) (9.3 versus 4.3 years). Discussions around long-term outcomes after emergency surgery remain difficult. Although age is an influencing factor, predicted life expectancy alone does not provide additional value to shared decision making.
| S-EPMC8504444 | biostudies-literature
Project description:As the deployment of electronic medical records (EMR) expands, so is the availability of long-term datasets that could serve to enhance public health surveillance. We hypothesized that EMR-based surveillance systems that incorporate seasonality and other long-term trends would discover outbreaks of acute respiratory infections (ARI) sooner than systems that only consider the recent past.We simulated surveillance systems aimed at discovering modeled influenza outbreaks injected into backgrounds of patients with ARI. Backgrounds of daily case counts were either synthesized or obtained by applying one of three previously validated ARI case-detection algorithms to authentic EMR entries. From the time of outbreak injection, detection statistics were applied daily on paired background+injection and background-only time series. The relationship between the detection delay (the time from injection to the first alarm uniquely found in the background+injection data) and the false-alarm rate (FAR) was determined by systematically varying the statistical alarm threshold. We compared this relationship for outbreak detection methods that utilized either 7 days (early aberrancy reporting system (EARS)) or 2-4 years of past data (seasonal autoregressive integrated moving average (SARIMA) time series modeling).In otherwise identical surveillance systems, SARIMA detected epidemics sooner than EARS at any FAR below 10%. The algorithms used to detect single ARI cases impacted both the feasibility and marginal benefits of SARIMA modeling. Under plausible real-world conditions, SARIMA could reduce detection delay by 5-16 days. It also was more sensitive at detecting the summer wave of the 2009 influenza pandemic.Time series modeling of long-term historical EMR data can reduce the time it takes to discover epidemics of ARI. Realistic surveillance simulations may prove invaluable to optimize system design and tuning.
| S-EPMC5791979 | biostudies-literature
Project description:Multistate models are used to characterize individuals' natural histories through diseases with discrete states. Observational data resources based on electronic medical records pose new opportunities for studying such diseases. However, these data consist of observations of the process at discrete sampling times, which may either be pre-scheduled and non-informative, or symptom-driven and informative about an individual's underlying disease status. We have developed a novel joint observation and disease transition model for this setting. The disease process is modeled according to a latent continuous-time Markov chain; and the observation process, according to a Markov-modulated Poisson process with observation rates that depend on the individual's underlying disease status. The disease process is observed at a combination of informative and non-informative sampling times, with possible misclassification error. We demonstrate that the model is computationally tractable and devise an expectation-maximization algorithm for parameter estimation. Using simulated data, we show how estimates from our joint observation and disease transition model lead to less biased and more precise estimates of the disease rate parameters. We apply the model to a study of secondary breast cancer events, utilizing mammography and biopsy records from a sample of women with a history of primary breast cancer.
| S-EPMC4415156 | biostudies-literature