Electronic Clinical Information Research Articles

The Impact of Prescription Time Limits on Phosphate Administration in the Intensive Care Unit: A Before-After Quality Improvement Study.

(1) Background: We aim to examine and improve phosphate prescribing as part of a quality assurance program by examining the change in the proportion of patients receiving phosphate with normal or high preceding serum phosphate concentrations before and after the introduction of the 24 h time limit to default phosphate prescription. (2) Methods: This was a quality assurance study conducted across three Australian adult intensive care units (ICUs). All adult patients with ICU lengths of stay greater than or equal to 48 h who had their serum phosphate concentrations measured were included. A 24 h time limit was introduced to the protocolised prescription in the electronic clinical information system for enteral and intravenous phosphate at participating ICUs. Patient characteristics, phosphate administration, and outcomes were compared before and after this time limit was introduced. The primary outcome was the proportion of patients to whom phosphate was prescribed after measurement of a normal or high serum phosphate level. Secondary outcomes were ICU length of stay, mortality, and discharge destination. (3) Results: A total of 1192 patients were included from three ICUs over the two periods. The proportion of patients with a normal or high measured phosphate level who then received phosphate supplementation was significantly lower in the second study period (30.3% vs. 9.9%; p < 0.001). This difference persisted when adjusted for potential confounders in a mixed-effects logistic regression model (an adjusted odds ratio for receiving phosphate with normal or high serum concentration 0.214, 95% confidence interval of 0.132-0.347; p < 0.001). No significant difference was seen in the typical ICU length of stay, in-hospital case-fatality rate, and hospital discharge destination between these groups. (4) Conclusions: This multicentre before-after study has demonstrated that the introduction of a 24 h limit on electronic phosphate prescriptions resulted in significantly fewer patients receiving phosphate when their serum phosphate concentration was normal or high, without any adverse impact on patient outcomes.

Automated differential diagnostics of respiratory diseases using an electronic stethoscope

Abstract Introduction: The outbreak of the coronavirus infection, which has escalated into a pandemic, has worsened the already unfavourable situation with respiratory system diseases in Ukraine. The burden on doctors has significantly increased, necessitating the exploration of simplified and expedited methods for conducting routine respiratory examinations. The research aims to describe a model for creating an automated differential diagnosis of respiratory noise using an electronic stethoscope, combining medical and clinical information about the types of respiratory noise characterizing the normal or pathological state of the respiratory system with a means of its information and technical processing. Material and methods: The research methods were analysis of theoretical information about the types of respiratory noise, analysis of technical information for choosing an information technology tool for processing biological signals; synthesis of the results; modelling. Results: The research resulted in a model of automated differential diagnosis based on the principle of auscultation, which includes the process of extracting the sound of air movement inside and outside the lungs and the classification of the extracted sounds. Automation of this process concerned only the classification of the extracted sounds since the principle of extraction itself was the same for both mechanical and automatic implementations. Conclusions: The automatic classification process was intended to reduce the time of the procedure and reduce the influence of the human factor, eliminating the possibility of medical error. To implement the process, a deep machine learning method was used, the array of information for which was to be a created phonotheque of acoustic signals of the respiratory system, which would include all types of respiratory noise concerning normal or pathological processes in the body.

Implementing Screening, Brief Intervention and Referral Intervention for Health Promotion and Disease Prevention in Hospital Settings in Alberta: A Pilot Study.

Objective: This study assessed the feasibility of implementing screening, brief intervention and referral (SBIR) intervention in hospital settings. Methods: This cross-sectional study evaluated the implementation of the SBIR intervention in a hospital in Alberta for tobacco use, alcohol intake, physical inactivity, and insufficient vegetable and fruit consumption. Patients were interviewed approximately 4-month later to collect data on the acceptability and effectiveness of the intervention received (n = 108). The data were primarily analyzed using descriptive statistics. Results: Of 108 patients, >80% agreed that "they were ok with being screened" for the risk factors during their hospital visit. Up to 68% of patients recalled the provider's brief education. At the follow-up, 20% of patients quit tobacco, 50% reduced alcohol use, 30% increased physical activity, and 25% increased vegetable and fruit intake. Conclusion: Risk factor screening was acceptable for patients. Patients recalled the brief education they received from healthcare providers. Patients reported risk-reducing changes in their risk factors. Our future work will integrate the SBIR approach within the Electronic Clinical Information System and use robust research methods to investigate the impact of SBIR on patients' behavior change.

A novel multistage ensemble approach for prediction and classification of diabetes.

Diabetes mellitus is a metabolic syndrome affecting millions of people worldwide. Every year, the rate of occurrence rises drastically. Diabetes-related problems across several vital organs of the body can be fatal if left untreated. Diabetes must be detected early to receive proper treatment, preventing the condition from escalating to severe problems. Tremendous health sciences and biotechnology advancements have resulted in massive data that generated massive Electronic Health Records and clinical information. The exponential increase of electronically gathered information has resulted in more complicated, accurate prediction models that can be updated continuously using machine learning techniques. This research mainly emphasizes discovering the best ensemble model for predicting diabetes. A new multistage ensemble model is proposed for diabetes prediction. In this model, accuracy is predicated on the Pima Indian Diabetes dataset. The accuracy of the proposed ensemble model is compared with the existing machine learning model, and the experimental results demonstrate the performance of the proposed model in terms of higher Precision, f-measure, Recall, and area under the curve.

Development and pilot implementation of a patient-oriented discharge summary for critically Ill patients.

BACKGROUNDPatients leaving the intensive care unit (ICU) often experience gaps in care due to deficiencies in discharge communication, leaving them vulnerable to increased stress, adverse events, readmission to ICU, and death. To facilitate discharge communication, written summaries have been implemented to provide patients and their families with information on medications, activity and diet restrictions, follow-up appointments, symptoms to expect, and who to call if there are questions. While written discharge summaries for patients and their families are utilized frequently in surgical, rehabilitation, and pediatric settings, few have been utilized in ICU settings. AIMTo develop an ICU specific patient-oriented discharge summary tool (PODS-ICU), and pilot test the tool to determine acceptability and feasibility.METHODSPatient-partners (i.e., individuals with lived experience as an ICU patient or family member of an ICU patient), ICU clinicians (i.e., physicians, nurses), and researchers met to discuss ICU patients’ specific informational needs and design the PODS-ICU through several cycles of discussion and iterative revisions. Research team nurses piloted the PODS-ICU with patient and family participants in two ICUs in Calgary, Canada. Follow-up surveys on the PODS-ICU and its impact on discharge were administered to patients, family participants, and ICU nurses.RESULTSMost participants felt that their discharge from the ICU was good or better (n = 13; 87.0%), and some (n = 9; 60.0%) participants reported a good understanding of why the patient was in ICU. Most participants (n = 12; 80.0%) reported that they understood ICU events and impacts on the patient’s health. While many patients and family participants indicated the PODS-ICU was informative and useful, ICU nurses reported that the PODS-ICU was “not reasonable” in their daily clinical workflow due to “time constraint”.CONCLUSIONThe PODS-ICU tool provides patients and their families with essential information as they discharge from the ICU. This tool has the potential to engage and empower patients and their families in ensuring continuity of care beyond ICU discharge. However, the PODS-ICU requires pairing with earlier discharge practices and integration with electronic clinical information systems to fit better into the clinical workflow for ICU nurses. Further refinement and testing of the PODS-ICU tool in diverse critical care settings is needed to better assess its feasibility and its effects on patient health outcomes.

Optimizing red blood cell transfusion practices in the intensive care unit: a multi-phased health technology reassessment

Health technology reassessment (HTR) is a process to manage existing health technologies to ensure ongoing optimal use. A model to guide HTR was developed; however, there is limited practical experience. This paper addresses this knowledge gap through the completion of a multi-phase HTR of red blood cell (RBC) transfusion practices in the intensive care unit (ICU). The HTR consisted of three phases and here we report on the final phase: the development, implementation, and evaluation of behavior change interventions aimed at addressing inappropriate RBC transfusions in an ICU. The interventions, comprised of group education and audit and feedback, were co-designed and implemented with clinical leaders. The intervention was evaluated through a controlled before-and-after pilot feasibility study. The primary outcome was the proportion of potentially inappropriate RBC transfusions (i.e., with a pre-transfusion hemoglobin of 70 g/L or more). There was marked variability in the monthly proportion of potentially inappropriate RBC transfusions. Relative to the pre-intervention phase, there was no significant difference in the proportion of potentially inappropriate RBC transfusions post-intervention. Lessons from this work include the importance of early and meaningful engagement of clinical leaders; tailoring the intervention modalities; and, efficient access to data through an electronic clinical information system. It was feasible to design, implement, and evaluate a tailored, multi-modal behavior change intervention in this small-scale pilot study. However, early evaluation of the intervention revealed no change in technology use leading to reflection on the important question of how the HTR model needs to be improved.

Clinical connectivity map for drug repurposing: using laboratory results to bridge drugs and diseases

BackgroundDrug repurposing, the process of identifying additional therapeutic uses for existing drugs, has attracted increasing attention from both the pharmaceutical industry and the research community. Many existing computational drug repurposing methods rely on preclinical data (e.g., chemical structures, drug targets), resulting in translational problems for clinical trials.ResultsIn this study, we propose a novel framework based on clinical connectivity mapping for drug repurposing to analyze therapeutic effects of drugs on diseases. We firstly establish clinical drug effect vectors (i.e., drug-laboratory results associations) by applying a continuous self-controlled case series model on a longitudinal electronic health record data, then establish clinical disease sign vectors (i.e., disease-laboratory results associations) by applying a Wilcoxon rank sum test on a large-scale national survey data. Eventually, a repurposing possibility score for each drug-disease pair is computed by applying a dot product-based scoring function on clinical disease sign vectors and clinical drug effect vectors. During the experiment, we comprehensively evaluate 392 drugs for 6 important chronic diseases (include asthma, coronary heart disease, congestive heart failure, heart attack, type 2 diabetes, and stroke). The experiment results not only reflect known associations between diseases and drugs, but also include some hidden drug-disease associations. The code for this paper is available at: https://github.com/HoytWen/CCMDRConclusionsThe proposed clinical connectivity map framework uses laboratory results found from electronic clinical information to bridge drugs and diseases, which make their relations explainable and has better translational power than existing computational methods. Experimental results demonstrate the effectiveness of our proposed framework, further case analysis also proves our method can be used to repurposing existing drugs opportunities.

Exploring hospital-based health information technology functions for patients with Alzheimer's Disease and related Dementias.

This study investigated whether hospital-adopted health information technology (HIT) is associated with a reduction in the frequency of preventable emergency department (ED) visits for patients with Alzheimer's Disease and Related Dementias (ADRD). We used data from the 2015 State Emergency Department Databases, Area Health Resources File, and the American Hospital Association Annual Survey Information Technology Supplement. We employed multivariable logistic regression models to examine the variation of the likelihood of having preventable ED visits by hospitals' adoption of HIT functions and adjusted for patient, hospital, and county-level factors. We focused on hospital-HIT functions related to patient engagement, routine integration and availability of electronic clinical information, frequency of hospital reported use of electronic patient information, and the provision of electronic notification to the patient's primary care provider. Approximately 23% of ADRD patients went to a hospital that often used electronic records from outside providers, and 75% of ADRD patients went to a hospital that provided electronic notification to the patient's primary care provider. Regression results showed that hospital reported use of electronic patient health information from outside providers (OR=0.88; p<0.001), provision of electronic notification to the patient's primary care physician inside and outside of the system (OR=0.91; p=0.013), and hospital-HIT patient engagement functionalities (OR=0.90; p<0.001) were associated with significantly lower preventable ED visit rates. The results of our study suggest that certain types of HIT functionalities may be useful for reducing preventable ED visits for ADRD patients.

Development and implementation of a clinical information system–based protocol to improve nurse satisfaction of end-of-life care in a single intensive care unit

BackgroundPatients treated in Australian intensive care units (ICUs) have an overall mortality rate of 5.05%. This is due to the critical nature of their disease, the increasing proportion of patients with multiple comorbidities, and advanced age. This has made treating patients during the end of life an integral part of intensive care practice and requires a high quality of care. With the increased use of electronic clinical information systems, a standardised protocol encompassing end-of-life care may provide an efficient method for documentation, communication, and timely delivery of comfort care. ObjectiveThe aim of the study was to determine if an electronic clinical information system–based end-of-life care protocol improved nurses' satisfaction with the practice of end-of-life care for patients in the ICU. DesignThis is a prospective single-centre observational study. SettingThe study was carried out at a 20-bed cardiothoracic and general ICU between 2015 and 2017. ParticipantsThe study participants were ICU nurses. InterventionElectronic clinical information–based end-of-life care protocol was used in the study. OutcomeThe primary outcome was nurse satisfaction obtained by a survey. ResultsThe number of respondents for the before survey and after survey was 58 (29%) and 64 (32%), respectively. There was a significant difference between the before survey and the after survey with regard to feeling comfortable in transitioning from curative treatment (median = 2 [interquartile range {IQR} = 2, 3] vs 3 [IQR = 2, 3], p = 0.03), feeling involved in the decision to move from curative treatment to end-of-life care (median = 2 [IQR = 2, 2] vs 2 [IQR 2, 3], p = 0.049), and feeling religious beliefs/rituals should be respected during the end-of-life process (median = 4 [IQR = 3, 4] vs. 4 [IQR = 4, 4], p = 0.02). There were some practices that had a low satisfaction rate on both the before survey and after survey. However, a high proportion of nurses were satisfied with many of the end-of-life care practices. ConclusionThe nurses were highly satisfied with many aspects of end-of-life care practices in this unit. The use of an electronic clinical information system–based protocol improved nurse satisfaction and perception of quality of end-of-life care practices for three survey questions.

Text mining with sentiment analysis on seafarers’ medical documents

Digital health systems contain large amounts of patient records, doctor notes, and prescriptions in text format. This information summarized over the electronic clinical information will lead to an improved quality of healthcare, the possibility of fewer medical errors, and low costs. Besides, seafarers are more vulnerable to have accidents, and prone to health hazards because of work culture, climatic changes, and personal habits. Therefore, text mining implementation in seafarers’ medical documents can generate better knowledge of medical issues that often happened onboard. Medical records are collected from digital health systems of Centro Internazionale Radio Medico (C.I.R.M.) which is an Italian Telemedical Maritime Assistance System (TMAS). Three years (2018–2020) patient data have been used for analysis. Adoption of both lexicon and Naïve Bayes’ algorithms was done to perform sentimental analysis and experiments were conducted over R statistical tool. Visualization of symptomatic information was done through word clouds and 96% of the correlation between medical problems and diagnosis outcome has been achieved. We validate the sentiment analysis with more than 80% accuracy and precision.

Abstract 334: Evaluating Sedation Regimens and Time to Awakening in Post Cardiac Arrest Patients

Introduction: Guidelines for post-arrest care recommend use of short acting sedation, but there is currently significant practice variation. We tested whether benzodiazepine use was associated with delayed awakening in this population. Methods: We performed a retrospective cohort study at a large academic medical center including comatose patients hospitalized after resuscitation from in- or out-of-hospital cardiac arrest from January 2010 to September 2019. We excluded patients with cardiac arrest secondary to primary neurological event or trauma, those with severe cerebral edema on initial head imaging, those who were awake post-arrest and those with severe shock for whom benzodiazepines might have been chosen for hemodynamic reasons. We extracted all medication information from the electronic medical record and standard clinical and outcome information from a prospective registry maintained at our center. We considered patients to be exposed to benzodiazepines if they received &gt; 10mg midazolam equivalents in the first 72 hours after cardiac arrest and censored cumulative mediation data at awakening for those who awakened before 72 hours. Our primary outcome of interest was days from arrest to awakening, which we defined as following verbal commands. We compared median time to awakening across sedation groups, then performed Cox regression to test the independent association of benzodiazepine exposure with time to awakening after adjusting for age, sex, weight, presenting rhythm, arrest location, initial serum creatinine, initial shock severity, initial neurological examination and presence of epileptiform. Results: Overall, 2,778 patients presented during the study period of which 621 met inclusion criteria for analysis and 209/621 (34%) awakened after a median of 4 [IQR 3 - 7] days. Patients who received benzodiazepines for sedation awakened significantly later than those who did not (5 days vs. 3 days, P=0.004). In adjusted regression, benzodiazepine exposure was independently associated with delayed awakening (adjusted hazard ratio 0.64 (95% CI 0.44 - 0.94)). Conclusion: Benzodiazepine exposure is associated with delayed awakening in comatose survivors of cardiac arrest.

The Association Between Pressure Ulcer/Injury Development and Short-term Mortality in Critically Ill Patients: A Retrospective Cohort Study.

The aim of this retrospective study was to examine the association between PU/I development and mortality in a large cohort of consecutively admitted critically ill patients. Data from adult patients ( >18 years of age) admitted to an intensive care unit (ICU) between 2010 and 2013 were extracted from the ICU electronic clinical information system. Patients were excluded if they had a PU/I present on admission, no recorded admission modified Jackson/Cubbin (mJ/C) or Sequential Organ Failure Assessment (SOFA) score, or their ICU outcome was undetermined. The mJ/C risk scale (score range 9-48) was used to assess the PU/I risk (the lower the score, the higher the PU/I risk), the SOFA score (score range 0-24; the higher the SOFA score, the sicker the patient, with a higher risk of death) was used to assess the severity of the condition and outcome. ICU outcome was defined as 1) moved from the ICU to a ward/recovering or 2) no response to ICU treatment/deceased. All data were transferred to statistical software for analysis. Logistic regression analysis was used to examine the outcome related to PU/I development, SOFA, and mJ/C scores. Descriptive contingency tables of different scenarios were used to further evaluate relationships among different risk factors related to mortality; the Wald χ2 test was used to assess the statistical significance of the contingency tables. Of the 6582 patients admitted, 6089 were included for analysis. Two hundred, one (201) had a PU/In on admission, 212 had missing mJ/C or SOFA scores, and ICU outcome was undetermined in 80 patients. Patient mean age was 61.1 ± 15.8 (range 18-94) years; 3891 (63.9%) were male, average length of stay (LOS) was 3.6 days, denoted by quartile (Q) (median 1.58 days; Q1: 0.9, Q3: 3.9 days), and 1589 (26.1%) stayed 3 days or more in the ICU. The incidence of PU/I was 6.9% (423 patients), and ICU mortality rate was 9.1% (n=553). The mean LOS of patients with PU/I was 13.35 ± 15.56 days (median 8.95, Q1: 4.88, Q3: 16.2) and 2.84 ± 3.87 days for patients with no PU/I (median: 1.20, Q1: 0.90, Q3: 3.17; P <.0001). Mean LOS was 3.42 ± 5.95 days (median: 1.30, Q1: 0.90, Q3: 3.70) among recovering and 5.00 ± 7.17 days among deceased patients (median 2.56, Q1: 1.26, Q3: 6.40; P <.0001). The proportion of patients with an admission mJ/C score of 29 or less ranged from 48.8% to 51.5%, and the mean SOFA score was 7.0 ± 3.2. PU/I development and SOFA or mJ/C scores were independent predictors of mortality. The probability of a negative outcome was higher in persons with PU/Is compared to persons with no PU/Is. Persons with lower SOFA scores (ie, less severely ill patients) and higher mJ/C scores for each factor separately (ie, at low risk of PU/I development) each factor separately had a lower mortality risk. PU/I development in critically ill patients treated at an ICU is an independent predictor of mortality, even though the PU/I incidence and hospital mortality were relatively low. The ICU admission SOFA and mJ/C score also were independent prognosticators of ICU mortality. Future research could focus on the role of different steps in the cascade of PU/I development, especially to the role of inflammation.

The prevalence and risk of non-infectious comorbidities in HIV-infected and non-HIV infected men attending general practice in Australia.

BackgroundNon-AIDS-related mortality rates among HIV-infected patients still exceed those of their uninfected peers. A major driver of this excess mortality is a higher risk of non-infectious comorbidities, including cardiovascular disease, chronic kidney disease, type 2 diabetes mellitus, osteoporosis and cancer. The prevalence of mental illness and other chronic non-infectious comorbidities is identified as a primary concern of antiretroviral prescribers in Australia.MethodsWe conducted a cross-sectional, observational study using data from MedicineInsight, a large-scale Australian primary care database comprising longitudinal data from electronic clinical information systems. The HIV-infected cohort included all men with a recorded diagnosis of HIV. The non-HIV-infected cohort comprised all other men from the same practices. The prevalence and risk of cardiovascular disease, chronic kidney disease, type 2 diabetes mellitus, osteoporosis, cancer, anxiety and depression were compared between the groups.ResultsWe included 2,406 HIV-infected males and 648,205 males with no record of HIV diagnosis attending primary care in this study. HIV-infected men were less socioeconomically disadvantaged and more urban-dwelling than men in the primary care cohort. We found that HIV-infected men attending primary care in Australia are at increased risk of chronic kidney disease, cancer, osteoporosis, anxiety and depression. There appears to be a risk of premature onset of cardiovascular disease, osteoporosis and cancer among younger HIV-infected patients. There is a high prevalence of anxiety and depression among HIV-infected men.ConclusionsIncreased prevalence of non-infectious comorbidities among HIV-infected men has broad implications for the effective management of those with these chronic conditions. Education to raise awareness among both HIV-infected men and their care providers, together with a greater focus on risk reduction, monitoring and preventive care, may be effective strategies in primary healthcare settings to further narrow the gap in health outcomes between people living with HIV and their uninfected counterparts.

Defining the high-risk patient

As the volume of surgery continues to grow worldwide, the identification of high-risk patients is an important goal to guide clinical decision making in the perioperative period. Risk stratification evolved over the last decade from simple risk stratification tools, still used widely in the clinical arena to more sophisticated risk prediction models based on machine learning and latent class analysis, which can be incorporated into a well-developed electronic patient record or critical care clinical information system. As the debate about which patients will benefit most from critical care admission and interventions is still ongoing, the identification of the high-risk patient is a continuing challenge. In this review we will summarise the latest developments in the use of these risk stratification tools and risk prediction models, which can be utilised to identify the high-risk surgical candidate.

Postponing intubation in spontaneously breathing major trauma patients upon emergency room admission does not impair outcome

BackgroundPre-hospital emergency anaesthesia and tracheal intubation are life-saving interventions in trauma patients. However, there is evidence suggesting that the risks associated with both procedures outweigh the benefits. Thus, we assessed whether induction of anaesthesia and tracheal intubation of trauma patients can be postponed in spontaneously breathing patients until emergency room (ER) admission without increasing mortality.MethodsRetrospective analysis of major trauma patients either intubated on-scene by an emergency medical service (EMS) physician (pre-hospital intubation, PHI) or within the first 10 min after admission at a level 1 trauma centre (emergency room intubation, ERI). Data was extracted from the German Trauma Registry, hospital patient data management and electronic clinical information system.ResultsFrom a total of 946 major trauma cases documented between 2010 and 2017, 294 patients matched the study inclusion criteria. Mortality rate of PHI (N = 258) vs. ERI (N = 36) patients was 26.4% vs. 16.7% (p = 0.3). After exclusion of patients with severe traumatic brain injury and/or pre-hospital cardiac arrest, mortality rate of PHI (N = 100) vs. ERI patients (N = 29) was 6% vs. 17.2%, (p = 0.07). Median on-scene time was significantly (p < 0.01) longer in PHI (30 min; IQR: 21–40) vs. ERI patients (20 min; IQR: 15–28).ConclusionsThere was no statistical difference in mortality rates of spontaneously breathing trauma patients intubated on-scene when compared with patients intubated immediately after hospital admission. Due to the retrospective study design and small case number, further studies evaluating the impact of airway management timing in sufficiently breathing trauma patients are warranted.

How the delivery of HIV care in Canada aligns with the Chronic Care Model: A qualitative study.

With the advent of continuous antiretroviral therapy, HIV has become a complex chronic, rather than acute, condition. The Chronic Care Model (CCM) provides an integrated approach to the delivery of care for people with chronic conditions that could therefore be applied to the delivery of care for people living with HIV. Our objective was to assess the alignment of HIV care settings with the CCM. We conducted a mixed methods study to explore structures, organization and care processes of Canadian HIV care settings. The quantitative results of phase one are published elsewhere. For phase two, we conducted semi-structured interviews with key informants from 12 HIV care settings across Canada. Irrespective of composition of the care setting or its location, HIV care in Canada is well aligned with several components of the CCM, most prominently in the areas of linkage to community resources and delivery system design with inter-professional team-based care. We propose the need for improvements in the availability of electronic clinical information systems and self-management support services to support better care delivery and health outcomes among people living with HIV in Canada.

Test collections for electronic health record-based clinical information retrieval.

ObjectivesTo create test collections for evaluating clinical information retrieval (IR) systems and advancing clinical IR research.Materials and MethodsElectronic health record (EHR) data, including structured and free-text data, from 45 000 patients who are a part of the Mayo Clinic Biobank cohort was retrieved from the clinical data warehouse. The clinical IR system indexed a total of 42 million free-text EHR documents. The search queries consisted of 56 topics developed through a collaboration between Mayo Clinic and Oregon Health & Science University. We described the creation of test collections, including a to-be-evaluated document pool using five retrieval models, and human assessment guidelines. We analyzed the relevance judgment results in terms of human agreement and time spent, and results of three levels of relevance, and reported performance of five retrieval models.ResultsThe two judges had a moderate overall agreement with a Kappa value of 0.49, spent a consistent amount of time judging the relevance, and were able to identify easy and difficult topics. The conventional retrieval model performed best on most topics while a concept-based retrieval model had better performance on the topics requiring conceptual level retrieval.DiscussionIR can provide an alternate approach to leveraging clinical narratives for patient information discovery as it is less dependent on semantics. Our study showed the feasibility of test collections along with a few challenges.ConclusionThe conventional test collections for evaluating the IR system show potential for successfully evaluating clinical IR systems with a few challenges to be investigated.

Model for the interoperability between health service providers (IPS), based on the electronic clinical information standard (HL7) and architecture to design and develop distributed systems (SOA)

This study addresses the need to exchange clinical records, efficiently and uniform among health institutions (IPS Spanish acronym for Instituciones Prestadoras de Salud), which is generated in clinical care users from using the Hospital Information Systems (HIS). From defining a model for interoperability, with reference to the regulations governing the General System of Social Security in Health in Colombia (SGSSS Spanish acronym for Sistema General de Seguridad Social en Salud), the standards to facilitate electronic exchange of clinical information Health Level Seven (HL7) and service oriented architecture (SOA). The model it wasdesigned in two dimensions, on the one hand horizontally would facilitate electronic exchange of clinical information between IPS and on the other side vertically was projected was obtained as they settled components for the exchange of healthcare and administrative records the SGSSS different actors, in this case with the health Promotion Companies (EPS Spanish acronym for Empresas Promotoras de Salud) and the Territorial Entities through health secretaries.

Validation and Clinical Impact of the Oncomine Myeloid Targeted DNA and RNA Ion Semiconductor Sequencing Assay

Introduction: The expanding diagnostic and clinical significance of genes associated with myeloid malignancies necessitates higher throughput testing. Targeted next-generation sequencing (NGS) of DNA and RNA may be an ideal approach to capture these variants and eventually streamline, or replace, conventional cytogenetic testing. We present our clinical validation of the OncomineTM Myeloid NGS assay and early experience regarding the clinical impact in patients with suspected or known myeloid malignancies.Methods: OncomineTM Myeloid (Thermo Fisher Scientific) panel (OMP) validation was conducted at Kingston Health Sciences Centre (KHSC) on anonymized and commercial samples according to IQMH and ACMG standards for NGS (PMID: 23887774). As of April 2018 the test has been formally validated and offered at KHSC. Prior to this, patients were consented at the time of blood (PB) or bone marrow (BM) collection for research-based testing. BM and PB samples were collected, gDNA and RNA extracted, and libraries prepared using the Ion ChefTM System. Sequencing was completed using the OMP on Ion PGM (research phase) and S5XL (clinical) sequencers. The OMP uses amplicon-based semiconductor sequencing technology to cover 40 DNA genes recurrently mutated in myeloid malignancies (23 hotspots and 17 full coding), 29 RNA fusion driver genes and 10 gene expression targets. Sequencing data were analyzed using Torrent Suite, Torrent Variant Caller, Ion Reporter (v.5.2-5.6) and Alamut software. The OMP includes a Torrent Suite FLT3-ITD “plug-in” and Ion Reporter “Oncomine filter”. Orthogonal clinical assays were performed where necessary for additional confirmation. Variants were interpreted based on a 4-tier classification system developed by Li et al (PMID: 27993330). Variants in the top 3 tiers were reported after assessment by at least one clinician and one certified medical geneticist. Actionability was assessed in the context of electronic diagnostic and clinical information and molecular board review.Results: Validation involved 24 paired DNA-RNA samples previously run at KHSC on an early access OMP version and also at an external site (kind exchange by Dr. N. Carson, Saint John, NB), along with SeraCareTM DNA and RNA controls. Validation run metrics were as follows: DNA means (mapped reads 1306216, read length 226bp, uniformity 98%, depth 2518), RNA means (mapped reads 260350, read length 114bp). Complete concordance was found for RNA variants while the DNA filter chain was only modified to better capture a JAK2 exon 12 variant in a SeraCare control. The minimum depth of coverage was subsequently set to 400X for somatic DNA variants and sensitivity set at 5% variant allele fraction (VAF) for clinical reporting. To date, we have performed sequencing for 38 samples from 35 unique patients (avg age = 64.5y). Of these, 12/35 (34%) involved suspected or known myelodysplastic syndromes (MDS), 12/35 (34%) with acute myeloid leukemia (AML), 4/35 (12%) with query myeloproliferative neoplasms (MPNs), 2/35 (5%) with MDS/MPN, and 5/35 (14%) other (2 B-ALL, 1 aplastic, 1 hairy cell + ?MDS, 1 ?CHIP). OMP detected 56 variants (in 80% of cases), including 43% tier 1, 48% tier 2, and 9% tier 3 variants. The most frequently mutated genes included TET2 (21%), SRSF2 (14%), SF3B1 (9%), TP53 (5%), and RUNX1 (5%). The average VAF was 36% for all samples, with an average of 1.5 variants per sample. Of detected variants, 73% were potentially actionable. Specifically, 51% of actionable variants facilitated or clarified diagnosis (38% of total variants), 32% (23%) affected prognosis, and 17% (13%) had the potential to affect treatment decisions. Among 10 patients with suspected (but subthreshold for) MDS or MPN, clonality was detected in 5, while 5 had no variants, prompting further investigation of reversible cytopenia or cytosis. We are rapidly accruing patients and expect to have OMP profiles for at least 100 patients at the time of the ASH 2018 meeting.Conclusions: Oncomine Myeloid DNA and RNA molecular profiling has found greatest clinical use at our centre in the realm of MDS and AML. In the majority of patients, OMP permits the identification of actionable variants that may aid clinicians in achieving or clarifying diagnoses, inform follow-up and prognosis, and guide treatment decisions. The OMP represents a promising strategy to address the challenge of expanding, important molecular features of myeloid malignancies. DisclosuresNo relevant conflicts of interest to declare.

The NIHR Health Informatics Collaborative: sharing electronic NHS clinical information to capture the hepatitis C treatment revolution

The NIHR Health Informatics Collaborative: sharing electronic NHS clinical information to capture the hepatitis C treatment revolution