Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pragmatic and Ethical Challenges of Incorporating the Genome into the Electronic Medical Record.

ABSTRACT: Recent successes in the use of gene sequencing for patient care highlight the potential of genomic medicine. For genomics to become a part of usual care, pertinent elements of a patient's genomic test must be communicated to the most appropriate care providers. Electronic medical records may serve as a useful tool for storing and disseminating genomic data. Yet, the structure of existing EMRs and the nature of genomic data pose a number of pragmatic and ethical challenges in their integration. Through a review of the recent genome-EMR integration literature, we explore concrete examples of these challenges, categorized under four key questions: What data will we store? How will we store it? How will we use it? How will we protect it? We conclude that genome-EMR integration requires a rigorous, multi-faceted and interdisciplinary approach of study. Problems facing the field are numerous, but few are intractable.

SUBMITTER: Nishimura AA

PROVIDER: S-EPMC4489153 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Pragmatic and Ethical Challenges of Incorporating the Genome into the Electronic Medical Record.

Nishimura Adam A AA Tarczy-Hornoch Peter P Shirts Brian H BH

Current genetic medicine reports 20141201 4

Recent successes in the use of gene sequencing for patient care highlight the potential of genomic medicine. For genomics to become a part of usual care, pertinent elements of a patient's genomic test must be communicated to the most appropriate care providers. Electronic medical records may serve as a useful tool for storing and disseminating genomic data. Yet, the structure of existing EMRs and the nature of genomic data pose a number of pragmatic and ethical challenges in their integration. T ...[more]

PMID: 26146597

Similar Datasets

A pragmatic method for electronic medical record-based observational studies: developing an electronic medical records retrieval system for clinical research.

Project description:The use of electronic medical record (EMR) data is necessary to improve clinical research efficiency. However, it is not easy to identify patients who meet research eligibility criteria and collect the necessary information from EMRs because the data collection process must integrate various techniques, including the development of a data warehouse and translation of eligibility criteria into computable criteria. This research aimed to demonstrate an electronic medical records retrieval system (ERS) and an example of a hospital-based cohort study that identified both patients and exposure with an ERS. We also evaluated the feasibility and usefulness of the method. The system was developed and evaluated. In total, 800 000 cases of clinical information stored in EMRs at our hospital were used. The feasibility and usefulness of the ERS, the method to convert text from eligible criteria to computable criteria, and a confirmation method to increase research data accuracy. To comprehensively and efficiently collect information from patients participating in clinical research, we developed an ERS. To create the ERS database, we designed a multidimensional data model optimised for patient identification. We also devised practical methods to translate narrative eligibility criteria into computable parameters. We applied the system to an actual hospital-based cohort study performed at our hospital and converted the test results into computable criteria. Based on this information, we identified eligible patients and extracted data necessary for confirmation by our investigators and for statistical analyses with our ERS. We propose a pragmatic methodology to identify patients from EMRs who meet clinical research eligibility criteria. Our ERS allowed for the efficient collection of information on the eligibility of a given patient, reduced the labour required from the investigators and improved the reliability of the results.

| S-EPMC3533000 | biostudies-literature

Overcoming the Challenges of Unstructured Data in Multisite, Electronic Medical Record-based Abstraction.

Project description:Unstructured data encountered during retrospective electronic medical record (EMR) abstraction has routinely been identified as challenging to reliably abstract, as these data are often recorded as free text, without limitations to format or structure. There is increased interest in reliably abstracting this type of data given its prominent role in care coordination and communication, yet limited methodological guidance exists.As standard abstraction approaches resulted in substandard data reliability for unstructured data elements collected as part of a multisite, retrospective EMR study of hospital discharge communication quality, our goal was to develop, apply and examine the utility of a phase-based approach to reliably abstract unstructured data. This approach is examined using the specific example of discharge communication for warfarin management.We adopted a "fit-for-use" framework to guide the development and evaluation of abstraction methods using a 4-step, phase-based approach including (1) team building; (2) identification of challenges; (3) adaptation of abstraction methods; and (4) systematic data quality monitoring.Unstructured data elements were the focus of this study, including elements communicating steps in warfarin management (eg, warfarin initiation) and medical follow-up (eg, timeframe for follow-up).After implementation of the phase-based approach, interrater reliability for all unstructured data elements demonstrated ?'s of ?0.89-an average increase of +0.25 for each unstructured data element.As compared with standard abstraction methodologies, this phase-based approach was more time intensive, but did markedly increase abstraction reliability for unstructured data elements within multisite EMR documentation.

| S-EPMC5024721 | biostudies-literature

Electronic Medical Record Inaccuracies: Multicenter Analysis of Challenges with Modified Lung Cancer Screening Criteria.

Project description:The National Comprehensive Cancer Network expanded their lung cancer screening (LCS) criteria to comprise one additional clinical risk factor, including chronic obstructive pulmonary disease (COPD). The electronic medical record (EMR) is a source of clinical information that could identify high-risk populations for LCS, including a diagnosis of COPD; however, an unsubstantiated COPD diagnosis in the EMR may lead to inappropriate LCS referrals. We aimed to detect the prevalence of unsubstantiated COPD diagnosis in the EMR for LCS referrals, to determine the efficacy of utilizing the EMR as an accurate population-based eligibility screening "trigger" using modified clinical criteria. We performed a multicenter review of all individuals referred to three LCS programs from 2012 to 2015. Each individual's EMR was searched for COPD diagnostic terms and the presence of a diagnostic pulmonary functionality test (PFT). An unsubstantiated COPD diagnosis was defined by an individual's EMR containing a COPD term with no PFTs present, or the presence of PFTs without evidence of obstruction. A total of 2834 referred individuals were identified, of which 30% (840/2834) had a COPD term present in their EMR. Of these, 68% (571/840) were considered unsubstantiated diagnoses: 86% (489/571) due to absent PFTs and 14% (82/571) due to PFTs demonstrating no evidence of postbronchodilation obstruction. A large proportion of individuals referred for LCS may have an unsubstantiated COPD diagnosis within their EMR. Thus, utilizing the EMR as a population-based eligibility screening tool, employing expanded criteria, may lead to individuals being referred, potentially, inappropriately for LCS.

| S-EPMC7136785 | biostudies-literature

Creating a Medication Therapy Observational Research Database from an Electronic Medical Record: Challenges and Data Curation

Project description: Not available

| S-EPMC10849827 | biostudies-literature

Genome-wide association study of hyperthyroidism based on electronic medical record from Taiwan.

Project description:Excess thyroid hormones have complex metabolic effects, particularly hyperthyroidism, and are associated with various cardiovascular risk factors. Previous candidate gene studies have indicated that genetic variants may contribute to this variable response. Electronic medical record (EMR) biobanks containing clinical and genomic data on large numbers of individuals have great potential to inform the disease comorbidity development. In this study, we combined electronic medical record (EMR) -derived phenotypes and genotype information to conduct a genome-wide analysis of hyperthyroidism in a 35,009-patient cohort in Taiwan. Diagnostic codes were used to identify 2,767 patients with hyperthyroidism. Our genome-wide association study (GWAS) identified 44 novel genomic risk markers in 10 loci on chromosomes 2, 6, and 14 (P < 5 × 10-14), including CTLA4, HCP5, HLA-B, POU5F1, CCHCR1, HLA-DRA, HLA-DRB9, TSHR, RPL17P3, and CEP128. We further conducted a comorbidity analysis of our results, and the data revealed a strong correlation between hyperthyroidism patients with thyroid storm and stroke. In this study, we demonstrated application of the PheWAS using large EMR biobanks to inform the comorbidity development in hyperthyroidism patients. Our data suggest significant common genetic risk factors in patients with hyperthyroidism. Additionally, our results show that sex, body mass index (BMI), and thyroid storm are associated with an increased risk of stroke in subjects with hyperthyroidism.

| S-EPMC9390483 | biostudies-literature

Electronic medical record implementation in tertiary care: factors influencing adoption of an electronic medical record in a cancer centre.

Project description:BackgroundElectronic Medical Records (EMRs) are one of a range of digital health solutions that are key enablers of the data revolution transforming the health sector. They offer a wide range of benefits to health professionals, patients, researchers and other key stakeholders. However, effective implementation has proved challenging.MethodsA qualitative methodology was used in the study. Interviews were conducted with 12 clinical and administrative staff of a cancer centre at one-month pre-launch and eight clinical and administrative staff at 12-months post-launch of an EMR. Data from the interviews was collected via audio recording. Audio recordings were transcribed, de-identified and analysed to identify staff experiences with the EMR.ResultsData from the pre-implementation interviews were grouped into four categories: 1) Awareness and understanding of EMR; 2) Engagement in launch process; 3) Standardisation and completeness of data; 4) Effect on workload. Data from the post-launch interviews were grouped into six categories: 1) Standardisation and completeness of data; 2) Effect on workload; 3) Feature completeness and functionality; 4) Interaction with technical support; 5) Learning curve; 6) Buy-in from staff. Two categories: Standardisation and completeness of data and effect on workload were common across pre and post-implementation interviews.ConclusionFindings from this study contribute new knowledge on barriers and enablers to the implementation of EMRs in complex clinical settings. Barriers to successful implementation include lack of technical support once the EMR has launched, health professional perception the EMR increases workload, and the learning curve for staff adequately familiarize themselves with using the EMR.

| S-EPMC7789279 | biostudies-literature

Electronic medical record use in pediatric primary care.

Project description:To characterize patterns of electronic medical record (EMR) use at pediatric primary care acute visits.Direct observational study of 529 acute visits with 27 experienced pediatric clinician users.For each 20 s interval and at each stage of the visit according to the Davis Observation Code, we recorded whether the physician was communicating with the family only, using the computer while communicating, or using the computer without communication. Regression models assessed the impact of clinician, patient and visit characteristics on overall visit length, time spent interacting with families, and time spent using the computer while interacting.The mean overall visit length was 11:30 (min:sec) with 9:06 spent in the exam room. Clinicians used the EMR during 27% of exam room time and at all stages of the visit (interacting, chatting, and building rapport; history taking; formulation of the diagnosis and treatment plan; and discussing prevention) except the physical exam. Communication with the family accompanied 70% of EMR use. In regression models, computer documentation outside the exam room was associated with visits that were 11% longer (p=0.001), and female clinicians spent more time using the computer while communicating (p=0.003).The 12 study practices shared one EMR.Among pediatric clinicians with EMR experience, conversation accompanies most EMR use. Our results suggest that efforts to improve EMR usability and clinician EMR training should focus on use in the context of doctor-patient communication. Further study of the impact of documentation inside versus outside the exam room on productivity is warranted.

| S-EPMC3005866 | biostudies-other

A genome-wide association study of heparin-induced thrombocytopenia using an electronic medical record.

Project description:Heparin-induced thrombocytopenia (HIT) is an unpredictable, potentially catastrophic adverse effect of heparin treatment resulting from an immune response to platelet factor 4 (PF4)/heparin complexes. No genome-wide evaluations have been performed to identify potential genetic influences on HIT. Here, we performed a genome-wide association study (GWAS) and candidate gene study using HIT cases and controls identified using electronic medical records (EMRs) coupled to a DNA biobank and attempted to replicate GWAS associations in an independent cohort. We subsequently investigated influences of GWAS-associated single nucleotide polymorphisms (SNPs) on PF4/heparin antibodies in non-heparin treated individuals. In a recessive model, we observed significant SNP associations (odds ratio [OR] 18.52; 95% confidence interval [CI] 6.33-54.23; p=3.18×10(-9)) with HIT near the T-Cell Death-Associated Gene 8 (TDAG8). These SNPs are in linkage disequilibrium with a missense TDAG8 SNP. TDAG8 SNPs trended toward an association with HIT in replication analysis (OR 5.71; 0.47-69.22; p=0.17), and the missense SNP was associated with PF4/heparin antibody levels and positive PF4/heparin antibodies in non-heparin treated patients (OR 3.09; 1.14-8.13; p=0.02). In the candidate gene study, SNPs at HLA-DRA were nominally associated with HIT (OR 0.25; 0.15-0.44; p=2.06×10(-6)). Further study of TDAG8 and HLA-DRA SNPs is warranted to assess their influence on the risk of developing HIT.

| S-EPMC4433536 | biostudies-literature

Electronic Health Record Skills Workshop for Medical Students.

Project description:Introduction:The adoption of electronic health records (EHRs) presents new challenges for information gathering, documentation, and patient care. Medical students spend a significant amount of time using the EHR during their clerkship experiences and will continue to do so as they progress to residency. However, formal training varies between institutions and leaves gaps in data-gathering skills, documentation skills, and order entry-these three skills formed the basis for our learning objectives. We designed a workshop using a simulated EHR to teach these skills. Methods:We offered the workshop during a class-wide transition-to-internship course for senior medical students. After a brief didactic, students worked in small groups using a simulated EHR to complete cases addressing each of the three learning objectives. Faculty facilitators assisted groups and then guided a large-group discussion of the challenges encountered during the cases. Results:Twenty-five senior medical students attended the first optional workshop. Of these students, 66.7% recommended that the workshop continue to be included in the curriculum. Comments from those who recommended otherwise suggested that many of them would recommend the workshop if it used our local EHR (Epic). Correct answers to the factual questions increased for most questions between the pretest and the posttest. Confidence to perform all skills targeted in the learning objectives increased between the pretest and the posttest. Discussion:This EHR workshop was well received by senior medical students and increased confidence in EHR skills, including data gathering, documentation, and handling unsolicited information with a plan including order entry.

| S-EPMC6946580 | biostudies-literature

A genome-wide association study of red blood cell traits using the electronic medical record.

Project description:The Electronic Medical Record (EMR) is a potential source for high throughput phenotyping to conduct genome-wide association studies (GWAS), including those of medically relevant quantitative traits. We describe use of the Mayo Clinic EMR to conduct a GWAS of red blood cell (RBC) traits in a cohort of patients with peripheral arterial disease (PAD) and controls without PAD.Results for hemoglobin level, hematocrit, RBC count, mean corpuscular volume, mean corpuscular hemoglobin, and mean corpuscular hemoglobin concentration were extracted from the EMR from January 1994 to September 2009. Out of 35,159 RBC trait values in 3,411 patients, we excluded 12,864 values in 1,165 patients that had been measured during hospitalization or in the setting of hematological disease, malignancy, or use of drugs that affect RBC traits, leaving a final genotyped sample of 3,012, 80% of whom had ?2 measurements. The median of each RBC trait was used in the genetic analyses, which were conducted using an additive model that adjusted for age, sex, and PAD status. We identified four genomic loci that were associated (P<5 × 10(-8)) with one or more of the RBC traits (HBLS1/MYB on 6q23.3, TMPRSS6 on 22q12.3, HFE on 6p22.1, and SLC17A1 on 6p22.2). Three of these loci (HBLS1/MYB, TMPRSS6, and HFE) had been identified in recent GWAS and the allele frequencies, effect sizes, and the directions of effects of the replicated SNPs were similar to the prior studies.Our results demonstrate feasibility of using the EMR to conduct high throughput genomic studies of medically relevant quantitative traits.

| S-EPMC2946914 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data