Dataset Information

Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center.

ABSTRACT: Next Generation Sequencing (NGS) methods are driving profound changes in biomedical research, with a growing impact on patient care. Many academic medical centers are evaluating potential models to prepare for the rapid increase in NGS information needs. This study sought to investigate (1) how and where sequencing data is generated and analyzed, (2) research objectives and goals for NGS, (3) workforce capacity and unmet needs, (4) storage capacity and unmet needs, (5) available and anticipated funding resources, and (6) future challenges. As a precursor to informed decision making at our institution, we undertook a systematic needs assessment of investigators using survey methods. We recruited 331 investigators from over 60 departments and divisions at the University of Pittsburgh Schools of Health Sciences and had 140 respondents, or a 42% response rate. Results suggest that both sequencing and analysis bottlenecks currently exist. Significant educational needs were identified, including both investigator-focused needs, such as selection of NGS methods suitable for specific research objectives, and program-focused needs, such as support for training an analytic workforce. The absence of centralized infrastructure was identified as an important institutional gap. Key principles for organizations managing this change were formulated based on the survey responses. This needs assessment provides an in-depth case study which may be useful to other academic medical centers as they identify and plan for future needs.

SUBMITTER: Geskin A

PROVIDER: S-EPMC4483235 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center.

Geskin Albert A Legowski Elizabeth E Chakka Anish A Chandran Uma R UR Barmada M Michael MM LaFramboise William A WA Berg Jeremy J Jacobson Rebecca S RS

PloS one 20150626 6

Next Generation Sequencing (NGS) methods are driving profound changes in biomedical research, with a growing impact on patient care. Many academic medical centers are evaluating potential models to prepare for the rapid increase in NGS information needs. This study sought to investigate (1) how and where sequencing data is generated and analyzed, (2) research objectives and goals for NGS, (3) workforce capacity and unmet needs, (4) storage capacity and unmet needs, (5) available and anticipated ...[more]

PMID: 26115441

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Project description:BACKGROUND:Electronic medical records (EMRs) contain a wealth of information that can support data-driven decision making in health care policy design and service planning. Although research using EMRs has become increasingly prevalent, challenges such as coding inconsistency, data validity, and lack of suitable measures in important domains still hinder the progress. OBJECTIVE:The objective of this study was to design a structured way to process records in administrative EMR systems for health services research and assess validity in selected areas. METHODS:On the basis of a local hospital EMR system in Singapore, we developed a structured framework for EMR data processing, including standardization and phenotyping of diagnosis codes, construction of cohort with multilevel views, and generation of variables and proxy measures to supplement primary data. Disease complexity was estimated by Charlson Comorbidity Index (CCI) and Polypharmacy Score (PPS), whereas socioeconomic status (SES) was estimated by housing type. Validity of modified diagnosis codes and derived measures were investigated. RESULTS:Visit-level (N=7,778,761) and patient-level records (n=549,109) were generated. The International Classification of Diseases, Tenth Revision, Australian Modification (ICD-10-AM) codes were standardized to the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) with a mapping rate of 87.1%. In all, 97.4% of the ICD-9-CM codes were phenotyped successfully using Clinical Classification Software by Agency for Healthcare Research and Quality. Diagnosis codes that underwent modification (truncation or zero addition) in standardization and phenotyping procedures had the modification validated by physicians, with validity rates of more than 90%. Disease complexity measures (CCI and PPS) and SES were found to be valid and robust after a correlation analysis and a multivariate regression analysis. CCI and PPS were correlated with each other and positively correlated with health care utilization measures. Larger housing type was associated with lower government subsidies received, suggesting association with higher SES. Profile of constructed cohorts showed differences in disease prevalence, disease complexity, and health care utilization in those aged above 65 years and those aged 65 years or younger. CONCLUSIONS:The framework proposed in this study would be useful for other researchers working with EMR data for health services research. Further analyses would be needed to better understand differences observed in the cohorts.

Project description:Introduction. The value of tablet computer use in medical education is an area of considerable interest, with preliminary investigations showing that the majority of medical trainees feel that tablet computers added value to the curriculum. This study investigated potential differences in tablet computer use between medical students and resident physicians. Materials & Methods. Data collection for this survey was accomplished with an anonymous online questionnaire shared with the medical students and residents at Southern Illinois University School of Medicine (SIU-SOM) in July and August of 2012. Results. There were 76 medical student responses (26% response rate) and 66 resident/fellow responses to this survey (21% response rate). Residents/fellows were more likely to use tablet computers several times daily than medical students (32% vs. 20%, p = 0.035). The most common reported uses were for accessing medical reference applications (46%), e-Books (45%), and board study (32%). Residents were more likely than students to use a tablet computer to access an electronic medical record (41% vs. 21%, p = 0.010), review radiology images (27% vs. 12%, p = 0.019), and enter patient care orders (26% vs. 3%, p < 0.001). Discussion. This study shows a high prevalence and frequency of tablet computer use among physicians in training at this academic medical center. Most residents and students use tablet computers to access medical references, e-Books, and to study for board exams. Residents were more likely to use tablet computers to complete clinical tasks. Conclusions. Tablet computer use among medical students and resident physicians was common in this survey. All learners used tablet computers for point of care references and board study. Resident physicians were more likely to use tablet computers to access the EMR, enter patient care orders, and review radiology studies. This difference is likely due to the differing educational and professional demands placed on resident physicians. Further study is needed better understand how tablet computers and other mobile devices may assist in medical education and patient care.

Project description:BackgroundIt is important to monitor the scope of clinical research of all types, to involve participants of all ages and subgroups in studies that are appropriate to their condition, and to ensure equal access and broad validity of the findings.ObjectiveWe conducted a review of clinical research performed at New York University with the following objectives: (1) to determine the utility of institutional administrative data to characterize clinical research activity; (2) to assess the inclusion of special populations; and (3) to determine if the type, initiation, and completion of the study differed by age.MethodsData for all studies that were institutional review board-approved between January 1, 2014, and November 2, 2016, were obtained from the research navigator system, which was launched in November 2013. One module provided details about the study protocol, and another module provided the characteristics of individual participants. Research studies were classified as observational or interventional. Descriptive statistics were used to assess the characteristics of clinical studies across the lifespan, by type, and over time.ResultsA total of 22%-24% of studies included children (minimum age <18 years) and 4%-5% focused exclusively on pediatrics. Similarly, 64%-72% of studies included older patients (maximum age >65 years) but only 5%-12% focused exclusively on geriatrics. Approximately 85% of the studies included both male and female participants. Of the remaining studies, those open only to girls or women were approximately 3 times as common as those confined to boys or men. A total of 56%-58% of projects focused on nonvulnerable patients. Among the special populations studied, children (12%-15%) were the most common. Noninterventional trial types included research on human data sets (24%), observational research (22%), survey research (16%), and biospecimen research (8%). The percentage of projects designed to test an intervention in a vulnerable population increased from 17% in 2014 to 21% in 2015.ConclusionsPediatric participants were the special population that was most often studied based on the number of registered projects that included children and adolescents. However, they were much less likely to be successfully enrolled in research studies compared with adults older than 65 years. Only 20% of the studies were interventional, and 20%-35% of participants in this category were from vulnerable populations. More studies are exclusively devoted to women's health issues compared with men's health issues.

Project description:ImportanceSome patients are avoiding essential care for fear of contracting coronavirus disease 2019 (COVID-19) in hospitals. There are few data, however, on the risk of acquiring COVID-19 in US hospitals.ObjectiveTo assess the incidence of COVID-19 among patients hospitalized at a large US academic medical center in the 12 weeks after the first inpatient case was identified.Design, setting, and participantsThis cohort study included all patients admitted to Brigham and Women's Hospital (Boston, Massachusetts) between March 7 and May 30, 2020. Follow-up occurred through June 17, 2020. Medical records for all patients who first tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse-transcription polymerase chain reaction (RT-PCR) on hospital day 3 or later or within 14 days of discharge were reviewed.ExposuresA comprehensive infection control program was implemented that included dedicated COVID-19 units with airborne infection isolation rooms, personal protective equipment in accordance with US Centers for Disease Control and Prevention recommendations, personal protective equipment donning and doffing monitors, universal masking, restriction of visitors, and liberal RT-PCR testing of symptomatic and asymptomatic patients.Main outcomes and measuresWhether infection was community or hospital acquired based on timing of tests, clinical course, and exposures.ResultsOver the 12-week period, 9149 patients (mean [SD] age, 46.1 [26.4] years; median [IQR] age, 51 years [30-67 years]; 5243 female [57.3%]) were admitted to the hospital, for whom 7394 SARS-CoV-2 RT-PCR tests were performed; 697 COVID-19 cases were confirmed, translating into 8656 days of COVID-19-related care. Twelve of the 697 hospitalized patients with COVID-19 (1.7%) first tested positive on hospital day 3 or later (median, 4 days; range, 3-15 days). Of these, only 1 case was deemed to be hospital acquired, most likely from a presymptomatic spouse who was visiting daily and diagnosed with COVID-19 before visitor restrictions and masking were implemented. Among 8370 patients with non-COVID-19-related hospitalizations discharged through June 17, 11 (0.1%) tested positive within 14 days (median time to diagnosis, 6 days; range, 1-14 days). Only 1 case was deemed likely to be hospital acquired, albeit with no known exposures.Conclusions and relevanceIn this cohort study of patients in a large academic medical center with rigorous infection control measures, nosocomial COVID-19 was rare during the height of the pandemic in the region. These findings may inform practices in other institutions and provide reassurance to patients concerned about contracting COVID-19 in hospitals.

Dataset Information

Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center.

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Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center.

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