Dataset Information

Inclusion of pediatric samples in an opt-out biorepository linking DNA to de-identified medical records: pediatric BioVU.

ABSTRACT: The Vanderbilt DNA repository, BioVU, links DNA from leftover clinical blood samples to de-identified electronic medical records (EMRs). After initiating adult sample collection, pediatric extension required consideration of ethical concerns specific to pediatrics and implementation of specialized DNA extraction methods. In the first year of pediatric sample collection, more than 11,000 samples from individuals younger than 18 years were included. We compared data from the pediatric BioVU cohort with those from the overall Vanderbilt University Medical Center pediatric population and found similar demographic characteristics; however, the BioVU cohort had higher rates of select diseases, medication exposures, and laboratory testing, demonstrating enriched representation of severe or chronic disease. The fact that the sample accumulation is not balanced may accelerate research in some cohorts while limiting the study of relatively benign conditions and the accrual of unaffected and unbiased control samples. BioVU represents a feasible model for pediatric DNA biobanking but involves both ethical and practical considerations specific to the pediatric population.

SUBMITTER: McGregor TL

PROVIDER: S-EPMC3686097 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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Inclusion of pediatric samples in an opt-out biorepository linking DNA to de-identified medical records: pediatric BioVU.

McGregor T L TL Van Driest S L SL Brothers K B KB Bowton E A EA Muglia L J LJ Roden D M DM

Clinical pharmacology and therapeutics 20121121 2

The Vanderbilt DNA repository, BioVU, links DNA from leftover clinical blood samples to de-identified electronic medical records (EMRs). After initiating adult sample collection, pediatric extension required consideration of ethical concerns specific to pediatrics and implementation of specialized DNA extraction methods. In the first year of pediatric sample collection, more than 11,000 samples from individuals younger than 18 years were included. We compared data from the pediatric BioVU cohort ...[more]

PMID: 23281421

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Project description:Autoimmune diseases represent a significant medical burden affecting up to 5-8% of the U.S. POPULATION:While genetics is known to play a role, studies of common autoimmune diseases are complicated by phenotype heterogeneity, limited sample sizes, and a single disease approach. Here we performed a targeted genetic association study for cases of multiple sclerosis (MS), rheumatoid arthritis (RA), and Crohn's disease (CD) to assess which common genetic variants contribute individually and pleiotropically to disease risk. Joint modeling and pathway analysis combining the three phenotypes were performed to identify common underlying mechanisms of risk of autoimmune conditions. European American cases of MS, RA, and CD, (n = 119, 53, and 129, respectively) and 1924 controls were identified using de-identified electronic health records (EHRs) through a combination of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) billing codes, Current Procedural Terminology (CPT) codes, medication lists, and text matching. As expected, hallmark SNPs in MS, such as DQA1 rs9271366 (OR = 1.91; p = 0.008), replicated in the present study. Both MS and CD were associated with TIMMDC1 rs2293370 (OR = 0.27, p = 0.01; OR = 0.25, p = 0.02; respectively). Additionally, PDE2A rs3781913 was significantly associated with both CD and RA (OR = 0.46, p = 0.02; OR = 0.32, p = 0.02; respectively). Joint modeling and pathway analysis identified variants within the KEGG NOD-like receptor signaling pathway and Shigellosis pathway as being correlated with the combined autoimmune phenotype. Our study replicated previously-reported genetic associations for MS and CD in a population derived from de-identified EHRs. We found evidence to support a shared genetic etiology between CD/MS and CD/RA outside of the major histocompatibility complex region and identified KEGG pathways indicative of a bacterial pathogenesis risk for autoimmunity in a joint model. Future work to elucidate this shared etiology will be key in the development of risk models as envisioned in the era of precision medicine.

Project description:Due to recently proposed changes in the Common Rule regarding the collection of research preferences, there is an increased need for efficient methods to document opt-in research preferences at a population level. Previously, our institution developed an opt-out paper-based workflow that could not be utilized for research in a scalable fashion. This project was designed to demonstrate the feasibility of implementing an electronic health record (EHR)-based active opt-in research preferences program. The first phase of implementation required creating and disseminating a patient questionnaire through the EHR portal to populate discreet fields within the EHR indicating patients' preferences for future research study contact (contact) and their willingness to allow anonymised use of excess tissue and fluid specimens (biobank). In the second phase, the questionnaire was presented within a clinic nurse intake workflow in an obstetrical clinic. These permissions were tabulated in registries for use by investigators for feasibility studies and recruitment. The registry was also used for research patient contact management using a new EHR encounter type to differentiate research from clinical encounters. The research permissions questionnaire was sent to 59,670 patients via the EHR portal. Within four months, 21,814 responses (75% willing to participate in biobanking, and 72% willing to be contacted for future research) were received. Each response was recorded within a patient portal encounter to enable longitudinal analysis of responses. We obtained a significantly lower positive response from the 264 females who completed the questionnaire in the obstetrical clinic (55% volunteers for biobank and 52% for contact). We demonstrate that it is possible to establish a research permissions registry using the EHR portal and clinic-based workflows. This patient-centric, population-based, opt-in approach documents preferences in the EHR, allowing linkage of these preferences to health record information.

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Project description:Abstract Background Sepsis guidelines recommend daily review to de-escalate or stop antibiotics in appropriate patients. We conducted a randomized controlled trial (NCT03517007) of an opt-out protocol to decrease unnecessary antibiotics in selected patients with suspected sepsis. Methods We evaluated non-ICU adults remaining on broad-spectrum antibiotics with negative blood cultures at 48-96 hours at ten U.S. hospitals during September 2018-May 2020. A 23-item safety check excluded patients with ongoing signs of infection, concerning or inadequate microbiologic data, or high-risk conditions (Figure 1). Eligible patients were randomized to the opt-out protocol vs. usual care. The primary outcome was 30-day post-enrollment antibacterial days of therapy (DOT). Clinicians caring for intervention patients were contacted by a pharmacist or physician to encourage antibiotic discontinuation or de-escalation using opt-out language, discuss rationale for continuing antibiotics, working diagnosis, and de-escalation and duration plans. Hurdle models separately compared the odds of antibiotic continuation and DOT distributions among those who continued antibiotics. Components of the De-Escalating Empiric Therapy: Opting-OUt of Rx in Selected patients with Suspected Sepsis (DETOURS) Trial Protocol Results Among 9606 screened, 767 (8%) were enrolled (Figure 2). Common reasons for exclusion were antibiotics given prior to blood culture (35%), positive culture from non-blood sites (26%), and increased oxygen requirement (21%). Intervention patients had 32% lower odds of antibiotic continuation (79% vs. 84%, OR 0.68, 95% confidence interval [0.47, 0.98]). DOT distributions among those who continued antibiotics were similar (ratio of means 1.06 [0.88-1.26], Figure 3). Fewer intervention patients were exposed to extended-spectrum agents (38% vs. 44%). Common reasons for continuing antibiotics were treatment of localized infection (76%) and belief that stopping antibiotics was not safe (31%). Safety outcomes such as mortality, readmission, sepsis relapse, C. difficile, and length of stay did not differ. DETOURS Trial Flow Diagram Flow of participants through the DETOURS Trial. Observed Days of Antibiotic Therapy Among Intervention and Control Subjects in the DETOURS Trial Post-enrollment days of antibiotic therapy among 767 DETOURS Trial participants in 10 US acute care hospitals within 30 days after enrollment. Dark pink color indicates percent overlap between intervention (purple) and control (light pink) groups. Conclusion In this patient-level randomized trial of a stewardship intervention, the opt-out de-escalation protocol targeting selected patients with suspected sepsis resulted in more antibiotic discontinuations but did not affect safety events. Disclosures Rebekah W. Moehring, MD, MPH, UpToDate, Inc. (Other Financial or Material Support, Author Royalties) Michael Z. David, MD PhD, GSK (Board Member) Michael Klompas, MD, MPH, UpToDate (Other Financial or Material Support, Chapter Author)

Dataset Information

Inclusion of pediatric samples in an opt-out biorepository linking DNA to de-identified medical records: pediatric BioVU.

Publications

Inclusion of pediatric samples in an opt-out biorepository linking DNA to de-identified medical records: pediatric BioVU.

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