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:Study questionWhat is the effect of default test offers--opt-in, opt-out, and active choice--on the likelihood of acceptance of an HIV test among patients receiving care in an emergency department?MethodsThis was a randomized clinical trial conducted in the emergency department of an urban teaching hospital and regional trauma center. Patients aged 13-64 years were randomized to opt-in, opt-out, and active choice HIV test offers. The primary outcome was HIV test acceptance percentage. The Denver Risk Score was used to categorize patients as being at low, intermediate, or high risk of HIV infection.Study answer and limitations38.0% (611/1607) of patients in the opt-in testing group accepted an HIV test, compared with 51.3% (815/1628) in the active choice arm (difference 13.3%, 95% confidence interval 9.8% to 16.7%) and 65.9% (1031/1565) in the opt-out arm (difference 27.9%, 24.4% to 31.3%). Compared with active choice testing, opt-out testing led to a 14.6 (11.1 to 18.1) percentage point increase in test acceptance. Patients identified as being at intermediate and high risk were more likely to accept testing than were those at low risk in all arms (difference 6.4% (3.4% to 9.3%) for intermediate and 8.3% (3.3% to 13.4%) for high risk). The opt-out effect was significantly smaller among those reporting high risk behaviors, but the active choice effect did not significantly vary by level of reported risk behavior. Patients consented to inclusion in the study after being offered an HIV test, and inclusion varied slightly by treatment assignment. The study took place at a single county hospital in a city that is somewhat unique with respect to HIV testing; although the test acceptance percentages themselves might vary, a different pattern for opt-in versus active choice versus opt-out test schemes would not be expected.What this paper addsActive choice is a distinct test regimen, with test acceptance patterns that may best approximate patients' true preferences. Opt-out regimens can substantially increase HIV testing, and opt-in schemes may reduce testing, compared with active choice testing.Funding, competing interests, data sharingThis study was supported by grant NIA 1RC4AG039078 from the National Institute on Aging. The full dataset is available from the corresponding author. Consent for data sharing was not obtained, but the data are anonymized and risk of identification is low.Trial registration Clinical trials NCT01377857.

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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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