VESPA Cohort: Vanderbilt Electronic Systems for Pharmacogenomic Assessment
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PROVIDER: PRJNA296728 | ENA |
REPOSITORIES: ENA
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Project description:<p>The Vanderbilt Electronic Systems for Pharmacogenomic Assessment (VESPA) Project is a large electronic medical record (EMR)- and biobank-based initiative for translational pharmacogenomics discoveries. Key research resources utilized in this effort include the BioVU DNA databank and associated Synthetic Derivative database of clinical information, and software tools developed to identify drugs and clinical events using EHR-derived structured and unstructured ("free text") data. Cohorts include subjects with primarily drug-response phenotypes, and most cases and controls identified include three data types: ICD-9 codes, medication regimens, and medical test results. Advanced informatics methods, such as natural language processing, were also used for some phenotypes. Algorithms used event-sequence analyses to establish temporal relationships between drugs and phenotypes. Both cases and control algorithms excluded records that contained specific comorbidities and were refined to achieve positive predictive value (PPV) > 90%. For automated algorithms failing to meet this threshold, manual review was coupled with algorithms to validate that the included cases were true positives.</p> <p>A total of 11,639 subjects met phenotyping criteria for a least one of the 28 phenotypes investigated. Across all phenotypes cases and controls, 90% were reused as either a case or control for a least one other phenotype. Data are deposited for individual phenotypes in the VESPA substudies.</p> <p><b>Substudies</b>: <li>VESPA: Genome Wide Association Study of Serum Creatinine during Vancomycin Therapy and Vancomycin Pharmacokinetics - <a href="./study.cgi?study_id=phs000894">phs000894</a></li> <li>VESPA: Genome Wide Study of Clinically Diagnosed Ace Inhibitor Cough - <a href="./study.cgi?study_id=phs000992">phs000992</a></li> </p>
| phs000991 | dbGaP
Project description:VESPA: Vanderbilt Electronic Systems for Pharmacogenomic Assessment
| PRJNA280021 | ENA
Project description:VESPA Cohort: Vanderbilt Electronic Systems for Pharmacogenomic Assessment
| PRJNA296729 | ENA
Project description:<p>An important potential enabling resource for Personalized Medicine is the combination of a DNA repository with Electronic Medical Record (EMR) systems sufficiently robust to provide excellence in clinical care and to serve as resources for analysis of disease susceptibility and therapeutic outcomes across patient populations. The Vanderbilt EMR is a state of the art clinical and research tool (that includes >1.7 million records), and is associated with a DNA repository which has been in development for over 3 years; these are the key components of VGER, the Vanderbilt Genome-Electronic Records project, a part of NHGRI's eMERGE network. The VGER model acquires DNA from discarded blood samples collected from routine patient care, and can link these to de-identified data extracted and readily updated from the EMR. The phenotype we analyze here is the QRS duration on the electrocardiogram, since slow conduction (indicated by longer QRS duration) is a marker of arrhythmia susceptibility.</p>
| phs000188.v1.p1 | EGA
Project description:This study developed a triple-negative breast cancer (TNBC) surrogate subtype classification that represents TNBC subtypes based on the Vanderbilt subtype classification The web-based subtyping tool TNBCtype was used to classify the TNBC cohort into Vanderbilt subtypes
2023-03-04 | GSE226289 | GEO