Tools and Resources
BioVU. BioVU is Vanderbilt's collection of DNA samples coupled to a deidentified image of the Vanderbilt electronic medical record system, termed the “Synthetic Derivative.” Established in 2007, BioVU contained >240,000 samples at the end of 2016 and is the largest collection of DNA samples coupled to EMRs at a single academic institution world-wide. BioVU has served as a critical platform for genomic discovery both at Vanderbilt and in collaboration with other institutions nationally and internationally. The rich phenotypic information in BioVU has enabled the development of the phenome wide association study (PheWAS). [Dan Roden, Josh Denny]
Phenotype Knowledgebase (PheKB). This resource is a collaborative environment for building and validating electronic algorithms to identify subsets of patients by case or control status within electronic health data. PheKB was functionally designed to enable such a workflow and has purposefully integrated tools and standards that guide the user in efficiently navigating from early stage development to public sharing and reuse. PheKB has tools to enable cross-site collaboration for algorithm development, validation, and sharing for reuse with confidence. [Josh Denny]
Health Information Privacy Laboratory (HIPLab). The HIPLab was founded to address the growing needs for privacy technology research and development for the emerging health information technologies sector. The goal of the HIPLab is to improve the protection of patients' privacy in health information systems while optimizing the utility of data for research. [Brad Malin]
MyCancerGenome. This site, founded and managed at Vanderbilt, presents information on variants identified in tumors, their possible therapeutic impact, and clinical trials for which patients carrying specific mutations may be eligible. [Mia Levy]
MyDrugGenome. This site is a resource to learn about how genetics can affect the way medications work and how genetic results can be incorporated into personalized patient care.
Sequence and Phenotype Integration Exchange (SPHINX). Available through the eMERGE Network, SPHINX is a web-based tool for exploring data for hypothesis generation, especially around drug response implications of genetic variation across the eMERGE PGx cohort.
PheWAScatalog provides a catalog of PheWAS results. Phenome-wide association studies (PheWAS) analyze many phenotypes compared to a single genetic variant (or other attribute). This method was originally described using electronic medical record (EMR) data from the Vanderbilt DNA biobank, BioVU, but can also be applied to other richly phenotyped sets. [Josh Denny]
Genotype-Tissue Expression (GTEx) Portal. The GTEx program provides valuable insights into the mechanisms of gene regulation by studying human gene expression and regulation in multiple tissues from healthy individuals, exploring disease-related perturbations in a variety of human diseases, and examining sexual dimorphisms in gene expression and regulation in multiple tissues. prediXcan is a gene-based association method for mapping traits using transcriptome data, and metaXcan is an extension of prediXcan using summary statistics-based gene level association. [Nancy Cox]