Description
Digitalization of patient medical charts in the form of electronic health record (EHR) promotes precision medicine, which promises to be inclusive of a broad view of a person’s care. Disease genetics and pharmacogenomics (PGx) contributes to the success of precision medicine by providing genetic insights from preemptive care and disease diagnosis to drug prescribing recommendation. However, integrating genomics with EHR-linked health care systems is challenging. The ever increasing scale of EHR-linked health care systems ensues an increasing need for automated, computational annotation of genetic information to support fast-paced clinical decision making. This workshop will introduce several bioinformatics tools that facilitate automatic, computable annotation of genetic information. Computable representation of genetic variants is one bottleneck for accurate genetic curation and automatic annotation in analyses following clinical genetic tests.
The first part of the workshop will focus on the Variation Representation Specification (VRS, pronounced “verse”), a recently published standard of the Global Alliance for Genomics and Health for the computable representation of biomolecular variation. VRS allows precise and federatable identification of genetic variants for downstream disease annotations and PGx annotations in EHR-linked health care systems. The associated VRSATILE (“versatile”) framework provides additional tools for representation of variation in computable genomic knowledge exchange. Exemplary applications of VRSATILE include knowledge and evidence retrieval across databases (e.g., functional and clinical databases) and computable representation of PGx variants. The second part of the workshop focuses on automating PGx annotations using PharmCAT (Pharmacogenomics Clinical Annotation Tool). PharmCAT is able to digest genetic information from VCFs, infer PGx named alleles and phenotypes, and generate detailed reports for clinical decision support. The capability of PharmCAT to automate PGx annotation makes it possible to translate clinical genetic test results to clinical decisions and actions at the scale of EHR-linked, large-scale health care systems. The workshop will provide an interactive, hands-on experience for participants and familiarize the audience with the latest bioinformatics tools that facilitate automation of genetic annotation and PGx annotation for large-scale, EHR-linked health care systems.
