PharmCAT
Team member on an open-source pharmacogenomics clinical annotation tool
Role: team member · University of Pennsylvania · 2024 – present
Links: pharmcat.clinpgx.org
What it is
PharmCAT is an open-source tool, developed by Stanford and Penn, that reads a patient’s genotype file (VCF) and turns it into drug-prescribing recommendations based on CPIC, DPWG and FDA guidelines.
My contribution
I was part of the PharmCAT team, with a focus on making the tool run where researchers actually work: the cloud platforms that host the large biobank and genomic datasets.
- Cross-platform testing. Ran and validated PharmCAT on the main research platforms:
- Pipeline templates. Built ready-to-use pipelines for these platforms, so other researchers can start from a working template instead of setting PharmCAT up from scratch.
Why it matters
Each platform has its own way of storing data, running jobs and controlling access. A tool that works on a laptop doesn’t automatically work inside a secure biobank environment. Templates that are tested on each platform lower the barrier for any researcher who wants to turn genotype data into pharmacogenomic insights at biobank scale.
Stack
PharmCAT · VCF · AnVIL · Terra · All of Us · UK Biobank RAP · DNAnexus · AWS