PharmCAT:
Pharmacogenomics Clinical Annotation Tool

Download v2.15.5 View on GitHub

PharmCAT (Pharmacogenomics Clinical Annotation Tool) is a bioinformatics tool that analyzes genetic variants to predict drug response and tailor medical treatment to an individual patient’s genetic profile. It does this in two phases:

1. Processes VCF files from next generation sequencing (NGS) or genotyping methods and identifies pharmacogenomic (PGx) genotypes and infers haplotypes, typically called star alleles.
2. Uses the pharmacogene diplotypes (combination of maternal and paternal star alleles) to predict PGx phenotypes and reports the corresponding drug-prescribing recommendations from CPIC guidelines, PharmGKB-annotated DPWG guidelines and PharmGKB-annotated FDA-approved drug labels.

PharmCAT was developed in a collaboration between the Pharmacogenomics Knowledgebase (PharmGKB) and the former PGRN Statistical Analysis Resource (P-STAR), with input from other groups. The work was originally based on established guidelines from the Clinical Pharmacogenetics Implementation Consortium (CPIC).

References:

• Commentary: TE Klein, MD Ritchie. PharmCAT: A Pharmacogenomics Clinical Annotation Tool. Clinical Pharmacology & Therapeutics (2018) 104(1):19-22.
• Methods paper: K Sangkuhl & M Whirl-Carrillo, et al. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clinical Pharmacology & Therapeutics (2020) 107(1):203-210.
• Tutorial paper: B Li & K Sangkuhl et al. How to Run the Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clinical Pharmacology & Therapeutics (2022).

PharmCAT is under active development.

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Documentation

See Genes & Drugs for a list of all genes and drugs supported by PharmCAT. We have detailed documentation in Gene Definition Exceptions for genes that require special handling.

Read the Methods to learn how PharmCAT works, including how it matches sample data to allele definitions and matches genotypes to drug recommendations.

Running PharmCAT

Learn how to run PharmCAT and all the different components that make up the PharmCAT tool. Please make sure to also read and understand PharmCAT's VCF requirements.

Tutorial videos are available on the PharmGKB YouTube channel. These videos provide step-by-step demonstrations on running PharmCAT. The first two videos cover:

1. An introduction to PharmCAT, modules, and reports
2. How to run PharmCAT - a hands-on example that walks through the setup and running PharmCAT

Future videos will cover more topics.

License

PharmCAT is licensed under the Mozilla Public License 2.0 (MPL-2.0).

Examples

We have an example collection of synthetic input and output files generated by PharmCAT.

View examples of input and output files.