# Pharmacogenomics Clinical Annotation Tool (PharmCAT)

> **NIH NIH U24** · UNIVERSITY OF PENNSYLVANIA · 2020 · $560,000

## Abstract

ABSTRACT
Approximately 2 million adverse drug reactions (ADRs) occur annually in the United
States; this results in roughly 100,000 deaths and costs upwards of $30 billion dollars
each year. Many of these hospitalizations and deaths are preventable. Developing the
infrastructure to identify the genetic variants in patients before prescribing the medications
known to cause ADRs is an active area of genomic medicine implementation at many
health care organizations and academic medical centers. The Clinical Pharmacogenetics
Implementation Consortium (CPIC), U.S Food & Drug Administration (FDA), the
Pharmacogenomics Knowledgebase (PharmGKB) and others have established
guidelines and recommendations surrounding gene-drug pairs that can and already lead
to prescribing modifications based on genetic variant(s). One of the greatest challenges
in implementing Pharmacogenomics (PGx) is extracting genomic variants and assigning
possible diplotypes (one haplotype on each chromosome, including star-allele definitions)
from genetic data derived from sequencing and genotyping technologies in order to apply
the prescribing recommendations. In a collaboration between the members of the former
PGRN-Statistical Analysis Resource (P-STAR), PharmGKB, the Clinical Genome
Resource (ClinGen), the electronic Medical Records and Genomics (eMERGE) network,
Implementing Genomics in Practice (IGNITE), CPIC, and others, we are developing a
software tool, PharmCAT, to extract PGx variants, beginning with those in published CPIC
guidelines, from a genetic dataset resulting from sequencing or genotyping technologies
(represented as a .VCF file), interpret the variant alleles, infer diplotypes, and generate
an interpretation report including CPIC, FDA, or other clinical guidance. The PharmCAT
report can then be used to inform prescribing decisions. This framework has been named
the Pharmacogenomics Clinical Annotation Toolkit (PharmCAT). The initial prototype of
PharmCAT has been developed by software developers at PharmGKB under the
direction of Dr. Teri Klein and software developers and her team at Stanford University
as well as Dr. Marylyn Ritchie and her team at the University of Pennsylvania. In this U24
genomics resources proposal, our goals are to further develop, test, and disseminate the
PharmCAT resource to the scientific community. This will enable the research and
implementation of PGx into clinical care in a standardized, reproducible, consistent
manner and accelerate PGx clinical implementation for precision medicine.

## Key facts

- **NIH application ID:** 10024591
- **Project number:** 1U24HG010862-01A1
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** TERI Ellen KLEIN
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $560,000
- **Award type:** 1
- **Project period:** 2020-08-07 → 2023-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10024591

## Citation

> US National Institutes of Health, RePORTER application 10024591, Pharmacogenomics Clinical Annotation Tool (PharmCAT) (1U24HG010862-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10024591. Licensed CC0.

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