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Related Experiment Video

Updated: Jan 22, 2026

Author Spotlight: Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans

Author Spotlight: Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans

Published on: September 8, 2023

Pharmacogenomics Clinical Annotation Tool (PharmCAT).

Katrin Sangkuhl¹, Michelle Whirl-Carrillo¹, Ryan M Whaley¹

¹Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA.

Clinical Pharmacology and Therapeutics

|July 16, 2019

Summary

This summary is machine-generated.

Pharmacogenomics Clinical Annotation Tool (PharmCAT) aids precision medicine by extracting genomic variants and assigning haplotypes for prescribing guidelines. Validation showed high concordance, enabling accurate pharmacogenomics reporting.

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mirMachine: A One-Stop Shop for Plant miRNA Annotation

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Published on: May 1, 2021

Area of Science:

Genomics
Pharmacogenomics
Precision Medicine

Background:

Implementing pharmacogenomics (PGx) requires extracting genomic variants and assigning haplotypes to apply prescribing recommendations.
Existing methods face challenges in consistent and accurate PGx data interpretation.

Purpose of the Study:

To introduce the Pharmacogenomics Clinical Annotation Tool (PharmCAT) for PGx variant extraction, haplotype inference, and report generation.
To validate PharmCAT's performance using pilot data from the 1000 Genomes Project and GeT-RM samples.

Main Methods:

PharmCAT extracts guideline-specified variants from genetic data (sequencing/genotyping).
It infers haplotypes and diplotypes.
Generates reports with genotype/diplotype-based annotations and CPIC/FDA/PharmGKB guideline recommendations.

Main Results:

PharmCAT demonstrated high concordance with Genetic Testing Reference Materials Coordination Program (GeT-RM) data.
The tool successfully processed 1000 Genomes Project sequences.

Conclusions:

PharmCAT provides a consistent and accurate method for PGx annotation and reporting.
The tool is available on GitHub to support the growing field of precision medicine.