ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole-genome sequencing data

Gennaro Calendo; Dara Kusic; Jozef Madzo; Jozef Madzo; Neda Gharani; Neda Gharani; Laura Scheinfeldt; Laura Scheinfeldt

doi:10.3389/fbinf.2024.1351620

Frontiers in Bioinformatics (Mar 2024)

ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole-genome sequencing data

Gennaro Calendo,
Dara Kusic,
Jozef Madzo,
Jozef Madzo,
Neda Gharani,
Neda Gharani,
Laura Scheinfeldt,
Laura Scheinfeldt

Affiliations

Gennaro Calendo: Coriell Institute for Medical Research, Camden, NJ, United States
Dara Kusic: Coriell Institute for Medical Research, Camden, NJ, United States
Jozef Madzo: Coriell Institute for Medical Research, Camden, NJ, United States
Jozef Madzo: Cooper Medical School of Rowan University, Camden, NJ, United States
Neda Gharani: Coriell Institute for Medical Research, Camden, NJ, United States
Neda Gharani: Gharani Consulting Limited, London, United Kingdom
Laura Scheinfeldt: Coriell Institute for Medical Research, Camden, NJ, United States
Laura Scheinfeldt: Cooper Medical School of Rowan University, Camden, NJ, United States

DOI: https://doi.org/10.3389/fbinf.2024.1351620
Journal volume & issue: Vol. 4

Abstract

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Long-read sequencing technologies offer new opportunities to generate high-confidence phased whole-genome sequencing data for robust pharmacogenetic annotation. Here, we describe a new user-friendly R package, ursaPGx, designed to accept multi-sample phased whole-genome sequencing data VCF input files and output star allele annotations for pharmacogenes annotated in PharmVar.

Published in Frontiers in Bioinformatics

ISSN: 2673-7647 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Medicine: Medicine (General): Computer applications to medicine. Medical informatics
Website: https://www.frontiersin.org/journals/bioinformatics

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