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

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

doi:10.3389/fbinf.2024.1351620

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

Front Bioinform. 2024 Mar 12:4:1351620. doi: 10.3389/fbinf.2024.1351620. eCollection 2024.

Authors

Gennaro Calendo¹, Dara Kusic¹, Jozef Madzo^{1

2}, Neda Gharani^{1

3}, Laura Scheinfeldt^{1

2}

Affiliations

¹ Coriell Institute for Medical Research, Camden, NJ, United States.
² Cooper Medical School of Rowan University, Camden, NJ, United States.
³ Gharani Consulting Limited, London, United Kingdom.

Abstract

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.

Keywords: R; annotation; pharmacogenetic; software; star allele.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This study was funded by NHGRI 5U24HG008736 to LS.