Pharmacogene Variation Consortium
About PharmVar
Updates
PharmVar announces the release of a major update. Notable new features include a revised haplotype naming system, the introduction of unique haplotype IDs, displaying impact next to the causative SNV in brackets and a revised allele (CYP2D6*14A is now *114). The new gene page design has customizable display options and allows the user to see variation info across reference sequences and genome builds and rsIDs without leaving the page.
The update also features nomenclature for the first non-CYP gene, NUDT15. Papers describing the new features, and how NUDT15 nomenclature was developed are close to being published in CPT. A presentation with an overview of PharmVar and highlights of the new features can be found under the ABOUT tab.
There are now over 10 genes in the database, among them are CYPs 2C9, 2C19, 2D6, and the first non-CYP gene NUDT15 – additional genes will be transitioned soon.
Announcement
CYP database is now PharmVar.org
After more than 15 years the Human Cytochrome P450 (CYP) Allele Nomenclature Database has transitioned...
...to the Pharmacogene Variation (PharmVar) Consortium at PharmVar.org
Learn all about it in our publication: The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database published in Clinical Pharmacology & Therapeutics
PharmVar Membership
The PharmVar welcomes members from academia and industry as well as government and non-government groups including patient advocacy groups, with an interest in pharmacogenetics and genomics.
PharmVar will serve as a central repository for pharmacogene variation to facilitate allele (haplotype) designation and the interpretation of pharmacogenetic test results to guide precision medicine.
PharmVar is a PGRN resource funded by NIGMS.
After September 26, 2017, please visit PharmVar.org to access content of the original P450 Nomenclature Database
Project narrative
Abstract
In the mid 1990’s, an international group of leading experts devised the star (*) nomenclature system to provide the field with a systematic way to catalogue allelic variants of Cytochrome P450s, a super family of genes responsible for a wide range of activity towards numerous clinically used drugs. To keep track of an increasing number of P450 allelic variants, the Human Cytochrome P450 (CYP) Allele Nomenclature Database (“Nomenclature website” for short) was established in 2002 and has become the primary hub for allele definitions as well as the authority of P450 nomenclature. The PGx field has readily embraced the star nomenclature system and heavily relies on the catalog of haplotype definitions that have been listed on the Nomenclature website for research and clinical applications alike.
The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. As a first step, the Nomenclature website has transitioned from its current location at the Karolinska Institute in Sweden to Children’s Mercy in Kansas City, USA, in September of 2017 and the interactive PhamVar database has been launched in early 2018. The high-priority CYP2C9, 2C19, and CYP2D6 genes have been transitioned into the database; other P450 genes will follow (once a gene is transferred into PharmVar, it will receive legacy status on the Nomenclature website). PharmVar has also introduced its first non-CYP gene, NUDT15 and other clinically actionable CPIC genes for which no standardized nomenclature exists will be added in the future. Highlights of the PharmVar database include a transparent submission and review process, versioning at a haplotype, gene and database level, a new haplotype versioning system, PharmVar IDs and other annotations. User-friendly database design allows the display of relevant information with just a few clicks. Pharmacogene variation data in PharmVar is freely available to all users.. The utility of PharmVar is being maximized through direct efforts with the PharmGKB, CPIC and other stakeholders to unify and standardize pharmacogene variation designation and translation into phenotype.
The PharmVar and PharmGKB teams bring rich expertise and existing collaborations to the Consortium, which are essential components for advancing genome-informed medicine and PGx-guided individualized drug therapy at large.
Stay tuned. More to come soon.
Have a question? Please contact Andrea Gaedigk at agaedigk@cmh.edu
Contact
Andrea Gaedigk
Director Pharmacogenetic Core Laboratory
Clinical Pharmacology, Toxicology & Therapeutic Innovation
Children's Mercy Kansas City
