ClinPGx Blog (Page 5)

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It’s national poetry month again!

I am not a mouse. It’s the reference allele (hg38). I am not a mouse. It's the common variant In these folks tested. Saw on minus strand G is the major allele In this group tested. C is the minor It’s the reference allele (hg38). Last

CYP2D6 allele function update

The CYP2D6 allele functionality file has been re-evaluated and updated by experts involved in CYP2D6-related CPIC guidelines. CYP2D6 functions are now assigned up to star allele 163. Part of the re-evaluation focused on alleles that include 100C>T (P34S) (*10 key SNP). Furthermore, the activity value of several decreased

ClinGen Pharmacogenomics Working Group (PGxWG) Follow-Up Survey

The ClinGen Pharmacogenomics Working Group (PGxWG) has just launched a second survey to solicit feedback about the criteria and terminology that should be used to define clinical validity and actionability for pharmacogenes and variants from both the PGx community and the wider genetics and medical communities. Please note that this

ClinGen Pharmacogenomics Working Group (PGxWG) Survey

The ClinGen Pharmacogenomics Working Group (PGxWG) has launched a survey to solicit feedback about the criteria and terminology that should be used to define clinical validity and actionability for pharmacogenes and variants. The ClinGen PGxWG is a multi-disciplinary team of researchers and professionals with expertise in pharmacogenomics (PGx), clinical pharmacology,

PharmVar updates for CYP3A4 star allele definitions

PharmVar announces several updates for CYP3A4 star allele definitions. Retirement of the CYP3A4*1G allele: this allele was defined by a common variant in intron 10 (c.1026+12G>A) which was also found on many other haplotypes (or star alleles). PharmVar transiently designated the CYP3A4*1G allele as

CYP4F2 is now fully curated by PharmVar

CYP4F2 contributes to the synthesis of cholesterol, steroids and other lipids. It has been shown to regulate the bioavailability of vitamin E and vitamin K, a co-factor that is critical to blood clotting. Variations in this important pharmacogene can affect vitamin K levels and thus, the dosing of vitamin K

PharmGKB selected in the first list of Global Core Biodata Resources

We are pleased to announce that PharmGKB is included in the first list of Global Core Biodata Resources (GCBRs), a collection of resources whose long term funding and sustainability is critical to life science and biomedical research worldwide. The Global Biodata Coalition (GBC) brings together major public and charitable funders,

CYP2C18 and knowledge gaps

Pablo Zubiaur & Andrea Gaedigk have an editorial online ahead of print in Pharmacogenomics calling for the inclusion of CYP2C18 in more studies of drug metabolism [PMID: 36331025]. CYP2C18 is in a cluster on chromosome 10 that has CYP2C18, CYP2C19, CYP2C9 and CYP2C8 that spans 500k bases (NCBI gene browser)

PharmCAT Version 2.0 Released

Version 2.0 of the Pharmacogenomics Clinical Annotation Tool (PharmCAT) has been released October 20, 2022. PharmCAT is a software tool that takes the genetic data (VCF file) of an individual as input, interprets the pharmacogene alleles, diplotypes, and phenotypes, and generates a report with genotype-based drug prescribing recommendations. In

There is no ontology term for Phenoconversion in BioPortal

There are two papers ahead of print in Pharmacogenomics both discussing how important phenoconversion is to consider in the implementation of PGx in clinical practice. Phenoconversion in the PGx context is a drug-drug interaction that impacts a drug metabolizing phenotype such that it mimics the effects of a metabolizer genotype.