ClinPGx Blog (Page 15)

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Public comment period for CPIC allele function assignment SOP

CPIC is inviting public comments on their draft SOP for assigning function to pharmacogenomic alleles.CPIC has been assigning “function” to pharmacogenomic alleles since its inception. This has already led to a Delphi process and consensus publication on standardizing terms used for allele function and pharmacogenetic phenotypes for some genes.

PharmGKB releases automated annotations

We are excited to announce that automated annotations of pharmacogenomic information in the scientific literature are now available from PharmGKB. These annotations have been produced using the PGxMine project, the result of a collaboration with Dr. Jake Lever at Stanford University.PGxMine uses a supervised machine learning algorithm to carry

CYP2D6 Gene Review by PharmVar published in CPT

The Pharmacogene Variation (PharmVar) Consortium just published the inaugural article of a gene-centered series of review papers in Clinical Pharmacology & Therapeutics. The reviews are covering clinical relevance, genetic variability, allele frequencies and function, ethnic differences, gene nomenclature before and within PharmVar, curation efforts, particular gene-specific challenges, PharmVar features and

ACLA writes to the FDA about PGx testing

The American Clinical Laboratory Association (ACLA) has written a letter to the US Food and Drug Administration (FDA) regarding the FDA’s recent communications about pharmacogenomic (PGx) testing. The letter details the ACLA’s concerns that the FDA’s actions will have a significant impact on both patients and the

Michelle Whirl-Carrillo -- Director of the PharmGKB!

We are happy to announce that Dr. Michelle Whirl-Carrillo has agreed to take on the position of Director of PharmGKB. Michelle has worked with the PharmGKB for over 15 years (not including a 1.5 year “sabbatical” at 23andme). She has served as lead curator, Assistant Director, and (since 2014)

Pilot study from Genomics England to report on DPYD variants

A pilot study from Genomics England is now reporting back DPYD variants in cancer patients as part of the 100,000 Genomes Project. The DPYD protein is responsible for degrading fluoropyrimidine drugs, which include 5-fluorouracil and capecitabine. These drugs are commonly used in the treatment of cancer. Decreased activity of

PharmCAT article published in Clinical Pharmacology & Therapeutics

The article describing the Pharmacogenomics Clinical Annotation Tool (PharmCAT) and a pilot validation using GeT-RM samples was recently published in Clinical Pharmacology & Therapeutics. PharmCAT (1) extracts variants specified in guidelines from a genetic dataset derived from sequencing or genotyping technologies; (2) infers haplotypes and diplotypes; and (3) generates a

CYP2C9, CYP2C19, and CYP2D6 core alleles

We recently blogged about the use of PharmVar core alleles as the basis for the PharmGKB/CPIC CYP2D6, CYP2C19, and CYP2C9 allele definition tables, which are available as part of the gene-specific information tables. In addition to the core variant(s), the definition includes ambiguous nucleotides to reflect variation present

CPIC to issue guidance on non-actionable pharmacogenes

The Clinical Pharmacogenetics Implementation Consortium (CPIC) hopes to provide more guidance in the future about gene-drug pairs which have a weak evidence base and are not clinically actionable, despite being heavily marketed to healthcare providers and the public. Many of these gene-drug pairs have already been curated by CPIC staff

PharmGKB ondansetron and tropisetron pathways published in Pharmacogenetics and Genomics

The PharmGKB pathways for ondansetron and tropisetron have been published in the June 2019 issue of Pharmacogenetics and Genomics. Ondansetron and tropisetron are serotonin receptor antagonists which are prescribed for their antiemetic activity. After an overview of the pharmacokinetics and pharmacodynamics of each drug, the publication discusses the current pharmacogenetic