Thursday, April 21, 2022

What does *1 really mean? And why does that matter?

A Haiku about PGx for National Poetry Month.

Diagnosed star one,

Yet severe toxicity.

What did the lab test?

What does *1 really mean? And why does that matter?

The star alleles of the drug metabolizing enzyme genes are an unusual way of defining variation and are perhaps one of the most misunderstood aspects of pharmacogenomics. Arising from attempts to describe and standardize the molecular basis of different drug phenotypes; debrisoquine poor metabolizer phenotype, etc [PMID: 7773298, PMID: 8807658].  Sometimes authors use the term “wild type”, even for humans, to describe the most common form of the gene or protein in a given population where it displays the expected drug metabolism phenotype. The *1 allele is generally used to denote the absence of the variants tested. However, it is not a stable assignment; a *1/*1 individual only tested at one locus may not have the same genetic sequence as a *1/*1 individual tested for a panel of 10 variants in the same gene. This really matters when evaluating the likelihood of drug phenotype - the "reference" is only as good as the number of variants that were checked. *1 is rather a placeholder, it is the absence of certainty, because even with a panel that covers variants that represent 99% of known variation (in the populations examined so far which are not representative of the full global population) there may still be rare variants with significant impact on protein function that we may not yet have documented. While a *1/*1 may not be at increased risk of toxicity (or other phenotypes), or require a change of dosage immediately, they still have the baseline level of risk and it shouldn’t be a huge surprise if they exhibit an adverse reaction to a drug. 

Recent publications of case studies that concluded a lack of involvement of known pharmacogenes without documenting what was tested: 

PMID:35180762 - “Acral Skin Rash Caused by Altered Mercaptopurine

Metabolism in Maintenance Therapy for B-Cell

Acute Lymphoblastic Leukemia”  excerpt “TPMT and NUDT15 genotype at diagnosis were wildtype alleles and therefore we started with full 6-MP dosing.”

This issue is not limited to pharmacogenes using star allele nomenclature: “5-Fluorouracil Neurotoxicity in the Absence of Dihydropyrimidine Dehydrogenase Deficiency Case Report” [PMID:35419161] excerpt “Our patient tested negative for DPD mutations, but it remains possible she harbored a genetic variant not accounted for in the genetic testing panel. Other known risk factors include mutations in the orotate phosphoribosyltransferase and thymidylate synthase genes… “

We recommend authors always include the list of all variants that were tested, and other features see [PMID:30406943].

Thursday, April 14, 2022

Update to PharmGKB Pediatric Drug Summaries

The third round of PharmGKB's pediatric drug summaries is now live on PharmGKB pediatric. This release includes over 20 additional drugs with a focus on those on the Best Pharmaceuticals for Children Act (BPCA) priority list, including:

These pediatric drug summaries contain key information relevant to prenatal, postnatal, and pediatric populations, manually curated from PharmGKB annotations, pathways, CPIC guidelines, and FDA-approved drug labels.

PharmGKB continues to add to the list of drugs with pediatric summaries.

Wednesday, April 6, 2022

"Ask a Curator" live zoom event

PharmGKB curators will hold a series of live Q&A events over Zoom to help people find and use different aspects of the knowledgebase. We hope this will be a great way to answer questions about PharmGKB and PGx which are specific to users’ individual needs or projects.  These events will demonstrate the full extent of the resources available on PharmGKB, as well as details about those resources and how to download, use, and cite data from PharmGKB. 

In order to tailor these events for users with similar needs from PharmGKB, the first event will focus on researchers. Future events geared towards educators and clinicians are in the works, as well as events hosted at different times for our global audience. We will also be recording this upcoming event along with future events for those who are unable to attend live. Recordings will be posted on the PharmGKB YouTube channel.

We are asking people to please register in advance with their questions so curators can better focus these events. There will also be the opportunity to ask questions during the event. Events will be limited to 20 participants to allow enough time for everyone’s questions to be answered.

Sign up here for Tuesday April 26th at 12pm EST, 9am PST, 5pm GMT

Can’t make it but want to sign up for a future Ask a Curator? Join our mailing list here.