New pathways on PharmGKB

The following pathways have been recently released on PharmGKB:

Acenocoumarol Pharmacokinetics

Phenprocoumon Pharmacokinetics

Piroxicam Pharmacokinetics

Siponimod Pharmacokinetics/Pharmacodynamics

Aminoglycoside Ototoxicity, Adverse Drug Reaction

These pathways cover gene-drug pairs which have been assigned level A or B by CPIC.A full list of PharmGKB pathways can be found at https://www.pharmgkb.org/pathways

PharmGKB User Survey

We have launched a user survey to help inform the future direction of PharmGKB. All user responses are greatly appreciated; no matter who you are, where you are in the world or how many times you have used PharmGKB. The survey is split into two parts. The first section takes ~1 minute to complete. If you have time to give us some more information, the second section will take an additional ~5 minutes. Thank you for your contribution.

SLCO1B1 added to PharmVar

PharmVar and PharmGKB are excited to share that SLCO1B1 nomenclature is now maintained by PharmVar. This important drug transporter, also known as OATP1B1, has been shown to facilitate the uptake of stains into the liver. Furthermore, genetic variation has been shown to cause musculoskeletal symptoms impeding statin effectiveness.

Star nomenclature has been used by manuscript authors in the past; allele designations were, however, self-assigned and there was no central repository providing oversight or keeping track of the reported allelic variants. The PharmVar SLCO1B1 gene experts have systematically reviewed and curated all information available in the literature. As the published star allele designations were not necessarily consistent in regard of criteria used for their definition, several alleles were merged and/or revised. In addition, new information gathered by the PharmVar Team were utilized to confirm published allele definitions, fill data gaps to facilitate updating some of the existing definitions, as well as discover novel haplotypes adding star alleles to the collection. Specific details of changes to allele definitions can be found on the PharmVar SLCO1B1 page and on the Change Log tab of the SLCO1B1 Allele Definition Table available from PharmGKB.

PharmGKB, PharmVar and CPIC have coordinated updates to their SLCO1B1 resources to reflect its release in PharmVar. The PharmVar SLCO1B1 gene page includes new allele functions assigned by CPIC as part of its forthcoming update to the guideline on SLCO1B1 and statins. These new PharmVar allele definitions and CPIC functions have been incorporated into the CPIC database and implementation resources for use with the current simvastatin guideline recommendations. All resources available through PharmGKB have also been updated accordingly. Standardized nomenclature for this drug transporter is an important step forward for clinical implementation of stain pharmacogenetics.

PharmGKB announces the launch of PharmGKB Pediatric

PharmGKB Pediatric (https://pediatric.pharmgkb.org) is a "view" of PharmGKB (https://www.pharmgkb.org) that highlights pharmacogenomic annotations that (1) are based on pediatric studies or (2) may be relevant to pediatrics.  All of the annotations found on PharmGKB are also on PharmGKB Pediatric.  

A quick way to access pediatric information is to click the blue "Pediatric Pharmacogenomics" button on the website homepage 

                           

and follow the link to the "Pediatric Annotations Dashboard".  

This dashboard gives an overview of what percentage of each type of PharmGKB annotation has pediatric information. 

A description of how annotations qualify for the pediatric tag can be found here.  Clicking on the link under a pie chart will take the user to a complete list of pediatric annotations that can be sorted, filtered or downloaded.

Also on PharmGKB Pediatric, the menu on the left-hand side of drug and gene page will have a "child" icon if there are pediatric annotations in a particular category (see example below).  Additionally, manually-curated summaries of the pediatric annotations and pediatric information from FDA-approved drug labels (see example below)

Example screenshot of warfarin page with pediatric icons and summary.

are available for over 80 drugs (as of 11 October 2021) that fall into these categories:  (1) CPIC guideline drugs and (2) drugs on the Best Pharmaceuticals for Children Act (BPCA) priority list AND that have at least one pediatric variant annotation.  

We continue to add to the list of drugs with pediatric summaries and develop the site for users.

NIH Request for Information on Scientific Data Sources

The U.S. National Institutes of Health (NIH) has put out a Request for Information (RFI) on User Experience with Scientific Data Sources and Tools in order to better understand the use of these resources by the scientific community.

We’re asking the pharmacogenomics community to consider responding to the survey and show their support for pharmacogenomics resources like PharmGKB and PharmVar. The RFI closes on October 15.