Tuesday, January 20, 2015

PharmGKB: an example of Precision Medicine

"21st century businesses will rely on American science, technology, research and development. I want the country that eliminated polio and mapped the human genome to lead a new era of medicine — one that delivers the right treatment at the right time. In some patients with cystic fibrosis, this approach has reversed a disease once thought unstoppable. Tonight, I’m launching a new Precision Medicine Initiative to bring us closer to curing diseases like cancer and diabetes — and to give all of us access to the personalized information we need to keep ourselves and our families healthier." - President Barack Obama January 20, 2015

PharmGKB ibuprofen pathways published in Pharmacogenetics and Genomics

We have published the PharmGKB summary: ibuprofen pathways in the Pharmacogenetics and Genomics Journal. This review summarizes the metabolism and transport of ibuprofen, its mechanism of action and discusses genetic variations affecting the pharmacokinetics, efficacy and toxicity of ibuprofen and their clinical significance.

Find out more...
View our ibuprofen PK and PD pathways on PharmGKB:
Ibuprofen pathway, pharmacokinetics
Ibuprofen pathway, pharmacodynamics

Read our new publication: 
PharmGKB summary: ibuprofen pathways
Pharmacogenet Genomics. 2015 Feb;25(2):96-106.

View all pathways on PharmGKB.

Monday, January 5, 2015

Live from PSB: Phil Bourne from the NIH


PharmGKB is at the Pacific Symposium on Biocomputing (PSB) on the big island of Hawaii.

We will broadcast Phil Bourne's talk on "NIH Big Data from Science to Careers" over the web via the BlueJeans teleconferencing system. There will also be a phone number to dial into for audio only as well.

The talk will be at 2:00 pm HST tomorrow, 1/6/2015.

Instructions for joining the teleconference have been posted to the PSB website.

Tuesday, December 23, 2014

December SNPits Summary

In the December issue of UF Health Personalized Medicine Program's e-newsletter, SNPits, a recent study by Lee, et al. entitled "DPYD variants as predictors of 5-fluorouracil toxicity in adjuvant colon cancer treatment" is reviewed.  The authors find a statistically significant association between DPYD*2A and rs67376798 (DPYD D949V) and increased toxicity in patients treated with 5-fluorouracil-based combination chemotherapy.  This large randomized phase III trial is important evidence supporting the clinical applicability of these variants.

CPIC's dosing recommendations for 5-FU dosing with DPYD variants is found on PharmGKB here.

Friday, December 19, 2014

CPIC Term Standardization

CPIC (Clinical Pharmacogenetics Implementation Consortium) is leading an effort to standardize terms for clinical pharmacogenetic tests.  The goal of the project is to create standardized terms to be used in CPIC guidelines (specifically Tables 1 and 2) and in the larger pharmacogenetics community.  A list of phenotype term options based on an extensive literature review and scanning of sample laboratory reports is being developed.  Refinement of the terms will be performed using a modified Delphi method in the context of expert opinions.

CPIC is actively engaging different constituencies including members of the PGRN, ClinGen, the CDC PGx nomenclature working group, clinical laboratories and the IOM PGx roundtable.  Further details about this project are described here. If you have questions or comments regarding this project, and/or if you are interested in participating in this process, please contact us at

Tuesday, December 2, 2014

Annotated PMDA drug labels now available on PharmGKB

PharmGKB now has annotated drug labels available from the Pharmaceutical and Medical Devices Agency (PMDA), Japan.

The PMDA is a regulatory agency responsible for scientific reviews for the approval of drugs or medical devices, as well as safety monitoring after approval. The PMDA website provides PDF copies of package inserts for approved drugs. However, these inserts are only available in Japanese, and until recently PharmGKB had been unable to search for or annotate PMDA package inserts containing relevant pharmacogenetic (PGx) information.

In a paper published in 2013 in the Journal of Clinical Pharmacy and Therapeutics, Shimazawa and Ikeda selected PMDA inserts to examine for PGx information based on the FDA's Table of Pharmacogenomic Biomarkers in Drug Labeling. In addition to a discussion of the differences in PGx biomarker information between labels from the United States, United Kingdom and Japan, the authors also provided a table in the supplementary information that gave translations of any PGx information present in the PMDA package inserts. Using these translations, PharmGKB was able to create annotated drug labels for the package inserts examined by Shimazawa and Ikeda that contained PGx information. As with the annotated FDA and EMA drug labels, PMDA labels are given a PGx level of evidence, and a PDF copy of the package insert with PGx information highlighted is available for each annotated label.

It is likely that there are other PMDA package inserts that contain PGx information, and PharmGKB welcomes any feedback regarding PGx information within PMDA package inserts or labels from other medicine agencies around the world.

See a list of drug labels available on PharmGKB:
PMDA labels on PharmGKB

Read the paper:
Differences in pharmacogenomic biomarker information in package inserts from the United States, the United Kingdom and Japan
Shimazawa R, Ikeda M. Journal of Clinical Pharmacy and Therapeutics 2013; 38(6): 468-75. PMID 23895776.

Wednesday, November 26, 2014

November SNPits Summary

The November issue of UF Health Personalized Medicine Program's e-newsletter, SNPits, is out.  This issue contains a summary of a recent paper by Nicholson and Formea in Clinical Chemistry that discusses implementing CPIC guidelines for CYP2D6 and codeine.  The authors highlight some of the difficulties that may arise in the clinic.  We are pleased that the larger clinical community is beginning to embrace PGx guidelines and practice.