Wednesday, June 28, 2017

Pharmacogenomics on Nightly News with Lester Holt

The Wednesday, June 28th edition of the Nightly News with Lester Holt featured a short segment on pharmacogenomics.

The piece briefly covered the Mayo Clinic's work in expanding the use of pharmacogenomics in the clinic. Dr. Richard Weinshilboum, co-director of the pharmacogenomics program at the Mayo Clinic, was also interviewed. Dr. Weinshilboum is a leader in the field, and has been a co-author on a number of PharmGKB publications, including multiple PharmGKB pathways and VIPs, as well as the International SSRI Pharmacogenomics Consortium (ISPC) publication. He is also a member of the Pharmacogenomics Research Network (PGRN); PharmGKB is a partner of the PGRN.

PharmGKB provides a page for clinically relevant pharmacogenomic summaries - a list of clinical annotations that contain variant-drug combinations featured in a guideline published by the Clinical Pharmacogenetics Implementation Consortium (CPIC) or other medical society, or implemented at a PGRN site or a major health system, such as the Mayo Clinic. This includes associations such as codeine and CYP2D6 or thiopurine drugs and TPMT; both of these associations have CPIC guidelines. The page also features variant-drug combinations that have a preponderance of evidence showing an association, and therefore may be clinically actionable, but are not currently featured in a guideline.

Tuesday, June 20, 2017

AMIA 10x10 Virtual Pharmacogenomics course with Stanford University begins June 26, 2017

The American Medical Informatics Association (AMIA) has partnered with the Biomedical Informatics program at Stanford University to present an online course in pharmacogenomics (PGx) as part of the AMIA 10 x 10 series. The course, Pharmacogenomics, will  introduce the field and cover topics relevant to PGx including pharmacology, genomics, genome wide association studies (GWAS) and high-throughput assay analyses, natural language processing (NLP), PGx resources such as PharmGKB, Drugbank and NCBI, relevant gene and drug classes as well as current challenges to the implementation of PGx testing in clinical care.  

Russ Altman, MD, PhD, Professor of Bioengineering, Genetics, Medicine, and Computer Science and Director of the Biomedical Informatics Training Program and Co-PI of PharmGKB is also the Director of the 10 x 10 Pharmacogenomics course. Additional instructors include Dr. Michelle Whirl-Carrillo, Associate Director of PharmGKB, Dr. Alison Fohner, former Scientific Curator at PharmGKB, Sara Hillenmeyer, and Dr. Natalia Khuri. 

The course begins June 26th. To learn more and to register, please click here

Tuesday, June 13, 2017

The Next Look for PharmGKB

PharmGKB is excited to show you our all-new website design. We’ve been working hard for months to create a new user interface that serves all of PharmGKB’s content in a clear and flexible way.

You can see the new design by visiting

The “next” site uses modern web technologies and frameworks to produce a clear interface no matter which device you’re using. This means mobile & small-screen devices will have a first-class user experience.

We’re using the new to power this next design. Page load speeds have increased dramatically especially when it comes to our most annotated genes like CYP2D6 and G6PD.

We’d love to know what you think of the new design! Please go to, use the site, and give us your feedback. Every message you send helps us understand how to help people looking to learn more about pharmacogenomics and precision medicine.

We plan to run as a preview of things to come while still showing our traditional design at After a short trial period we will move the “next” design over to

If you have something you’d like us to know about the redesign, please use the feedback button on the bottom-right of any page.

We hope you find this new design as exciting and useful as we do. We look forward to your feedback!

Thursday, June 1, 2017

Curators' Favorite Papers

Concordance between Research Sequencing and Clinical Pharmacogenetic Genotyping in the eMERGE-PGx Study
Authors: Rasmussen-Torvik LJ, Almoguera B, Doheny KF, Freimuth RR, Gordon AS, Hakonarson H, Hawkins JB, Husami A, Ivacic L, Kullo IJ, Linderman MD, Manolio TA, Obeng AO, Pellegrino R, Prows CA, Ritchie MD, Smith M, Stallings SC, Wolf WA, Zhang K, Scott SA.

A new paper in “The Journal of Molecular Diagnostics” examines whether “orthogonal confirmation” of next generation sequencing (NGS) results is necessary. The authors examined data from subjects enrolled as part of the Electronic Medical Records and Genomics Pharmacogenomics (eMERGE-PGx) study. The authors found that for 4077 patients (and 67,900 variants) the per-sample concordance rate was 0.972, while the per-variant concordance rate was 0.997. Source of error for the NGS sequencing results were attributed to the accidental swapping of samples. The source of error in clinical genotyping was attributed to the presence of rare variants near primer annealing sites which may have disrupted hybridization and led to amplification of the other allele ("allele drop-out"). The authors conclude that high concordance between the two sequencing modalities obviates the need for orthogonal sequence confirmation in NGS samples and that concordance could be improved by implementing practices known to further reduce error. 

Drugs in space: Pharmacokinetics and pharmacodynamics in astronauts
Authors: Johannes Kasta, Yichao Yua, Christoph N. Seubertb, Virginia E. Wotringc,d, Hartmut Derendorfa,

A review in “The European Journal of Pharmaceutical Sciences” discusses factors that may affect drug pharmacokinetics and pharmacodynamics, as well as drug safety and efficacy in a very particular situation: space. In addition to the expected effects of microgravity on drug absorption, distribution, metabolism, and elimination (ADME), studies in space have also shown that drug stability, the immune system, and bacterial growth patterns are also affected by microgravity and all must be taken into consideration to ensure drug efficacy and safety during spaceflight.