Wednesday, May 24, 2017

IGNITE Network Analysis of Genomic Medicine Implementation Published in BMC Medical Genomics

A new paper in BMC Medical Genomics describes a multi-case study of six IGNITE (Implementing GeNomics In pracTicE) network sites currently implementing genomics, including pharmacogenomics, into patient care. The authors discuss challenges to implementation as well as subsequent strategies to address those challenges. 

All participating IGNITE institutions cited low prioritization of genomic data integration into electronic health records (EHR) as a challenge to implementation and four sites addressed this challenge with data warehousing techniques. An additional challenge was the unfamiliarity of many health care providers with interpretation and implementation of genomic data into patient care, which several institutions addressed with the development of educational materials for healthcare providers, facilitation of educational meetings and workshops targeted to physicians as well as stakeholders at various levels, and educational outreach with trained specialists to assist providers in clinical settings. The third most commonly cited challenge was engaging and informing patients. All IGNITE sites utilized various media platforms (e.g. local and national TV and radio, social media, newspapers) to disseminate information about genomic medicine research. Additional strategies included seeking patient input at panels, encouraging patients to assist with the development of educational materials, as well as teaching patients about evidence-based clinical decisions to help them become active in their own care.

You may read the article in its entirety here

Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network.
BMC Medical Genomics May 22, 2017

Nina R. Sperber, Janet S. Carpenter, Larisa H. Cavallari, Laura J. Damschroder, Rhonda M. Cooper-DeHoff, Joshua C. Denny, Geoffrey S. Ginsburg, Yue Guan, Carol R. Horowitz, Kenneth D. Levy, Mia A. Levy, Ebony B. Madden, Michael E. Matheny, Toni I. Pollin, Victoria M. Pratt, Marc Rosenman, Corrine I. Voils, Kristen W. Weitzel, Russell A. Wilke, R. Ryanne Wu and Lori A. Orlando

Tuesday, May 23, 2017

CPIC Survey Available Online

An important function of CPIC (Clinical Pharmacogenetics Implementation Consortium) is to receive feedback from, and give feedback to, our user communities.  CPIC has posted a survey that is part of that feedback and contains questions regarding priorities for CPIC guidelines, as well as feedback on SNOMED CT term submissions.  CPIC requests completion of the survey by May 31st:

Tuesday, May 16, 2017

Voriconazole and Macrolide Antibiotic Pathways featured on PG&G Covers

PharmGKB was pleased to see our pathways featured on two successive covers of the journal Pharmacogenetics and Genomics. Our macrolide antibiotic pharmacokinetics and pharmacodynamics pathway was featured on the cover of the April issue, and our voriconazole pharmacokinetics pathway was featured on the cover of the May issue. PharmGKB curators Dr. Alison Fohner and Julia Barbarino were the respective lead authors on these pathways.

Voriconazole is an antifungal agent used primarily in immunocompromised patients, such as those undergoing organ transplantation. CYP2C19 is the primary enzyme responsible for voriconazole metabolism, and the metabolism and clearance of voriconazole are influenced by CYP2C19 genotype. The voriconazole pathway can be viewed on the PharmGKB website. The Clinical Pharmacogenetics Implementation Consortium (CPIC) also recently released guidelines for voriconazole dosing based on CYP2C19 genotype.

Macrolides are a class of broad spectrum antibiotics of large molecular size, including erythromycin, clarithromycin and azithromycin. Macrolide antibiotics exhibit a number of pharmacogenetic associations with the genes encoding drug transporters and metabolizing enzymes. More information can be found on the macrolide pathway on the PharmGKB website.

Wednesday, May 3, 2017

NHGRI’s Genomic Medicine X: Pharmacogenomics Meeting

On May 2 and 3, 2017, the National Human Genome Research Institute (NHGRI) held its 10th Genomic Medicine meeting, focusing on pharmacogenomics.

PharmGKBPharmCAT and CPIC were presented, as well as a review of the deposition of PharmGKB and CPIC data to ClinVar.  We thank Mary Relling from St Jude Children's Research Hospital,  Marylyn Ritchie from Geisinger and Heidi Rehm from Parnters for highlighting these activities at the meeting.

Wednesday, April 26, 2017

Curators' Favorite Papers

Electronic medical record-integrated pharmacogenomics and related clinical decision support concepts
Authors: Caraballo PJ Bielinski SJ St Sauver JL Weinshilboum RM

The authors of this article from Clinical Pharmacology and Therapeutics, discuss the challenges to successful integration of pharmacogenetic/pharmacogenomic (PGx) clinical decision support (CDS) tools into electronic health and medical records (EMR). They provide examples of medical systems that have already done so and they specifically highlight the success of the Mayo Clinic where CDS tools for eleven PGx genes and nineteen drug-gene interactions have been successfully integrated into EMRs and patient care.

Celebrating parasites
Authors: Greene CS, Garmire LX, Gilbert JA, Ritchie MD, Hunter LE.

This correspondence to Nature Genetics is a response to a controversial 2016 editorial from the the New England Journal of Medicine in which the term, “research parasites” was coined. The term described those researchers who do secondary analyses of data generated by other researchers. The authors argue that “parasites” serve an important purpose in research and that the critical re-analysis of data is crucial for the practice of science. To honor such research, they announce two inaugural award categories at this year's Pacific Symposium on Biocomputing: the Junior Parasite Award and the Sustained Parasite Award.

Sunday, April 23, 2017

March for Science

On April 22, 2017 — members of the PharmGKB team, participated with thousands of other scientists and non-scientists alike, in the March for Science. Please join us, as did Russ Altman (Co-Prinicipal Investigator, PharmGKB) and the larger scientific community in the continuation of evidence-based science.

Monday, April 17, 2017

Thiopurine Pathway updated with new candidate genes

Thiopurines and TPMT have long been a cornerstone of PGx research. As such the Thiopurine Pathway was one of the earliest pathways in PharmGKB to be published in Pharmacogenetics and Genomics [PMID:19952870]. In collaboration with Jun Yang, Takaya Moriyama and Rina Nishii from St Judes, we have substantially updated the Thiopurine Pathway to include new candidate genes in particular NUDT15. NUDT15 will also be featured in a new VIP summary next month. 

The new Thiopurine Pathway figure focuses more on the drug metabolites (which are clickable and linked to Pubchem structures and publications) and candidates for their formation. We have also updated the text to include the kind of summary and literature review PharmGKB pathways are known for, and have a more detailed underlying set of components to allow for data export/analysis.