Tuesday, April 24, 2018

Curators' Favorite Papers

The first paper comes from the journal Pharmacogenomics (Clinical pharmacogenetics: how do we ensure a favorable future for patients?) and it discusses the factors that have impeded the implementation of pharmacogenomic (PGx) testing into routine clinical care. Randomized clinical trials (RCT) are the current gold-standard for clinical research for new drug approvals, but the nature of PGx studies is ill-suited to the RCT format. The authors propose alternatives to RCTs such as demonstration of non-inferiority to standard of care, N-of-1 trials for individuals or “hybrid effectiveness-implementation” clinical trials (trials that blend design components investigating clinical effectiveness with implementation research). They also emphasize that implementation of PGx data would require comprehensive, pre-emptive testing, population specific PGx considerations, and storage of results in electronic medical records (EMR) with adequate clinical decision support (CDS) tools. Finally, they make the case for testing for genetic variants with robust evidence of a PGx association, and specifically cite the Clinical Pharmacogenenomics Implementation Consortium (CPIC) as a “promising place to start” in selecting PGx genes to test as well as PharmGKB as a resource for information on gene-drug PGx associations.

The second paper, authored by the International Society for Biocuration (Biocuration: Distilling data into knowledge), comes from the journal PLoS Biology. It explains the specific role that biocurators play within teams that manage biological information resources and databases. Beginning with the premise that data is an asset whose value increases each time it is shared, the authors argue that biocurators maximize value by assuring the “accuracy, comprehensiveness, integration, accessibility, and reuse” of data through the process of extracting knowledge (such as data) from unstructured forms (usually publications) into structured and machine readable forms to enhance its usability and sharing. The authors note that there is encouraging development with regard to data reporting tools, an increase in demand and support for data standards and a growth in the use of biocuration tools by researchers, and all of these are expected to facilitate data curation, data sharing and ultimately, scientific progress.

Wednesday, April 18, 2018

The Clobazam Pathway on the Cover of Pharmacogenetics and Genomics

One of our newest pathways, the Clobazam Pathway, Pharmacokinetics, is featured on the cover of the April issue of the journal Pharmacogenetics and Genomics. PharmGKB Scientific Curator Dr. Rachel Huddart is the first author on this pathway. Clobazam is a benzodiazepine and is used primarily as an anti-epileptic.  The primary metabolizing enzyme is CYP2C19, but additional metabolizing enzymes include CYP3A4CYP2B6 and CYP2C18. You can now view the interactive Clobazam Pathway, Pharmacokinetics on PharmGKB.

Thursday, April 5, 2018

Curator's Favorite Papers

Genetics has been shown to have a profound effect on response to treatment in patients with major depressive disorder (MDD) and may account for as much as 42% of the variability in treatment response, according to some studies. In addition, personality traits, as defined by “the Big-Five" (openness, conscientiousness, extraversion, agreeableness, and neuroticism), which are likely to also be influenced by genetics, may also associate with response to anti-depression treatment. A new study (Association of the Polygenic Scores for Personality Traits and Response to Selective Serotonin Reuptake Inhibitors in Patients with Major Depressive Disorder) intended to uncover gene variants associated with the cross-trait associations between “the Big-Five” and treatment response using data from the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomic Study (N = 529) and the International SSRI Pharmacogenomics Consortium (N = 865). Evidence points to an overlap in association between specific personality traits and SSRI treatment outcomes and that the association is partly due to genetics. Specifically, the study evaluated the combined effect of multiple genes (polygenic score, PGS) and their association with one of the five personality traits, as well as response and remission in patients with MDD who are prescribed SSRIs. The PGS for openness personality with treatment response was statistically significant in the ISPC cohort and statistically significant with remission in the PGRN-AMPS sample. PGS for conscientiousness was associated with response, but not remission. Cross-trait meta-analysis of GWAS uncovered eight overlapping genetic loci with previously reported associations with response to SSRIs as well as certain personality traits, particularly neuroticism.  Of note, several PharmGKB members were co-authors on this study: Katrin Sangkuhl, Scientific Curator, Ryan Whaley, Technical Lead, Russ Altman, Co-PI of PharmGKB and Teri Klein, Director and Co-PI of PharmGKB. 

You can find more information about pharmacogenetic guided dosing for SSRIs on cpicpgx.org as well as on the PharmGKB annotation of the CPIC Guideline for SSRIs and CYP2D6 and CYP2C19.