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annotation

A collection of 13 issues

There is no ontology term for Phenoconversion in BioPortal

There are two papers ahead of print in Pharmacogenomics both discussing how important phenoconversion is to consider in the implementation of PGx in clinical practice. Phenoconversion in the PGx context is a drug-drug interaction that impacts a drug metabolizing phenotype such that it mimics the effects of a metabolizer genotype.

Rollout of genotype picker tool on DPWG guideline annotations

The allele pull-down menu (also known as the genotype-picker tool) on PharmGKB annotations of CPIC guidelines is an extremely popular feature among users. We are pleased to now expand this functionality to annotations of guidelines from the Royal Dutch Association for the Advancement of Pharmacy - Pharmacogenetics Working Group (DPWG)

PharmGKB introduces scoring system for variant and clinical annotations and updated Levels of Evidence

Since their introduction in 2010, clinical annotations have become one of the most popular features of PharmGKB. Each clinical annotation summarizes a phenotypic association between a drug and genetic variant, shows relevant findings from the curated literature as variant annotations and is assigned a level of evidence to indicate the

PharmGKB releases automated annotations

We are excited to announce that automated annotations of pharmacogenomic information in the scientific literature are now available from PharmGKB. These annotations have been produced using the PGxMine project, the result of a collaboration with Dr. Jake Lever at Stanford University.PGxMine uses a supervised machine learning algorithm to carry

Combining large PGx datasets from cancer cell lines

Testing cancer cell lines in vitro for drug sensitivity is a cornerstone of preclinical drug development. Large publically available datasets can be found at The Genomics of Drug Sensitivity in Cancer Project(GDSE) and The Cancer Cell Line Encyclopedia (CCLE). Studies attempting to combine large public datasets and analyzing for

Concordance of Drug Labels and Clinical Annotations

Some drug labels have been identified by the FDA as containing pharmacogenetic biomarker information, but occasionally these variants are not listed in the Clinical Annotations on PharmGKB. The Clinical Annotations are based on literature available in peer reviewed journals and focus on germline variants. As a result, there are a

ABCB5 and haloperidol-induced toxicity: Results from a new study

Approximately 50% of patients treated with the antipsychotic drug haloperidol will develop extrapyramidal symptoms, a category that includes tremors, parkinsonism and decreased spontaneous movement. However, studies looking into the genetic variations associated with the development of these symptoms have been limited. In a study recently published in PLOS Medicine, Zheng

PharmGKB PGx summaries now available in the Genetic Testing Registry

The Genetic Testing Registry (GTR) now contains summaries written by PharmGKB Curators regarding the association between genes and drug responses that have CPIC therapeutic recommendations. These can be found on the GTR website under Conditions/Phenotypes and links to relevant clinical tests are provided on each page: * Warfarin response * Codeine

Visualizing Levels of Evidence

PharmGKB Clinical Annotations provide a summary of an association between a genetic variant and a drug response. Each is assigned a level of evidence by our curators, based on established criteria. We have created an illustration to help users understand the 4 levels of evidence:

Tailored therapy in asthma? ADRB2 genotype in the context of salmeterol therapy

In a recent trial, asthmatic children homozygous for the beta2-adrenergic receptor Arg16 variant (ADRB2 gene, rs1042713 genotype AA) were randomized and treated with either salmeterol (a beta2-adrenergic receptor agonist) or montelukast (a leukotriene receptor antagonist), both combined with fluticasone. Those in the montelukast treatment group displayed significantly better responses in