PharmVar announces the release of a major update. Notable new features include a revised haplotype naming system, the introduction of unique haplotype IDs, displaying impact next to the causative SNV in brackets and a revised allele (CYP2D6*14A is now *114). The new gene page design has customizable display options and allows the user to see variation info across reference sequences and genome builds and rsIDs without leaving the page.
The update also features nomenclature for the first non-CYP gene, NUDT15. Papers describing the new features, and how NUDT15 nomenclature was developed are close to being published in CPT. A presentation with an overview of PharmVar and highlights of the new features can be found under the ABOUT tab. It’s pretty cool – check it out at www.pharmvar.org
The PGRN Hub congratulates the Trainee Abstract Award Winners from the poster session at the 2018 PGRN-ASHG Symposium!
Best Trainee Abstract Award Winners
We also recognize the following trainees for Honorable Mention: Osatohanmwen J. Enogieru (UCSF), Andrew M. Glazer (Vanderbilt), Britt Drogemoller (UBC), Meghan J. Chenoweth (UToronto), Robert J. Autry (St. Jude), Xinyuan Zhang (UPenn).
We congratulate all participants for their excellent presentations of cutting-edge pharmacogenomics research.
Great news from the Clinical Pharmacogenetics Implementation Consortium (CPIC) team! Drs. Mary Relling of St. Jude Children's Research Hospital (SJCRH) and Teri Klein of Stanford University, will receive $5 million over the next 5 years from the National Institutes of Health (NIH) to continue and expand CPIC, to facilitating use of pharmacogenetic tests into patient care.
NHGRI, released two funding opportunities relevant to laboratory and clinical research to translate genomic and genetic research into understanding and treating human diseases.
Investigator-Initiated Genomic Medicine Research
PAR-18-735 & PAR-18-736
This supports research opportunities designed to advance the understanding and implementation of genomic information about an individual to inform clinical care, and the health outcomes of that clinical use.
Novel Approaches for Relating Genetic Variation to Function & Disease
PA-18-867 & PA-18-868
Genome-wide association studies have found many variants that are statistically associated with disease and other traits. In addition, clinical genomic sequencing studies have identified many variants in healthy and diseased individuals, where the pathogenicity of such variants is often unknown, leading to their classification as variants of uncertain significance (VUS). This program aims to support the development of novel and generalizable approaches to study how genetic variants lead to differences in function and to study how such functional differences affect human health and disease processes, or how this knowledge can be used clinically.
NIGMS is recruiting for an accomplished scientist with experience in the pharmacological sciences to join the Pharmacological and Physiological Sciences (PPS) Branch of the Division of Pharmacology, Physiology, and Biological Chemistry. The successful applicant will have responsibility for scientific and administrative management of a portfolio of grants, both research and training, in the Division.
Interested? Please learn more: https://loop.nigms.nih.gov/2018/09/wanted-program-director-pharmacological-and-physiological-sciences-branch/. The application process is not difficult (but it does end on Sept. 26), and Alison Cole and Rochelle Long want to know in advance if you will be applying. It’s a good group to work with on interesting science. Don’t hesitate to contact them for more information.
PharmVar is pleased to announce that 8 more genes have been added to the interactive database. All genes in the database are highlighted with the PharmVar logo.
Next generation sequencing technologies have been around since the last decade, however, its used in pharmacogenetic studies are limited and in general include fewer samples (Weeke et al. 2014, Yang et al. 2018, Chua et al., 2015, Li et al. 2018). Recently, the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium and investigators from USA and other countries performed the first and the largest whole-genome sequencing pharmacogenetic study from 1,441 children with asthma from the tails of the bronchodilator drug response distribution (Mak et al. 2018). The aim of the study was to identify common and rare variants associated with albuterol, a bronchodilator, response in ethnically diverse children. A genomewide significant locus and several suggestive loci near to genes related to lung function and immunity were identified. This first whole-genome pharmacogenetics study using the tails of the drug response is a promising approach and hopefully other kinds of pharmacogenomics studies using whole-genome or whole–exome sequencing will become more widely used in future.
Based on scientific merits and feasibility of the project, two projects have been selected for the pilot gene editing service described below:
PharmVar is delighted to announce a new feature that just went live! Variants of genes in the PharmVar database can now be downloaded in sequence (FASTA and VCF) and table (TSV) formats. Options include to the download variants of interest, all variants of a gene or the entire PharmVar database.
Check out the link “Additional Data Download Information” on the gene page for more information.
There are currently three genes in the database, CYPs 2C9, 2C19 and 2D6 – additional genes will be transitioned soon.
The Hub team