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 African American Pharmacogenomic Consortium Network Transdisciplinary Collaborative Center
(ACCOuNT TCC) was created to:
The University of Florida seeks doctorally prepared clinicians and researchers who are poised to lead the next generation of scientists into an era where genomic medicine approaches are a routine part of patient care. The Program for Applied Research and Development in Genomic Medicine, or PARADIGM, is funded by the National Institutes of Health’s National Human Genomic Research Institute and will prepare trainees to be leaders in genomic medicine research and implementation. Trainees will receive didactic training tailored to their needs, extensive mentoring from world-renowned scientists, valuable clinical exposure in multiple areas of genomic medicine and stimulating career development opportunities in a robust, interdisciplinary research environment at UF.
Doctorally prepared clinicians and researchers are encouraged to apply by April 15, 2018.
To capitalize on the opportunities presented by advances in data science, the National Institutes of Health (NIH) is developing a Strategic Plan for Data Science. This plan describes NIH’s overarching goals, strategic objectives, and implementation tactics for promoting the modernization of the NIH-funded biomedical data science ecosystem. As part of the planning process, NIH has published a draft of the strategic plan, along with a Request for Information (RFI) to seek input from stakeholders, including members of the scientific community, academic institutions, the private sector, health professionals, professional societies, advocacy groups, patient communities, as well as other interested members of the public. Please submit responses using the link below by April 2, 2018.
The deadline to nominate a colleague for the inaugural FNIH Trailblazer Prize for Clinician-Scientists (Trailblazer Prize) is March 30, 2018 at 1pm EDT. This annual prize and $10,000 honorarium presented by the FNIH recognizes the outstanding contributions of early career clinician-scientists in the United States whose work has the potential to or has led to innovations in patient care.
According to the American Medical Association, the percentage of physicians engaged in research and teaching has decreased in past decades. This concerning statistic means that there are fewer clinician-scientists that play the vital role of understanding basic biology and scientific discovery while considering the potential benefits to patients. Through the Trailblazer Prize, the FNIH celebrates the transformational work of clinician-scientists, whose research translates basic scientific observations into new paradigm-shifting approaches for diagnosing, preventing, treating or curing disease and disability.
Andrea Gaedigk, PhD, Director of the Pharmacogenetics Core Laboratory at Children’s Mercy Hospital Kansas City and the PI of the PharmVar Consortium, and Neil Miller, Director of Bioinformatics, Center for Pediatric Genomic Medicine at Children’s Mercy Hospital Kansas City
Understanding individual response to drugs plays a central role in precision medicine. As pharmacogenetic testing becomes more and more prevalent, it’s crucial that the clinical and research communities have a global resource that provides nomenclature for defining and reporting genetic variants that help guide drug choice and dosing in adults and children. This resource also needs to keep up with the new era of genomics and the rate at which we’re finding new allelic variants.
After more than 15 years, the Human Cytochrome P450 Allele Nomenclature website, which has been the established authority for issuing and maintaining allele designations, has been transitioned to the Pharmacogene Variation (PharmVar) Consortium. This new home will serve as a centralized “Next-Generation” Pharmacogene Variation data repository and support the continued development of pharmacogene nomenclature.
The first version of the PharmVar database will be launched by the end of March and will contain the high-priority CYP2C9, CYP2C19 and CYP2D6 genes, while other P450 genes will be transferred into the PharmVar database soon thereafter. One particular feature of the new database is easy switching between different reference sequences making finding positions of sequence variants a breeze. The database will eventually also feature customizable tables showing alleles and regions of interest, an API for programmatic access, sequence alignments, and user options of downloading variant sequences.
Anyone in academia, industry or clinical test labs can submit new allele definitions. Data will be included in the database after review by a group of experts. This is truly a community process involving gene experts from around the world that will help provide new definitions and high-quality data for everyone to use.
In addition to a transparent submission and review process, the PharmVar database will assign unique version numbers to haplotype definitions, genes and database releases to enable robust tracking of nomenclature data and simplifying the task of determining the exact allele definitions used in a particular analysis or described in a publication.
It’s important for the community to have one place that keeps track of all these variations because it allows us to standardize the names we use to describe the variants and ensure we are all speaking the same language.
Pharmacogenomics is positioned at the leading edge of genomic medicine, and there have been huge advances made in using DNA testing to guide drug choice and dosage. This individualized approach allows for treatment to be customized to a particular patient instead of the one-size-fits all dosing model. Pharmacogenetic testing is increasingly used at our institution and many others to guide treatment for behavioral disorders such as ADHD. The next frontier is using genomics in everyday health care for every patient.
Right now, a lot of actionable data is sitting in silos in hospitals and data centers around the world, because we are sure many of our peers just haven’t found a home for it yet. PharmVar hopes to address this by establishing one place to keep track of variation. Providing a systematic catalog is a key part to successful implementation of pharmacogenetics into the clinic, and we hope this resource will have an impact on individualized patient care and health outcomes.
From Francis Collins' 1/11/18 blog post:
The Hub team