Glossary¶
This page describes glossaries for PyPGx.
1000 Genomes Project (1KGP)¶
The 1000 Genomes Project created a catalogue of common human genetic variation, using openly consented samples from people who declared themselves to be healthy. The reference data resources generated by the project remain heavily used by the biomedical science community.
Clinical Pharmacogenetics Implementation Consortium (CPIC)¶
The Clinical Pharmacogenetics Implementation Consortium (CPIC) is an international consortium whose primary goal is to facilitate use of PGx tests for patient care by creating, curating, and posting freely available, peer-reviewed, evidence-based, updatable, and detailed gene/drug clinical practice guidelines.
Canadian Pharmacogenomics Network for Drug Safety (CPNDS)¶
The Canadian Pharmacogenomics Network for Drug Safety (CPNDS) is a multicenter active surveillance and pharmacogenomics consortium. It was founded in 2004 with the goal to uncover the genetic and mechanistic basis of drug response phenotypes and develop clinical pharmacogenetic implementation tools to improve the safety and efficacy of medications used in children and adults. It is a multidisciplinary team of scientists and practicing physicians from across Canada and around the world.
Dutch Pharmacogenetics Working Group (DPWG)¶
The Dutch Pharmacogenetics Working Group (DPWG) was established in 2005 by the Royal Dutch Pharmacist’s Association. The DPWG is multidisciplinary and includes clinical pharmacists, physicians, clinical pharmacologists, clinical chemists, epidemiologists, and toxicologists.
Genetic Testing Reference Materials Coordination Program (GeT-RM)¶
The goal of the Centers for Disease Control and Prevention–based Genetic Testing Reference Materials Coordination Program (GeT-RM) is to coordinate a self-sustaining community process to improve the availability of appropriate and characterized reference materials.
Next-generation sequencing (NGS)¶
Next-generation sequencing (NGS) is a massively parallel sequencing technology that offers ultra-high throughput, scalability, and speed.
Pharmacogenomics (PGx)¶
According to this PharmGKB post:
In general pharmacogenetics usually refers to how variation in one single gene influences the response to a single drug. Pharmacogenomics is a broader term, which studies how all of the genes (the genome) can influence responses to drugs. However, these terms are often used interchangeably.
Pharmacogene Variation Consortium (PhamVar)¶
The Pharmacogene Variation Consortium (PhamVar) is an international group of experts that maintains a systematic nomenclature system for allelic variations of genes that affect the metabolism of drugs. The database is focused on cytochrome P450 enzymes, but is being expanded into other classes of enzymes. The original nomenclature was maintained by the Human CYP Allele Nomenclature Database. However PhamVar took over this function in 2017.
Pharmacogenomics Knowledge Base (PharmGKB)¶
The Pharmacogenomics Knowledge Base (PharmGKB) is a publicly available, online knowledge base responsible for the aggregation, curation, integration and dissemination of knowledge regarding the impact of human genetic variation on drug response. PharmGKB annotates PGx-based drug dosing guidelines published by CPIC, DPWG, CPNDS, and other professional societies. PharmGKB annotations present a brief summary of the genotype-based dosing recommendations and links to the source publications/documents.
Structural variation (SV)¶
Structural variation (SV) is generally defined as a region of DNA approximately 1 kb and larger in size and can include inversions and balanced translocations or genomic imbalances (duplications and deletions), commonly referred to as copy number variants (CNVs). Additionally, for pharmacogenes that are known to have one or more pseudogenes (e.g. CYP2D6), SV can be often found in the form of hybrid genes (e.g. CYP2D6/CYP2D7).
Whole genome sequencing (WGS)¶
WGS is a comprehensive method for analyzing entire genomes, as opposed to selectively sequencing targeted regions (e.g. whole exome sequencing).