Glossary
********

This page describes glossaries for PyPGx.

1000 Genomes Project (1KGP)
===========================

The `1000 Genomes Project <https://www.internationalgenome.org/>`__ 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)
<https://cpicpgx.org/>`__ 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)
<http://cpnds.ubc.ca/>`__ 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) <https://www.knmp.nl/
producten/gebruiksrecht-g-standaard/informatie-over-de-g-standaard/
the-g-standaard-the-medicines-standard-in-healthcare>`__ 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) 
<https://www.cdc.gov/labquality/get-rm/index.html>`__ 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 <https://www.pharmgkb.org/page/faqs#what-
is-the-difference-between-pharmacogenetics-and-pharmacogenomics>`__:

  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)
<https://www.pharmvar.org/>`__ 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)
<https://www.pharmgkb.org/>`__ 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).