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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Pharmacogenetics and Pharmacogenomics: Overview01:29

Pharmacogenetics and Pharmacogenomics: Overview

Pharmacogenetics and pharmacogenomics examine how genetic factors influence an individual's response to drugs. While pharmacogenetics focuses on the impact of specific genetic variants on drug effects, pharmacogenomics takes a broader approach, studying how genetic variation across populations contributes to differences in drug responses. These fields aim to explain why individuals may experience varying levels of efficacy or adverse reactions to the same medication.Variability in drug...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu01:29

Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu

Genetic variations significantly influence drug response through pharmacokinetics, receptor interactions, and biologic milieu modifications. Pharmacokinetic alterations impact drug metabolism and clearance, affecting efficacy and toxicity. Variants in drug-metabolizing enzymes, such as CYP2C9 and CYP2C19, alter drug activation and elimination. For example, CYP2C9 loss-of-function variants require lower warfarin doses to prevent excessive bleeding, while CYP2C19 variants reduce clopidogrel...
Pharmacogenetics of Drug Metabolism: Overview01:27

Pharmacogenetics of Drug Metabolism: Overview

Genetic polymorphism in drug metabolism is crucial to the inter-individual variability observed in drug responses. Drug metabolism primarily involves the chemical modification of drugs and other xenobiotics to enhance their elimination by increasing their polarity. Two main classes of enzymes mediate this biotransformation process: Phase I enzymes, primarily cytochrome P450s, catalyze oxidation and reduction reactions, while other enzymes, such as esterases, mediate hydrolysis, and Phase II...
Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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A New Cloud-Native Tool for Pharmacogenetic Analysis.

David Yu Yuan1, Jun Hyuk Park2, Zhenyu Li3

  • 1European Nucleotide Archive, European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, Cambridge CB10 1SD, UK.

Genes
|March 28, 2024
PubMed
Summary
This summary is machine-generated.

A new bioinformatics pipeline, Pgxtools, enhances pharmacogenetic (PGx) testing by accurately analyzing genomic data and supporting clinical decisions. This tool improves variant identification for diverse populations using next-generation sequencing (NGS).

Keywords:
bioinformatics pipelinecloud-native technologiesgenomic data analysispharmacogeneticsworkflow

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Area of Science:

  • Genomics
  • Bioinformatics
  • Pharmacogenetics

Background:

  • Next-generation sequencing (NGS) enables large-scale pharmacogenetic (PGx) studies and pre-emptive testing.
  • Current NGS-based PGx testing lacks comprehensive computational tools for genetic data analysis and clinical decision support.

Purpose of the Study:

  • To develop a bioinformatics pipeline for analyzing genomic sequence data and reporting PGx genotypes.
  • To integrate a database for filtering actionable PGx variants and clinical interpretations.
  • To provide a tool supporting clinical decisions in pharmacogenetics.

Main Methods:

  • Utilized bioinformatics utilities for human genomics and cloud-based technologies.
  • Developed a pipeline integrating a database for variant filtering and clinical interpretation.
  • Performed quality verification using whole genome sequencing (WGS) data from the 1000 Genomes Project (G1K) and validated accuracy with CDC reference materials.

Main Results:

  • The Pgxtools pipeline analyzes genomic data, identifies actionable variants in 13 PGx genes, and generates annotated reports with clinical recommendations.
  • Pgxtools demonstrated higher accuracy in variant identification compared to G1K dataset results on GRCh37 and GRCh38, verified by independent methods.

Conclusions:

  • Pgxtools offers an integrated workflow for large-scale genomic data analysis and PGx clinical decision support.
  • Its cloud-native implementation ensures portability across various computing environments, from laptops to HPC clusters and cloud platforms.