Concept

Clinical metagenomic sequencing

Clinical metagenomic next-generation sequencing (mNGS) is the comprehensive analysis of microbial and host genetic material (DNA or RNA) in clinical samples from patients by next-generation sequencing. It uses the techniques of metagenomics to identify and characterize the genome of bacteria, fungi, parasites, and viruses without the need for a prior knowledge of a specific pathogen directly from clinical specimens. The capacity to detect all the potential pathogens in a sample makes metagenomic next generation sequencing a potent tool in the diagnosis of infectious disease especially when other more directed assays, such as PCR, fail. Its limitations include clinical utility, laboratory validity, sense and sensitivity, cost and regulatory considerations. Outside of clinical medicine, similar work is done to identify genetic material in environmental samples, such as ponds or soil. Next-generation sequencing uses the techniques of metagenomics to identify and characterize the genome of bacteria, fungi, parasites, and viruses without the need for a prior knowledge of a specific pathogen directly from clinical specimens. The capacity to detect all the potential pathogens in a sample makes metagenomic next generation sequencing a potent tool in the diagnosis of infectious disease especially when other more directed assays, such as PCR, fail. A typical mNGS workflow consists of the following steps: Sample acquisition: the most commonly used samples for metagenomic sequencing are blood, stool, cerebrospinal fluid (CSF), urine, or nasopharyngeal swabs. Among these, blood and CSF are the cleanest, having less background noise, while the others are expected to have a great amount of commensals and/or opportunistic infections and thus have more background noise. Samples should be collected with much caution as surgical specimens could be contaminated during handling of the biopsy; for example, lumbar punctures to obtain CSF specimens may be contaminated during the procedure. RNA/DNA extraction: the DNA and the RNA of the sample is extracted by using an extraction kit.

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Cours associés (2)
ENV-621: Hands-on bioinformatics for microbial meta-omics
This course will train doctoral students to use bioinformatic tools to analyse amplicon and metagenomic sequences. In addition, we will also touch upon meta-transcriptomics and meta-proteomics.
CH-413: Nanobiotechnology
This course concerns modern bioanalytical techniques to investigate biomolecules both in vitro and in vivo, including recent methods to image, track and manipulate single molecules. We cover the basic
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NGS Data Analysis: Outils et modèles
Explore des outils et des modèles pour l'analyse de données de séquençage de nouvelle génération, couvrant les technologies de séquençage de l'ADN, les pipelines d'analyse de données et les modèles statistiques.
Génomique : la révolution du séquençage à haut débit
Couvre la révolution du séquençage Illumina à haut débit et le compare à d'autres technologies comme Pacific Biosciences et Nanopore Sequencing.
Méthodes de séquençage de l'ADN
Explore les méthodes de séquençage de l'ADN comme Sanger, le pyroséquençage et les technologies de synthèse.
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Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...
Amer Soc Microbiology2024
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