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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Sequences01:29

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Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Arithmetic Sequences01:30

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An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...
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Plants present a rich source of nutrients for many organisms, making it a target for herbivores and infectious agents. Plants, though lacking a proper immune system, have developed an array of constitutive and inducible defenses to fend off these attacks.
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Updated: Feb 3, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
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Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.

Wei Gu1, Steve Miller1, Charles Y Chiu1,2

  • 1Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;

Annual Review of Pathology
|October 26, 2018
PubMed
Summary

Next-generation sequencing (NGS) offers a powerful method for detecting and identifying infectious agents in clinical samples. This technology enhances the diagnosis of infectious diseases, especially when traditional methods fall short.

Keywords:
clinical diagnosticsinfectious diseasemetagenomicsnanopore sequencingnext-generation sequencingpathogen detection

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Area of Science:

  • Clinical Microbiology
  • Infectious Diseases
  • Genomics

Background:

  • Infectious agents possess DNA or RNA genomes, making sequencing a viable detection strategy.
  • High-throughput sequencing costs have significantly decreased, enabling broader clinical applications.
  • Next-generation sequencing (NGS) is revolutionizing pathogen detection and characterization in clinical settings.

Purpose of the Study:

  • To review the application of untargeted metagenomic NGS in diagnosing infectious diseases.
  • To highlight NGS's utility in clinical scenarios where conventional diagnostics are limited.
  • To provide a comprehensive overview of NGS technologies, workflows, and data analysis for infectious disease diagnosis.

Main Methods:

  • Review of NGS technologies and common platforms.
  • Description of NGS assay workflows in clinical microbiology laboratories.
  • Explanation of bioinformatics analysis for metagenomic NGS data.
  • Discussion of validation and use cases for NGS in infectious disease diagnosis.
  • Presentation of significant case reports and studies.

Main Results:

  • NGS enables sensitive detection and taxonomic characterization of microorganisms from clinical samples.
  • Untargeted metagenomic NGS provides a comprehensive approach to identifying pathogens.
  • The review covers key aspects from technology to clinical application and validation.

Conclusions:

  • Next-generation sequencing is a transformative technology for diagnosing infectious diseases.
  • NGS enhances the ability to diagnose, interrogate, and track infectious disease outbreaks.
  • This approach holds significant promise for improving clinical microbiology and public health surveillance.