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Related Concept Videos

Sanger Sequencing01:57

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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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RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Next-generation Sequencing03:00

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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.
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Maxam-Gilbert Sequencing01:05

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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Related Experiment Video

Updated: Mar 19, 2026

Detection of Low Copy Number Integrated Viral DNA Formed by In Vitro Hepatitis B Infection
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Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing.

Vincent Montoya1, Andrea Olmstead1, Patrick Tang2

  • 1BC Centre for Disease Control, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
|June 11, 2016
PubMed
Summary

Deep sequencing enhances hepatitis C virus (HCV) transmission cluster identification by capturing minority variants. This method offers a more accurate view of viral evolution and spread compared to traditional Sanger sequencing.

Keywords:
Deep sequencingHepatitis C virusPhylogeneticsQuasispeciesTransmission

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Area of Science:

  • Virology
  • Evolutionary Biology
  • Epidemiology

Background:

  • Hepatitis C virus (HCV) remains a significant public health concern, necessitating effective surveillance and treatment.
  • Phylogenetic analysis is crucial for understanding viral evolution and transmission dynamics.
  • Traditional Sanger sequencing provides consensus sequences, potentially underestimating viral quasispecies complexity in rapidly mutating viruses like HCV.

Purpose of the Study:

  • To compare the effectiveness of deep sequencing versus Sanger sequencing in identifying hepatitis C virus transmission clusters.
  • To assess the utility of deep sequencing for characterizing viral quasispecies and improving phylogenetic analyses.

Main Methods:

  • Deep sequencing was applied to a characterized HCV-infected population.
  • Phylogenetic clusters were identified using deep sequencing with a sample-specific threshold.
  • Results were compared against clusters identified using consensus Sanger sequencing with various phylogenetic distance thresholds.

Main Results:

  • Deep sequencing identified additional transmission clusters and excluded individuals misclassified by Sanger sequencing.
  • A Sanger sequencing phylogenetic distance threshold of 0.03 offered the best agreement with deep sequencing results.
  • Out of 77 individuals, 10 were clustered by both methods, with deep sequencing identifying 4 more and excluding 8 others.

Conclusions:

  • Deep sequencing provides a more comprehensive characterization of viral quasispecies, leading to improved discrimination of HCV transmission clusters.
  • This approach offers a more effective tool for understanding HCV transmission dynamics compared to conventional Sanger sequencing.