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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

86.7K
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
Although all next-generation methods use different technologies, they all share a set of standard features....
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Sanger Sequencing01:57

Sanger Sequencing

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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...
752.0K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

10.8K
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.
Challenges of the Maxam-Gilbert Method
The...
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
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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RNA-seq03:21

RNA-seq

9.8K
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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Updated: May 22, 2025

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
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JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.

Ivan Specht1, Gage K Moreno1, Taylor Brock-Fisher1,2

  • 1The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Medrxiv : the Preprint Server for Health Sciences
|March 17, 2025
PubMed
Summary
This summary is machine-generated.

JUNIPER reconstructs disease transmission networks by analyzing pathogen genetic data, including within-host variations. This tool enhances understanding of pathogen spread and aids targeted control strategies for outbreaks like H5N1 and COVID-19.

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Area of Science:

  • Epidemiology
  • Computational Biology
  • Genomics

Background:

  • Understanding disease transmission is crucial for effective public health interventions.
  • Existing tools for transmission reconstruction face scalability and methodological limitations.

Purpose of the Study:

  • To develop a highly scalable tool, JUNIPER (Joint Underlying Network Inference for Phylogenetic and Epidemiological Reconstructions), for reconstructing pathogen transmission networks.
  • To incorporate intrahost variation and incomplete sampling into outbreak reconstruction models.

Main Methods:

  • Developed JUNIPER, integrating a statistical model for within-host variant frequencies from next-generation sequencing data.
  • Combined within-host variation models with population-level evolutionary and transmission models for simultaneous inference of phylogenies and transmission trees.
  • Validated JUNIPER on simulated and real-world outbreak data, including SARS-CoV-2, H5N1, and COVID-19 datasets.

Main Results:

  • JUNIPER accurately infers transmission links and phylogenies, outperforming existing methods.
  • Quantified elevated H5N1 transmission rates in California and identified high-confidence transmission events.
  • Demonstrated the efficacy of vaccination in reducing SARS-CoV-2 transmission.

Conclusions:

  • JUNIPER overcomes computational and methodological limitations in outbreak reconstruction.
  • Provides a robust framework for large-scale pathogen spread studies.
  • Enables critical insights into disease dynamics for targeted control measures.