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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.
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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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Updated: Sep 30, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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Detecting structural variations with precise breakpoints using low-depth WGS data from a single oxford nanopore

Henry C M Leung1, Huijing Yu1, Yifan Zhang1

  • 1Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong.

Scientific Reports
|March 17, 2022
PubMed
Summary
This summary is machine-generated.

Low-depth whole-genome sequencing (WGS) with Oxford Nanopore is effective for detecting structural variations (SVs). A new tool, SENSV, accurately identifies pathogenic SVs crucial for diagnosing genetic disorders.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Medical Genetics

Background:

  • Structural variations (SVs) are a significant cause of genetic disorders.
  • Low-depth whole-genome sequencing (WGS) data, specifically 4× coverage from Oxford Nanopore (ONT), presents challenges for existing SV detection software.
  • Pathogenic SVs, including deletions, duplications, and translocations, are often missed by current tools.

Purpose of the Study:

  • To demonstrate that 4× ONT WGS is sufficient for sensitive detection of SVs, particularly pathogenic ones for clinical diagnosis.
  • To introduce SENSV, a novel SV calling software designed for high sensitivity and breakpoint precision.
  • To evaluate SENSV's performance against existing software using real patient data and simulated datasets.

Main Methods:

  • Utilized low-depth (4×) whole-genome sequencing data generated by a single Oxford Nanopore MinION flow cell.
  • Developed and implemented a new SV calling software named SENSV, incorporating novel algorithms.
  • Compared SENSV performance with existing SV callers on 24 patient samples diagnosed with genetic disorders and simulated data.

Main Results:

  • SENSV achieved high sensitivity across all SV types with breakpoint precision typically within ±100 bp.
  • SENSV successfully identified pathogenic SVs in 22 out of 24 patient cases (heterozygous, size from hundreds of kbp to a few Mbp).
  • Existing SV calling software detected pathogenic SVs in 10 or fewer cases, even with relaxed breakpoint criteria (±2000 bp).

Conclusions:

  • Low-depth 4× ONT WGS is a viable method for sensitive detection of pathogenic structural variations.
  • SENSV significantly outperforms existing software in identifying clinically relevant SVs from low-depth WGS data.
  • SENSV offers a promising tool for improving the clinical diagnosis of genetic disorders caused by structural variations.