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Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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DNAscent v2: detecting replication forks in nanopore sequencing data with deep learning.

Michael A Boemo1

  • 1Department of Pathology, University of Cambridge, Cambridge, UK. mb915@cam.ac.uk.

BMC Genomics
|June 10, 2021
PubMed
Summary

DNAscent v2 software accurately detects thymidine analogue BrdU incorporation using Oxford Nanopore Technologies sequencing. This advancement enables precise measurement of DNA replication dynamics and origin identification for cancer research.

Keywords:
Budding yeastDNA replicationDNAscentOxford nanoporeReplication forksReplication originsResidual neural networks

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Area of Science:

  • Genomics and Molecular Biology
  • Computational Biology and Bioinformatics

Background:

  • High-throughput, single-molecule measurement of DNA replication dynamics is crucial for understanding fundamental cell biology and developing cancer therapeutics.
  • Oxford Nanopore Technologies (ONT) sequencing offers a promising high-throughput, long-read method for detecting base analogues like BrdU, surpassing traditional techniques.

Purpose of the Study:

  • To introduce DNAscent v2, an advanced software tool for accurate and rapid detection of BrdU incorporation from ONT sequencing data.
  • To leverage DNAscent v2 for precise identification of DNA replication origins and termination sites with single-nucleotide resolution.

Main Methods:

  • Development of DNAscent v2, employing a residual neural network for BrdU detection and an autoencoder for interpreting BrdU patterns.
  • Utilizing ONT sequencing to generate long reads and mapping them to the genome for analysis.

Main Results:

  • DNAscent v2 achieves state-of-the-art accuracy in BrdU calling and DNA replication origin identification, outperforming previous versions and existing tools like NanoMod and RepNano.
  • The software demonstrates enhanced speed, versatility across experimental protocols, and single-nucleotide resolution in BrdU detection.
  • DNAscent v2 can identify BrdU without requiring sequencing of unmodified DNA and detects more origins than RepNano.

Conclusions:

  • DNAscent v2 represents a significant advancement in high-throughput, single-molecule analysis of replication fork dynamics.
  • The improved accuracy facilitates the study of DNA replication in large genomes and opens avenues for genome stability research, including DNA repair detection.