Recent advances in the detection of base modifications using the Nanopore sequencer

Xu, Lai; Seki, Masahide

doi:10.1038/s10038-019-0679-0

Cited by 116 publications

(93 citation statements)

References 79 publications

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“…Several consecutive nucleobases in the narrowest region of the pore can influence the ionic current. Translating a sequence of current values into a DNA sequence is therefore a non-trivial task typically solved using hidden Markov models [15,16] or recurrent neural networks [17,18]; for review [9]. Importantly, such approaches can discriminate methylated and hydroxymethylated from unmodified cytosines [7,8], suggesting that detection of modified nucleobases incorporated in newly replicated DNA should be feasible.…”

Section: Brdu Produces a Distinct Nanopore Electrical Signalmentioning

confidence: 99%

FORK-seq: replication landscape of theSaccharomyces cerevisiaegenome by nanopore sequencing

Hennion

Arbona

Lacroix

et al. 2020

Preprint

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Genome replication mapping methods profile cell populations, masking cell-tocell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200 nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,651 replication tracks reproducing populationbased replication directionality profiles and map 4,964 and 4,485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.

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Section: Brdu Produces a Distinct Nanopore Electrical Signalmentioning

confidence: 99%

FORK-seq: replication landscape of theSaccharomyces cerevisiaegenome by nanopore sequencing

Hennion

Arbona

Lacroix

et al. 2020

Preprint

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“…This technology has already permitted the identification, annotation and characterization of tens of thousands of structural variants (SV) from a human genome [42]. Although the accuracy of nanopore sequencing is not yet comparable with that of short-read sequencing (for example, Illumina platforms claim 99.9% of accuracy), updates are constant and ongoing develops aim to expand the range of genomes and further improve accuracy of the technology [37,43].…”

Section: Third-generation Sequencersmentioning

confidence: 99%

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

Pereira

Oliveira

Sousa

2020

JCM

181

119

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Clinical genetics has an important role in the healthcare system to provide a definitive diagnosis for many rare syndromes. It also can have an influence over genetics prevention, disease prognosis and assisting the selection of the best options of care/treatment for patients. Next-generation sequencing (NGS) has transformed clinical genetics making possible to analyze hundreds of genes at an unprecedented speed and at a lower price when comparing to conventional Sanger sequencing. Despite the growing literature concerning NGS in a clinical setting, this review aims to fill the gap that exists among (bio)informaticians, molecular geneticists and clinicians, by presenting a general overview of the NGS technology and workflow. First, we will review the current NGS platforms, focusing on the two main platforms Illumina and Ion Torrent, and discussing the major strong points and weaknesses intrinsic to each platform. Next, the NGS analytical bioinformatic pipelines are dissected, giving some emphasis to the algorithms commonly used to generate process data and to analyze sequence variants. Finally, the main challenges around NGS bioinformatics are placed in perspective for future developments. Even with the huge achievements made in NGS technology and bioinformatics, further improvements in bioinformatic algorithms are still required to deal with complex and genetically heterogeneous disorders.

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“…The nanopore technology has the advantage of reading native DNA molecules and can distinguish modified from natural bases because they affect the electrical current flowing through the pore differently [32] . We analysed the electric signal to detect the 5-methylcytosine (5mC) in the CpG context of the whole genome of B. napus Darmor-bzh.…”

Section: Detection Of Modified Basesmentioning

confidence: 99%

Long-reads assembly of theBrassica napusreference genome, Darmor-bzh

Rousseau‐Gueutin

Belser

Silva

et al. 2020

Preprint

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BackgroundThe combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allow to access the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like telomeres and centromeres. The Brassica genus is not exempt and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the Brassica genus.FindingsHere, we report the new long-reads assembly of Darmor-bzh genome (Brassica napus) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.ConclusionUsing these cutting edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable for the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

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Recent advances in the detection of base modifications using the Nanopore sequencer

Cited by 116 publications

References 79 publications

FORK-seq: replication landscape of theSaccharomyces cerevisiaegenome by nanopore sequencing

FORK-seq: replication landscape of theSaccharomyces cerevisiaegenome by nanopore sequencing

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

Long-reads assembly of theBrassica napusreference genome, Darmor-bzh

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