Literature DB >> 31037722

Nanopore sequencing: Review of potential applications in functional genomics.

Nobuaki Kono1, Kazuharu Arakawa1.   

Abstract

Molecular biology has been led by various measurement technologies, and increased throughput has developed omics analysis. The development of massively parallel sequencing technology has enabled access to fundamental molecular data and revealed genomic and transcriptomic signatures. Nanopore sequencers have driven such evolution to the next stage. Oxford Nanopore Technologies Inc. provides a new type of single molecule sequencer using protein nanopore that realizes direct sequencing without DNA synthesizing or amplification. This nanopore sequencer can sequence an ultra-long read limited by the input nucleotide length, or can determine DNA/RNA modifications. Recently, many fields such as medicine, epidemiology, ecology, and education have benefited from this technology. In this review, we explain the features and functions of the nanopore sequencer, introduce various situations where it has been used as a critical technology, and expected future applications.
© 2019 Japanese Society of Developmental Biologists.

Keywords:  long reads; nanopore sequencing; next generation sequencing

Year:  2019        PMID: 31037722     DOI: 10.1111/dgd.12608

Source DB:  PubMed          Journal:  Dev Growth Differ        ISSN: 0012-1592            Impact factor:   2.053


  68 in total

Review 1.  mRNA Editing, Processing and Quality Control in Caenorhabditis elegans.

Authors:  Joshua A Arribere; Hidehito Kuroyanagi; Heather A Hundley
Journal:  Genetics       Date:  2020-07       Impact factor: 4.562

2.  The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.

Authors:  I-Min A Chen; Ken Chu; Krishnaveni Palaniappan; Anna Ratner; Jinghua Huang; Marcel Huntemann; Patrick Hajek; Stephan Ritter; Neha Varghese; Rekha Seshadri; Simon Roux; Tanja Woyke; Emiley A Eloe-Fadrosh; Natalia N Ivanova; Nikos C Kyrpides
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

Review 3.  Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing.

Authors:  Lauren M Petersen; Isabella W Martin; Wayne E Moschetti; Colleen M Kershaw; Gregory J Tsongalis
Journal:  J Clin Microbiol       Date:  2019-12-23       Impact factor: 5.948

4.  Ribosome Fingerprinting with a Solid-State Nanopore.

Authors:  Mukhil Raveendran; Anna Rose Leach; Tayah Hopes; Julie L Aspden; Paolo Actis
Journal:  ACS Sens       Date:  2020-10-28       Impact factor: 7.711

5.  Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk.

Authors:  Nobuaki Kono; Hiroyuki Nakamura; Masaru Mori; Yuki Yoshida; Rintaro Ohtoshi; Ali D Malay; Daniel A Pedrazzoli Moran; Masaru Tomita; Keiji Numata; Kazuharu Arakawa
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-03       Impact factor: 11.205

Review 6.  Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time.

Authors:  Mariana Lopes; Sandra Louzada; Margarida Gama-Carvalho; Raquel Chaves
Journal:  Int J Mol Sci       Date:  2021-04-29       Impact factor: 5.923

7.  BoardION: real-time monitoring of Oxford Nanopore sequencing instruments.

Authors:  Aimeric Bruno; Jean-Marc Aury; Stefan Engelen
Journal:  BMC Bioinformatics       Date:  2021-05-13       Impact factor: 3.169

8.  Re-examination of two diatom reference genomes using long-read sequencing.

Authors:  Gina V Filloramo; Bruce A Curtis; Emma Blanche; John M Archibald
Journal:  BMC Genomics       Date:  2021-05-24       Impact factor: 3.969

9.  Target-capture full-length double-strand cDNA sequencing for alternative splicing analysis.

Authors:  Hiroki Ura; Sumihito Togi; Yo Niida
Journal:  RNA Biol       Date:  2021-01-20       Impact factor: 4.652

10.  WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates.

Authors:  Astrid P Heikema; Rick Jansen; Saskia D Hiltemann; John P Hays; Andrew P Stubbs
Journal:  BMC Microbiol       Date:  2021-06-07       Impact factor: 3.605

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