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Evaluation and application of RNA-Seq by MinION.

Authors :
Seki M
Katsumata E
Suzuki A
Sereewattanawoot S
Sakamoto Y
Mizushima-Sugano J
Sugano S
Kohno T
Frith MC
Tsuchihara K
Suzuki Y
Source :
DNA research : an international journal for rapid publication of reports on genes and genomes [DNA Res] 2019 Feb 01; Vol. 26 (1), pp. 55-65.
Publication Year :
2019

Abstract

The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure for full-length cDNA sequencing using the Nanopore sequencer MinION. We applied MinION RNA-Seq for various applications, which would not always be easy using the usual RNA-Seq by Illumina. First, we examined and found that even though the sequencing accuracy was still limited to 92.3%, practically useful RNA-Seq analysis is possible. Particularly, taking advantage of the long-read nature of MinION, we demonstrate the identification of splicing patterns and their combinations as a form of full-length cDNAs without losing precise information concerning their expression levels. Transcripts of fusion genes in cancer cells can also be identified and characterized. Furthermore, the full-length cDNA information can be used for phasing of the SNPs detected by WES on the transcripts, providing essential information to identify allele-specific transcriptional events. We constructed a catalogue of full-length cDNAs in seven major organs for two particular individuals and identified allele-specific transcription and splicing. Finally, we demonstrate that single-cell sequencing is also possible. RNA-Seq on the MinION platform should provide a novel approach that is complementary to the current RNA-Seq.<br /> (© The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)

Details

Language :
English
ISSN :
1756-1663
Volume :
26
Issue :
1
Database :
MEDLINE
Journal :
DNA research : an international journal for rapid publication of reports on genes and genomes
Publication Type :
Academic Journal
Accession number :
30462165
Full Text :
https://doi.org/10.1093/dnares/dsy038