Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA librar...

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Bibliographic Details
Published in:Scientific reports Vol. 6; no. 1; p. 31602
Main Authors: Oikonomopoulos, Spyros, Wang, Yu Chang, Djambazian, Haig, Badescu, Dunarel, Ragoussis, Jiannis
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 24.08.2016
Nature Publishing Group
Subjects:
38/23
38/39
38/91
45
45/23
45/91
631/1647/2017/2003
631/1647/2217/2018
631/208/514/1949
631/208/514/2254
Agreements
Animals
DNA, Complementary - genetics
Gene expression
Gene Library
HEK293 Cells
High-Throughput Nucleotide Sequencing - methods
Humanities and Social Sciences
Humans
Isoforms
multidisciplinary
Nanopores
Performance assessment
Performance evaluation
Polyadenylation
Population
Science
ISSN:2045-2322, 2045-2322
Online Access:Get full text
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Summary:To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (r pearson  = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (r pearson  = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules.
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ISSN:2045-2322
2045-2322
DOI:10.1038/srep31602