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MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing

William S Taylor, John Pearson, Allison Miller, Sebastian Schmeier, Frank A Frizelle, Rachel V Purcell
doi: https://doi.org/10.1101/662270
William S Taylor
1Department of Surgery, University of Otago, Christchurch, New Zealand
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John Pearson
2Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
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Allison Miller
3Gene Structure and Function Laboratory, University of Otago, Christchurch, New Zealand
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Sebastian Schmeier
4Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
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Frank A Frizelle
1Department of Surgery, University of Otago, Christchurch, New Zealand
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Rachel V Purcell
1Department of Surgery, University of Otago, Christchurch, New Zealand
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  • For correspondence: rachel.purcell@otago.ac.nz
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Abstract

Recent evidence suggests a role for the gut microbiome in the development and progression of colorectal cancer. In this study we compare MinION sequencing with meta-transcriptomics and amplicon-based sequencing for microbiome analysis of colorectal tumour tissue samples. DNA and RNA were extracted from 11 colorectal tumour samples. RNA-Sequencing, 16S rRNA amplicon sequencing and MinION genomic sequencing was carried out and resulting data used as input for taxonomic classification using Kraken2. Taxonomic concordance between the three platforms at different taxonomic levels was tested on a per sample basis. The average number of reads per sample using RNA-Sequencing was more than 129 times that generated using MinION sequencing. However, the average read length of MinION sequences was more than 13 times that of RNA or 16S rRNA amplicon sequencing. 16S sequencing was less informative beyond the genus level, and both RNA-Sequencing and MinION sequencing could detect more phyla and genera in the same samples, compared to 16S sequencing. Long-read sequences generated using MinION sequencing can compensate for low numbers of reads for bacterial classification. MinION sequencing can discriminate between bacterial strains and plasmids and shows potential as a tool for microbiome sequencing of colorectal cancers in a clinical setting.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted June 06, 2019.
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MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing
William S Taylor, John Pearson, Allison Miller, Sebastian Schmeier, Frank A Frizelle, Rachel V Purcell
bioRxiv 662270; doi: https://doi.org/10.1101/662270
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MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing
William S Taylor, John Pearson, Allison Miller, Sebastian Schmeier, Frank A Frizelle, Rachel V Purcell
bioRxiv 662270; doi: https://doi.org/10.1101/662270

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