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Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations

Riccardo Panero, Maddalena Arigoni, Martina Olivero, Francesca Cordero, View ORCID ProfileAlessandro Weisz, Marco Beccuti, Maria Flavia Direnzo, View ORCID ProfileRaffaele A Calogero
doi: https://doi.org/10.1101/301010
Riccardo Panero
University of Torino, Italy;
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Maddalena Arigoni
University of Torino, Italy;
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Martina Olivero
University of Torino, Italy;
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Francesca Cordero
University of Torino, Italy;
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Alessandro Weisz
University of Salerno;
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Marco Beccuti
University of Torino, Italy;
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Maria Flavia Direnzo
University of Torino, Italy;
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Raffaele A Calogero
University of Torino
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  • For correspondence: raffaele.calogero@unito.it
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Abstract

Background RNA-seq represents an attractive methodology for the detection of functional genomic variants because it allows the integration of variant frequency and their expression. However, although specific statistic frameworks have been designed to detect SNVs/INDELS/gene fusions in RNA-seq data, very little has been done to understand the effect of library preparation protocols on transcript variant detection in RNA-seq data. Results Here, we compared RNA-seq results obtained on short reads sequencing platform with two protocols: one based on polyA+ RNA selection protocol (POLYA) and the other based on exonic regions capturing protocol (ACCESS). Our data indicate that ACCESS detects 10% more coding SNV/INDELs with respect to POLYA, making this protocol more suitable for this goal. Furthermore, ACCESS requires less reads for coding SNV detection with respect to POLYA. On the other hand, if the analysis aims at identifying SNV/INDELs also in the 5' and 3' UTRs, POLYA is definitively the preferred method. No particular advantage comes from the usage of ACCESS or POLYA in the detection of fusion transcripts. Conclusion Data show that a careful selection of the wet protocol adds specific features that cannot be obtained with bioinformatics alone.

Copyright 
The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
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  • Posted April 14, 2018.

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Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations
Riccardo Panero, Maddalena Arigoni, Martina Olivero, Francesca Cordero, Alessandro Weisz, Marco Beccuti, Maria Flavia Direnzo, Raffaele A Calogero
bioRxiv 301010; doi: https://doi.org/10.1101/301010
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Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations
Riccardo Panero, Maddalena Arigoni, Martina Olivero, Francesca Cordero, Alessandro Weisz, Marco Beccuti, Maria Flavia Direnzo, Raffaele A Calogero
bioRxiv 301010; doi: https://doi.org/10.1101/301010

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