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Validation of the Oncomine™ Focus Panel for Next Generation Sequencing of clinical tumour samples

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Williams2018_Article_ValidationOfTheOncomineFocusPa.pdf (1.516Mb)
Date
13/08/2018
Author
Williams, Hannah L.
Walsh, Kathy
Diamond, Austin
Oniscu, Anca
Deans, Zandra C.
Keywords
Next-generation sequencing
Molecular pathology
Clinical validation
FFPE
RB Pathology
RC0254 Neoplasms. Tumors. Oncology (including Cancer)
T Technology
DAS
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Abstract
The clinical utility of next-generation sequencing (NGS) for a diverse range of targets is expanding, increasing the need for multiplexed analysis of both DNA and RNA. However, translation into daily use requires a rigorous and comprehensive validation strategy. The aim of this clinical validation was to assess the performance of the Ion Torrent Personal Genome Machine (IonPGM™) and validate the Oncomine™ Focus DNA and RNA Fusion panels for clinical application in solid tumour testing of formalin-fixed, paraffin-embedded (FFPE) tissue. Using a mixture of routine FFPE and reference material across a variety of tissue and specimen types, we sequenced 86 and 31 samples on the Oncomine™ Focus DNA and RNA Fusion assays, respectively. This validation considered a number of parameters including the clinical robustness of the bioinformatics pipeline for variant detection and interpretation. The Oncomine™ Focus DNA assay had a sample and variant-based sensitivity of 99.1 and 97.1%, respectively, and an assay specificity of 100%. The Oncomine™ Focus Fusion panel had a good sensitivity and specificity based upon the samples assessed, however requires further validation to confirm findings due to limited sample numbers. We observed a good sequencing performance based upon amplicon, gene (hotspot variants within gene) and sample specific analysis with 92% of clinical samples obtaining an average amplicon coverage above 500X. Detection of some indels was challenging for the routine IonReporter™ workflow; however, the addition of NextGENe® software improved indel identification demonstrating the importance of both bench and bioinformatic validation. With an increasing number of clinically actionable targets requiring a variety of methodologies, NGS provides a cost-effective and time-saving methodology to assess multiple targets across different modalities. We suggest the use of multiple analysis software to ensure identification of clinically applicable variants.
Citation
Williams , H L , Walsh , K , Diamond , A , Oniscu , A & Deans , Z C 2018 , ' Validation of the Oncomine™ Focus Panel for Next Generation Sequencing of clinical tumour samples ' , Virchows Archiv , vol. First Online . https://doi.org/10.1007/s00428-018-2411-4
Publication
Virchows Archiv
Status
Peer reviewed
DOI
https://doi.org/10.1007/s00428-018-2411-4
ISSN
0945-6317
Type
Journal article
Rights
© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
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  • University of St Andrews Research
URI
http://hdl.handle.net/10023/15810

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