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dc.contributor.authorWilliams, Hannah L.
dc.contributor.authorWalsh, Kathy
dc.contributor.authorDiamond, Austin
dc.contributor.authorOniscu, Anca
dc.contributor.authorDeans, Zandra C.
dc.date.accessioned2018-08-13T09:30:08Z
dc.date.available2018-08-13T09:30:08Z
dc.date.issued2018-08-13
dc.identifier254608713
dc.identifierb26c8382-722c-432a-89a1-ed6260e6c01a
dc.identifier85051872040
dc.identifier000446380500011
dc.identifier.citationWilliams , 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/s00428-018-2411-4en
dc.identifier.issn0945-6317
dc.identifier.urihttps://hdl.handle.net/10023/15810
dc.description.abstractThe 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.
dc.format.extent15
dc.format.extent1589934
dc.language.isoeng
dc.relation.ispartofVirchows Archiven
dc.subjectNext-generation sequencingen
dc.subjectMolecular pathologyen
dc.subjectClinical validationen
dc.subjectFFPEen
dc.subjectRB Pathologyen
dc.subjectRC0254 Neoplasms. Tumors. Oncology (including Cancer)en
dc.subjectT Technologyen
dc.subjectDASen
dc.subjectSDG 3 - Good Health and Well-beingen
dc.subject.lccRBen
dc.subject.lccRC0254en
dc.subject.lccTen
dc.titleValidation of the Oncomine™ Focus Panel for Next Generation Sequencing of clinical tumour samplesen
dc.typeJournal articleen
dc.contributor.institutionUniversity of St Andrews. School of Medicineen
dc.identifier.doi10.1007/s00428-018-2411-4
dc.description.statusPeer revieweden


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