Towards a Next-Generation Sequencing Diagnostic Service for Tumour Genotyping: A Comparison of Panels and Platforms

BioMed Research International
George J BurghelMargaret A Knowles

Abstract

Detection of clinically actionable mutations in diagnostic tumour specimens aids in the selection of targeted therapeutics. With an ever increasing number of clinically significant mutations identified, tumour genetic diagnostics is moving from single to multigene analysis. As it is still not feasible for routine diagnostic laboratories to perform sequencing of the entire cancer genome, our approach was to undertake targeted mutation detection. To optimise our diagnostic workflow, we evaluated three target enrichment strategies using two next-generation sequencing (NGS) platforms (Illumina MiSeq and Ion PGM). The target enrichment strategies were Fluidigm Access Array custom amplicon panel including 13 genes (MiSeq sequencing), the Oxford Gene Technologies (OGT) SureSeq Solid Tumour hybridisation panel including 60 genes (MiSeq sequencing), and an Ion AmpliSeq Cancer Hotspot Panel including 50 genes (Ion PGM sequencing). DNA extracted from formalin-fixed paraffin-embedded (FFPE) blocks of eight previously characterised cancer cell lines was tested using the three panels. Matching genomic DNA from fresh cultures of these cell lines was also tested using the custom Fluidigm panel and the OGT SureSeq Solid Tumour panel. Each panel...Continue Reading

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Citations

Nov 14, 2015·Clinical Pharmacology and Therapeutics·D J Dickson, J D Pfeifer
Jul 1, 2016·Annual Review of Genomics and Human Genetics·Shawn E Levy, Richard M Myers
Feb 2, 2017·International Journal of Molecular Sciences·Rick KampsAndrea Romano
Mar 24, 2017·Journal for Immunotherapy of Cancer·David F StroncekBarbara Seliger
Aug 25, 2020·Annals of Laboratory Medicine·Yiming ZhongMarilyn M Li
May 26, 2017·Journal of Pathology and Translational Medicine·Jihun KimUNKNOWN Molecular Pathology Study Group of Korean Society of Pathologists
Nov 24, 2016·Brain Tumor Pathology·Lien BekaertEmmanuèle Lechapt-Zalcman
Dec 2, 2020·Journal of Personalized Medicine·Nerea Vega-Garcia On Behalf Of The Group Of Leukemia Of The Spanish Society Of Pediatric Hematology And Oncology Sehop

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Methods Mentioned

BETA
biopsies
Illumina Sequencing
PCR
genotyping
AmpliSeq

Software Mentioned

Ion Reporter
Mutation Surveyor
MiSeq Control Software ( MCS )
SureSeq Virtual Machine ( SSVM )
NextGene
Illumina Experiment Manager
Fluidigm
NextGene Viewer

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