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Open AccessArticle

Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma

1
Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool L7 8XT, UK
2
Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool L69 3GA, UK
3
Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7BT, UK
4
St. Paul’s Eye Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool L7 8XP, UK
5
Department of Medical Physics and Clinical Engineering, Liverpool University Hospitals NHS Foundation Trust, 1st Floor Duncan Building, Liverpool L7 8XP, UK
*
Author to whom correspondence should be addressed.
Cancers 2020, 12(4), 1039; https://doi.org/10.3390/cancers12041039
Received: 27 February 2020 / Revised: 1 April 2020 / Accepted: 21 April 2020 / Published: 23 April 2020
Uveal melanoma (UM) has well-characterised somatic copy number alterations (SCNA) in chromosomes 1, 3, 6 and 8, in addition to mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, SF3B1 and EIF1AX, most being linked to metastatic-risk. To gain further insight into the molecular landscape of UM, we designed a targeted next-generation sequencing (NGS) panel to detect SCNA and mutations in routine clinical UM samples. We compared hybrid-capture and amplicon-based target enrichment methods and tested a larger cohort of primary UM samples on the best performing panel. UM clinical samples processed either as fresh-frozen, formalin-fixed paraffin embedded (FFPE), small intraocular biopsies or following irradiation were successfully profiled using NGS, with hybrid capture outperforming the PCR-based enrichment methodology. We identified monosomy 3 (M3)-UM that were wild-type for BAP1 but harbored SF3B1 mutations, novel frameshift deletions in SF3B1 and EIF1AX, as well as a PLCB4 mutation outside of the hotspot on exon 20 coinciding with a GNAQ mutation in some UM. We observed samples that harboured mutations in both BAP1 and SF3B1, and SF3B1 and EIF1AX, respectively. Novel mutations were also identified in TTC28, KTN1, CSMD1 and TP53BP1. NGS can simultaneously assess SCNA and mutation data in UM, in a reliable and reproducible way, irrespective of sample type or previous processing. BAP1 and SF3B1 mutations, in addition to 8q copy number, are of added importance when determining UM patient outcome. View Full-Text
Keywords: next-generation sequencing; uveal melanoma; prognostication; mutation; clinical samples; chromosome; copy number next-generation sequencing; uveal melanoma; prognostication; mutation; clinical samples; chromosome; copy number
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Thornton, S.; Coupland, S.E.; Olohan, L.; Sibbring, J.S.; Kenny, J.G.; Hertz-Fowler, C.; Liu, X.; Haldenby, S.; Heimann, H.; Hussain, R.; Kipling, N.; Taktak, A.; Kalirai, H. Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma. Cancers 2020, 12, 1039.

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