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

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Thornton, Sophie, Coupland, Sarah E ORCID: 0000-0002-1464-2069, Olohan, Lisa, Sibbring, Julie S ORCID: 0000-0001-9178-6851, Kenny, John G, Hertz-Fowler, Christiane ORCID: 0000-0002-0729-6479, Liu, Xuan, Haldenby, Sam, Heimann, Heinrich, Hussain, Rumana ORCID: 0000-0001-8208-5009 et al (show 3 more authors) , Kipling, Natalie, Taktak, Azzam and Kalirai, Helen ORCID: 0000-0002-4440-2576 (2020) Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma. CANCERS, 12 (4). E1039-. ISSN 2072-6694, 2072-6694

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Abstract

Uveal melanoma (UM) has well-characterised somatic copy number alterations (SCNA) in chromosomes 1, 3, 6 and 8, in addition to mutations in <i>GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, SF3B1</i> and <i>EIF1AX</i>, 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 <i>BAP1</i> but harbored <i>SF3B1</i> mutations, novel frameshift deletions in <i>SF3B1</i> and <i>EIF1AX</i>, as well as a <i>PLCB4</i> mutation outside of the hotspot on exon 20 coinciding with a <i>GNAQ</i> mutation in some UM. We observed samples that harboured mutations in both <i>BAP1</i> and <i>SF3B1</i>, and <i>SF3B1</i> and <i>EIF1AX</i>, respectively. Novel mutations were also identified in <i>TTC28, KTN1, CSMD1</i> and <i>TP53BP1</i>. NGS can simultaneously assess SCNA and mutation data in UM, in a reliable and reproducible way, irrespective of sample type or previous processing. <i>BAP1</i> and <i>SF3B1</i> mutations, in addition to 8q copy number, are of added importance when determining UM patient outcome.

Item Type:	Article
Uncontrolled Keywords:	next-generation sequencing, uveal melanoma, prognostication, mutation, clinical samples, chromosome, copy number
Depositing User:	Symplectic Admin
Date Deposited:	04 May 2020 10:33
Last Modified:	07 Dec 2024 19:27
DOI:	10.3390/cancers12041039
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3085684