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

AI Article Synopsis

  • - Uveal melanoma (UM) is characterized by specific genetic changes, particularly in chromosomes 1, 3, 6, and 8, which relate to the risk of developing metastases and involve various mutations.
  • - Researchers created a targeted next-generation sequencing (NGS) panel to analyze these genetic changes in UM clinical samples, comparing two methods of target enrichment and finding that hybrid capture was the more effective approach.
  • - The study successfully identified new mutations and changes in UM samples, highlighting the importance of certain genetic alterations in predicting patient outcomes, while showcasing NGS's ability to reliably analyze diverse sample types.

Article Abstract

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

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7226611PMC
http://dx.doi.org/10.3390/cancers12041039DOI Listing

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