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

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.

Multiplex ligation-dependent probe amplification of uveal melanoma: correlation with metastatic death.

PURPOSE: To evaluate multiplex ligation-dependent probe amplification (MLPA) of uveal melanoma as a predictive tool for metastatic death. METHODS: Uveal melanoma specimens of 73 patients treated between 1998 and 2000 were included. DNA samples were analyzed with MLPA evaluating 31 loci on chromosomes 1, 3, 6 and 8, and the results were correlated with metastatic death. RESULTS: The patients (27 women; 46 men) had a median age of 60.6 years and a median follow-up of 6.2 years. Metastatic death occurred in 28 patients, correlating most strongly with chromosome 3 losses and gains on 8q (Cox univariate analysis, P < 0.001). Chromosome 6, region p25, gains correlated with good survival (Cox univariate analysis, P = 0.003). Prediction of metastatic death was improved by considering equivocal chromosome 3 losses as abnormal and by taking account of multiple risk factors, such as 8q gains, tumor diameter, and histologic features indicative of high-grade malignancy. CONCLUSIONS: MLPA analysis of uveal melanoma predicts metastatic death if statistically insignificant losses of chromosome 3 are considered together with gains in 8q as well as clinical stage and histologic grade of malignancy.

The human LMX1B gene: transcription unit, promoter, and pathogenic mutations.

LMX1B is a LIM-homeodomain transcription factor required for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Heterozygous loss-of-function mutations in LMX1B cause nail patella syndrome (NPS). To further understand LMX1B gene regulation and to identify pathogenic mutations within the coding region, a detailed analysis of LMX1B gene structure was undertaken. 5' -RACE and primer extension identified a long 5' -untranslated region of 1.3 kb that contains two upstream open-reading frames (uORFs). Transient transfection assays showed that sequences required for basal promoter activity extend no further than 112 bp upstream. An additional 47 mutations have been identified in the coding region, as well as nine deletions of large portions of the gene, but not in the promoter or highly conserved intronic sequences. The range of mutations and the identification of uORFs suggest further complexity in the regulation of LMX1B expression.