Fig. 4
Analysis of our prospective cohort of uveal melanomas (n = 5). (A) Two-dimensional UMAP analysis of cohort-wide GEP and application of TCGA-derived GEP-classifier in relation to the RNA- and DNA-based detectability of genetic alterations. (B) Representative examples of RNA-inferred allelic (im)balances to identify chromosomal alterations. In UM-4 and UM-5, imbalanced expression of genes of chromosome 3 correctly indicates the presence of a copy number alteration affecting this chromosome. In contrast, in UM-4, no imbalance is observed on chromosome 8q, in line with a disomy 8q, but an alteration and consequent imbalance is present in UM-5. The figures for all tumours from our cohort can be found in Supplementary Data 2. (C) BAP1 alterations (mutations and mutation-associated alternative splicing) as observed in the RNA sequencing data. (D) Analysis of the previously described signature of alternative splicing to identify SF3B1-mutant tumours.
