ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
Fig 2
(A) Validation of the HLA type prediction from tumor RNA-seq data. We show the predictions for MHC Class I (HLA-A, HLA-B, HLA-C) and II (HLA-DQA, HLA-DQB, HLA-DRB) with PHLAT (red) and SeqHLA (blue). Each bar corresponds to the proportion of samples (over a total of 24 small cell lung cancer samples) for which the prediction on the tumor sample coincides with the prediction on the matched normal sample (B) For each cell line, CA46, HL-60 and THP-1, we show the number of different splicing alterations measured (dark blue) and the number of cases leading to a change in the encoded open reading frame (light blue). Alterations shown are alternative (5’/3’) splice-site (A5_A3), de novo exonizations (Exonization), intron retentions (IR), and new exon skipping events (Neoskipping). (C) Number of splicing-derived neoepitopes (splicing-neoepitopes) (red) and splicing-affected self-epitopes (self-epitopes) (blue) detected for each of the splicing alterations in each of cell lines analyzed (CA46, HL-60 and THP-1). (D) as in (C) but separated by HLA-type. (E) Example of a splicing-neoepitope validated with MHC-I associated mass spectrometry data and derived from a neoskipping event in the gene ERF. The peptides are given in the same orientation as the 5’ to 3’ direction of the gene.