Extended Data Fig. 5: HLA LOH analysis.

a) Example of HLA-A alleles copy-number estimation in patient MEL-3. The horizontal axis shows HLA-A exons and on the Y axis are shown (top to bottom) estimated b-allele frequency (BAF), LogR, copy-numbers (CN), depth ratio and RNAseq support (% RNAseq reads) between HLA-A*25:01:01 (red) and HLA-A*02:05:01 (blue). b) Example of the two naive Bayes classifiers trained on MEL-3 exome-wide copy-number estimations for the prediction of HLA copy numbers. Density of the copy-numbers depth ratio used for training classifier one is shown at the top left. Bottom left shows the confusion matrix of classifier one. Density of the copy-numbers allele frequency alone and in combination with the depth ratio, both used for the training of classifier two, are shown at the top center and right, respectively. Bottom right shows the confusion matrix of the classifier two. c) Immunogenicity assessment of REP TILs from sample MEL-2 (IFNγ SFU per 10⁶ cells, mean +/− SD). CD8 (in green) and CD4 (in violet) neoantigen reactivity was validated by CD137 upregulation. Predicted HLA binder is annotated below the peptide sequence. d) Separate channels of mIF staining of a tumor tissue sample derived from patient MEL-2 (n = 1 slide). e) Separate channels of mIF staining of a tumor tissue sample derived from patient MEL-3 (n = 1 slide).