Of note, one of these D3 tumours (MELA_0800) had a low BAP1 variant allele frequency (VAF = 9/80) suggesting it was only present in a subclone, and as copy number tools are not as sensitive as mutation callers, it is possible that the subclone had loss of heterozygosity (LOH) that was not detected by the algorithm. This evidence concerns the gene BAP1 and neoplasm.