Homo sapiens Raw sequence reads

Malignant Pleural Mesothelioma (MPM) is typically diagnosed 20-50 years after exposure to asbestos and evolves along an unknown evolutionary trajectory. To elucidate this path, we conducted multi-regional exome sequencing of 90 tumour samples from 22 MPMs acquired at surgery. Exomic intratumour heterogeneity varied widely across the cohort. Phylogenetic tree topology ranged from linear to highly branched, reflecting a steep gradient of genomic instability. Using transfer learning, we detected repeated evolution, resolving 5 clusters that were prognostic, with temporally ordered clonal drivers. BAP1/- 3p21 and FBXW7/-chr4 events were always early clonal. In contrast, NF2/-22q events leading to Hippo pathway inactivation were predominantly late clonal, positively selected, and when subclonal, exhibited parallel evolution indicating an evolutionary constraint. Very late somatic alteration of NF2/22q occurred in one patient 12 years after surgery. Clonal architecture and evolutionary clusters dictated MPM inflammation and immune evasion. These results are the first to report potentially drugable evolutionary bottlenecking in MPM, and a significant impact of clonal architecture on shaping the immune landscape, with potential to dictate the clinical response to checkpoint immunotherapy.