Genomic foundation models extend clinicopathologic and transcriptomic prognostication in soft tissue sarcoma

Evo2, a genomic foundation model, was used to embed short variants, fusions and rearrangements from 102 patients with soft tissue sarcoma and 129 TCGA-SARC cases into patient-level genomic representations for Cox survival modelling. Adding Evo2 to SARCULATOR raised the OS C-index from 0.620 to 0.770 in the study cohort and from 0.595 to 0.716 in TCGA-SARC; in TCGA-SARC it also improved CINSARC-based OS prediction from 0.476 to 0.653. These descriptive point estimates support altered tumor sequence context as an independent prognostic layer for sarcoma risk stratification.