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

Background

Clinicopathologic (SARCULATOR) and transcriptomic (CINSARC) models are established prognostication tools in soft tissue sarcoma, but neither directly represent the sequence context of tumor genomic alterations. Evo2 is a genomic foundation model trained to learn the grammar of DNA/RNA sequences. We tested whether Evo2-derived features from tumor short variants, fusions, and rearrangements improve survival prognostication beyond clinicopathologic and transcriptomic risk models.