Inferring Multi-Stage Pathway Progression Models from Tumor Phylogenies

Abstract

Cancer progression is an evolutionary process driven by the accumulation and selection of somatic mutations, giving rise to genetically diverse subclonal populations within tumors. Understanding the dependencies among mutations and identifying recurrent evolutionary trajectories is critical for understanding cancer progression and informing therapeutic strategies. Recent advances in genomic sequencing and phylogenetic reconstruction now enable large-scale inference of tumor phylogenies, providing detailed representations of intratumor evolutionary histories across patient cohorts. However, modeling cancer progression from these data remains challenging due to extensive inter- and intratumor heterogeneity, often arising from mutations in different genes within the same pathway that confer similar fitness advantages. Existing methods to infer pathway-level progression models summarize each tumor by a single consensus genotype, ignoring intra-tumor heterogeneity, while phylogeny-based methods typically focus on individual mutations and do not model pathways. We introduce PhyloStage, an algorithm for inferring multi-stage pathway-level cancer progression models from large cohorts of tumor phylogenies. PhyloStage represents progression as a partial order over pathways, permitting independent mutations in incomparable pathways while constraining the order of mutations within the same or dependent pathways. The framework also incorporates uncertainty in tumor phylogenies, resolves mutation clusters with unknown ordering, and stratifies patients by progression stage. Applied to a cohort of 120 acute myeloid leukemia (AML) tumor phylogenies, PhyloStage infers progression models that are aligned with known AML progression. On 99 non-small cell lung cancer (NSCLC) patients, PhyloStage stratifies patients into progression stages such that later stages have larger tumor sizes, corroborating phenotypic tumor progression.