biostudies-literatureMohaghegh Neyshabouri MSwedish Foundation for Strategic ResearchHorizon 2020e1010732https://www.ebi.ac.uk/biostudies/studies/S-EPMC9754607biostudies-literatureUnknown18(12)Identifying the interrelations among cancer driver genes and the patterns in which the driver genes get mutated is critical for understanding cancer. In this paper, we study cross-sectional data from cohorts of tumors to identify the cancer-type (or subtype) specific process in which the cancer driver genes accumulate critical mutations. We model this mutation accumulation process using a tree, where each node includes a driver gene or a set of driver genes. A mutation in each node enables its children to have a chance of mutating. This model simultaneously explains the mutual exclusivity patterns observed in mutations in specific cancer genes (by its nodes) and the temporal order of events (by its edges). We introduce a computationally efficient dynamic programming procedure for calculatiPLoS computational biologyToMExO: A probabilistic tree-structured model for cancer progression.PMC9754607BD15-0043MSCA-ITN-2017-766030Mohaghegh Neyshabouri MLagergren JfalseToMExO: A probabilistic tree-structured model for cancer progression.Identifying the interrelations among cancer driver genes and the patterns in which the driver genes get mutated is critical for understanding cancer. In this paper, we study cross-sectional data from cohorts of tumors to identify the cancer-type (or subtype) specific process in which the cancer driver genes accumulate critical mutations. We model this mutation accumulation process using a tree, where each node includes a driver gene or a set of driver genes. A mutation in each node enables its children to have a chance of mutating. This model simultaneously explains the mutual exclusivity patterns observed in mutations in specific cancer genes (by its nodes) and the temporal order of events (by its edges). We introduce a computationally efficient dynamic programming procedure for calculati2022-01-01T00:00:00Z2022 Dec2025-04-04T19:11:37.279Z2025-04-04T19:11:37.279ZS-EPMC97546073646954010.1371/journal.pcbi.1010732