Fig. 1

Toy example of the OncoNEM scoring model. a Hypothesis of a clonal lineage tree that describes the subpopulations of a tumor (grey circles) and their relationships (black arrows). b This tree can be represented as a prediction matrix that predicts the mutation pattern we expect to see across all k cells for a mutation that occurred in a certain clone θ. c Assuming that we know the originating clone of every mutation (blue lines in clonal lineage tree), we can extend the prediction matrix to a full matrix of expected genotypes. d To score the tree, expected genotypes are compared to observed genotypes. The more mismatches there are, the lower the likelihood of the tree given the data. Since the origin of a mutation is unknown a priori, the full likelihood of the lineage tree is calculated by marginalizing over all possible origins for every mutation. FN false negative, FP false positive