gpps: An ILP-based approach for inferring cancer progression with mutation losses from single cell data

Abstract

MotivationIn recent years, the well-known Infinite Sites Assumption (ISA) has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progression where mutations are accumulated through histories. However, some recent studies leveraging Single Cell Sequencing (SCS) techniques have shown evidence of mutation losses in several tumor samples [19], making the inference problem harder.\n\nResultsWe present a new tool, gpps, that reconstructs a tumor phylogeny from single cell data, allowing each mutation to be lost at most a fixed number of times.\n\nAvailabilityThe General Parsimony Phylogeny from Single cell (gpps) tool is open source and available at https://github.com/AlgoLab/gppf.