Figure 1

The intra-tumor phylogeny problem. (A) Molecular profiles obtained from a bulk sequenced heterogeneous tumor are shown. They consist, in this example, of three clones (red squares, blue triangles, and green discs) and normal cells (small grey discs). The intra-tumor phylogeny problem is to infer the population structure of the tumor, i.e., to identify the different clones and to elucidate how they relate to each other. (B) Classical phylogenetic trees and hierarchical clustering methods place the observed molecular profiles at the leaf nodes of a tree, while the inner nodes represent unobserved common ancestors. Here, leaf nodes are defined as the nodes without any child nodes and inner nodes as the nodes that have at least one child node. (C) Unlike classical phylogenetic tree models, BitPhylogeny clusters molecular profiles to identify subclones and places them as both inner (blue triangle) and leaf nodes (red square, green disc) of a tree describing the hierarchy of the tumor cell population.