TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors - Fig 2

(A) Example of the true T for 6 hypothetical subclones. (B) Distance matrices reconstructed from the event distance based on alleles (DA) and somatic SNVs (DS). ‘X’ indicates that a subclone cannot be the parent of another subclone. (C) and (D) Edges can be restricted or penalized based on LOH. Each row in the matrix represents a measurement position on the genome. The measured LAF and the inferred by TargetClone are shown in separate columns. A grey color represents a balanced situation, orange allelic imbalance, and red LOH. The first two measurements are not shown in the tree in panel (A). (E) If different parental alleles are lost, edges can be restricted. The ground truth alleles are AA in the grey subclone, but TargetClone will report the alleles as BB. (F) Edges can be penalized if the loss of somatic SNVs is unlikely. (G) Example of the MSA for the subclones shown in (A). The red cross indicates that an edge in the MSA is removed when resolving the ISA. The dashed line indicates a newly added edge after resolving the ISA.