Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data.
Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. OncoNEM identifies homogeneous cellular subpopulations and infers their genotypes as well as a tree describing their evolutionary relationships. In simulation studies, we assess OncoNEM's robustness and benchmark its performance against competing methods. Finally, we show its applicability in case studies of muscle-invasive bladder cancer and essential thrombocythemia.
Genome biology. 2016 Apr 15*** epublish ***
Edith M Ross, Florian Markowetz
Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK., Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK.