OncoNEM: Inferring tumour evolution from single-cell sequencing data
Ross, Edith M
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Ross, E. M., & Markowetz, F. (2016). OncoNEM: Inferring tumour evolution from single-cell sequencing data. Genome Biology, 17 https://doi.org/10.1186/s13059-016-0929-9
Single-cell sequencing promises a high resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumour evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present oncoNEM, a probabilistic method for inferring intra-tumour 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.
tumour evolution, cancer evolution, tumour heterogeneity, single-cell sequencing, phylogenetic tree
The authors would like to acknowledge the support of the University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited. This work was funded by CRUK core grant C14303/A17197.
Cancer Research UK (C14303_do not transfer)
Cancer Research UK (CB4320)
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External DOI: https://doi.org/10.1186/s13059-016-0929-9
This record's URL: https://www.repository.cam.ac.uk/handle/1810/254951