SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.
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References in zbMATH (referenced in 8 articles )
Showing results 1 to 8 of 8.
- He, Shai; Schein, Aaron; Sarsani, Vishal; Flaherty, Patrick: A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data (2021)
- Caravagna, Giulio: Measuring evolutionary cancer dynamics from genome sequencing, one patient at a time (2020)
- Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
- Zeng, Li; Warren, Joshua L.; Zhao, Hongyu: Phylogeny-based tumor subclone identification using a Bayesian feature allocation model (2019)
- Zhou, Tianjian; Sengupta, Subhajit; Müller, Peter; Ji, Yuan: TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data (2019)
- Robinson, Peter N.; Piro, Rosario Michael; Jäger, Marten: Computational exome and genome analysis (2018)
- Busse, J.-E.; Gwiazda, P.; Marciniak-Czochra, A.: Mass concentration in a nonlocal model of clonal selection (2016)
- Ji, Yuan; Sengupta, Subhajit; Lee, Juhee; Müller, Peter; Gulukota, Kamalakar: Estimating latent cell subpopulations with Bayesian feature allocation models (2015)