PyClone

PyClone: statistical inference of clonal population structure in cancer. We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination. Single-cell sequencing validation demonstrates PyClone’s accuracy.


References in zbMATH (referenced in 11 articles )

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  1. He, Shai; Schein, Aaron; Sarsani, Vishal; Flaherty, Patrick: A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data (2021)
  2. Caravagna, Giulio: Measuring evolutionary cancer dynamics from genome sequencing, one patient at a time (2020)
  3. Zhou, Tianjian; Sengupta, Subhajit; Müller, Peter; Ji, Yuan: RNDClone: tumor subclone reconstruction based on integrating DNA and RNA sequence data (2020)
  4. Zeng, Li; Warren, Joshua L.; Zhao, Hongyu: Phylogeny-based tumor subclone identification using a Bayesian feature allocation model (2019)
  5. Zhou, Tianjian; Sengupta, Subhajit; Müller, Peter; Ji, Yuan: TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data (2019)
  6. Behr, Merle; Holmes, Chris; Munk, Axel: Multiscale blind source separation (2018)
  7. Xie, Fangzheng; Zhou, Mingyuan; Xu, Yanxun: Baycount: a Bayesian decomposition method for inferring tumor heterogeneity using RNA-seq counts (2018)
  8. Della Vedova, Gianluca; Patterson, Murray; Rizzi, Raffaella; Soto, Mauricio: Character-based phylogeny construction and its application to tumor evolution (2017)
  9. Zhou, T., Müller, P., Sengupta, S., Ji, Y.: PairClone: A Bayesian Subclone Caller Based on Mutation Pairs (2017) arXiv
  10. Ji, Yuan; Sengupta, Subhajit; Lee, Juhee; Müller, Peter; Gulukota, Kamalakar: Estimating latent cell subpopulations with Bayesian feature allocation models (2015)
  11. Lee, Juhee; Müller, Peter; Gulukota, Kamalakar; Ji, Yuan: A Bayesian feature allocation model for tumor heterogeneity (2015)