PyClone: statistical inference of clonal population structure in cancer
By Andrew Roth, J. Khattra, Damian Boon Siew Yap, A. Wan, E. Laks, Justina Biele, G. Ha, S. Aparicio, Alexandre Bouchard-Côté, Sohrab P. Shah. Nature Methods, 2014
958 citations recorded by the source corpus.
Subfields: Cancer Research, Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/0c64c08fb357eab7f3b4b596db17a3e3bf6613e4
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In Cancer Research
In Genetics
- Florian Markowetz
- Roland F. Schwarz
- Richard K. Wilson
- Niko Beerenwinkel
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- Obi L. Griffith
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In Molecular Biology
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Citations in the corpus
- Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab (2017, neutral): “Patients with CR/PR had high frequencies of tumor clonal and subclonal variants that decreased in prevalence after Nivo therapy and, in many cases, were not detected on-therapy (mutational contraction) (Figure 2A; STAR Methods).”
- Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy (2018, positive): “For each sample,MuTect-called somatic SNVswith variant allele frequency information, combined with Sequenza output allele-specific copy number and cellularity estimation, were input to PyClone to estimate cellular prevalence for all somatic SNVs. Mutational clonality was also inferred through the cl”
- SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution (2014, methodology): “As a comparison for our results, we applied an MCMC method, PyClone [11,30], to the same variants in copy-number neutral, LOH-free regions.”
- Cancer Evolution: Mathematical Models and Computational Inference (2014, methodology): “The second assumption implies that the clone with the higher clonal frequency, that is, the larger number of cells carrying the SNV, must be the ancestor (Fig.”