notes

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index

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cancer evolution

See cevo notes on overleaf

Todo regarding analysis of stochastic processes

Read review Resolving genetic heterogeneity in cancer by Turajlic, Graham, and Swanton et al 2019

Read Tug-of-war between driver and passenger mutations in cancer and other adaptive processes by McFarland Mirny and Korolev in 2014 @est(2h) @high

Read review Measuring Clonal Evolution in Cancer with Genomics by Williams, Sottoriva, and Graham in 2019. @est(2h) @high

Compare models from Quantification of subclonal selection in cancer from bulk sequencing data by Williams and Graham in 2018 and Tug-of-war between driver and passenger mutations in cancer and other adaptive processes by McFarland Mirny and Korolev in 2014, and Attolini Michor to those in Durrett book @est(6h) @low

Run julia code from Williams/Graham papers @est(2h) @high

Read Branching process models of cancer by Durrett in 2015

Read Exact solution of a two-type branching process clone size distribution in cell division kinetics by Antal and Krapivsky in 2010

Read review Tumour heterogeneity and the evolutionary trade-offs of cancer by Hausser and Alon in 2020

Todo regarding (cancer) phylogenetics

Watch Luay Nakhleh lecture on SiCloneFit

SiCloneFit Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data by Zafar and Nakhleh in 2019

Todo with Ximo

  • Study integration of ReMixT with pyclone in Interfaces of Malignant and Immunologic ClonalDynamics in Ovarian Cancer by Zhang and Shah in 2018 including Shah’s lecture https://youtu.be/8cwFV7bWawc
  • Integrate ReMixT output with our own pyro/pymc3 implementation of pyclone
  • Complete our own implement of ReMixT and pyclone in pyro/pymc3

references

  • Clonal inference with phylogeny

    • Vavoulis, D. V., Cutts, A., Taylor, J. C., & Schuh, A. (2020). A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data. BioRxiv, 2020.01.20.913236. https://doi.org/10.1101/2020.01.20.913236
    • Review Miura, S., Vu, T., Deng, J., Buturla, T., Oladeinde, O., Choi, J., & Kumar, S. (2020). Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing
    • Myers, M. A., Satas, G., & Raphael, B. J. (2019). CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples. Cell Systems, __8__(6), 514-522.e5. https://doi.org/10.1016/j.cels.2019.0
    • Review Schwartz, R., & Schäffer, A. A. (2017, April 1). The evolution of tumour phylogenetics: Principles and practice. Nature Reviews Genetics. Nature Publishing Group. https://doi.org/10.1038/nrg.2016.170
    • Deshwar, A. G., Vembu, S., Yung, C. K., Jang, G. H., Stein, L., & Morris, Q. (2015). PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biology, __16__(1), 1–20. https://doi.org/10.1186/s13059-015-0602-8
    • Jiao, W., Vembu, S., Deshwar, A. G., Stein, L., & Morris, Q. (2014). Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinformatics, __15__(1), 35. https://doi.org/10.1186/1471-2105-15-35
    • Roth, A., Khattra, J., Yap, D., Wan, A., Laks, E., Biele, J., … Shah, S. P. (2014). PyClone: Statistical inference of clonal population structure in cancer. Nature Methods, __11__(4), 396–398. https://doi.org/10.1038/nmeth.2883

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