Inferring and visualizing clonal evolution in multi-sample cancer sequencing.

• ClonEvol is published in Annals of Oncology
• A vignette on how to perform clonal evolution analysis (primarily via using ClonEvol) is now available (PDF).
• There has been major overhaul of code and features, including sphere of cells, annotated branch-based clonal evolution tree visualizations. Make sure you are running the latest version of ClonEvol when following the vignette.
• Also join clonEvol mailing list for update annoucements.
• Have a question, found a bug, please create an issue here.

The following figure demonstrates the reanalysis of a relapse acute myeloid leukemia case (AML1) published in Ding et al., Nature (2012). Top panel shows the original published fishplot, and the bottom panel shows the model inferred and visualized by ClonEvol.

Fig. 1. ClonEvol reanalysis of AML1 (a) Original model, represented by a fishplot (b-f) Matching model predicted and visualized by ClonEvol.

A tutorial is available (PDF).

The following are some of the publications that have utilized ClonEvol to study clonal evolution, which may also be useful:

• Dong, Weilai, et al. "Clonal Evolution Analysis of Paired Anaplastic and Well‐Differentiated Thyroid Carcinomas Reveals Shared Common Ancestor." Genes, Chromosomes and Cancer (2018).
• Jung, S. H., Kim, S. Y., An, C. H., Lee, S. H., Jung, E. S., Park, H. C., ... & Lee, S. H. (2018). Clonal structures of regionally synchronous gastric adenomas and carcinomas. Clinical Cancer Research, clincanres-0345.
• Miller, C. A., Dahiya, S., Li, T., Fulton, R., Smyth, M. D., Dunn, G. P., ... & Mardis, E. R. (2018). Resistance promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient. Molecular Case Studies, mcs-a002444.
• Joung, Je-Gun, et al. "Tumor heterogeneity predicts metastatic potential in colorectal cancer." Clinical Cancer Research (2017): clincanres-0306.
• Uy, Geoffrey L., et al. "Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy." Leukemia 31.4 (2017): 872.
• Mahlokozera, Tatenda, et al. "Biological and therapeutic implications of multisector sequencing in newly diagnosed glioblastomas." Neuro-oncology (2017).
• Xiong, Donghai, et al. "Novel mutational landscapes and expression signatures of lung squamous cell carcinoma." Oncotarget 9.7 (2017): 7424-7441.
• Hoadley, Katherine A., et al. "Tumor evolution in two patients with basal-like breast cancer: a retrospective genomics study of multiple metastases." PLoS medicine 13.12 (2016): e1002174.
• Miller, Christopher A., et al. "Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers." Nature communications 7 (2016): 12498.
• Griffith, Malachi, et al. "Optimizing cancer genome sequencing and analysis." Cell systems 1.3 (2015): 210-223.

Dang, H. X., White, B. S., Foltz, S. M., Miller, C. A., Luo, J., Fields, R. C., & Maher, C. A. (2017). ClonEvol: clonal ordering and visualization in cancer sequencing. Annals of Oncology, 28(12), 3076-3082.

Ha X. Dang @ haxdang (at) gmail (dot) com