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E-scape: Interactive visualization of single cell phylogenetics and spatio-temporal evolution in cancer

By Maia A Smith, Cydney Nielsen, Fong Chun Chan, Andrew McPherson, Andrew Roth, Hossein Farahani, Daniel Machev, Adi Steif, Sohrab P Shah

Posted 20 Nov 2016
bioRxiv DOI: 10.1101/080622 (published DOI: 10.1038/nmeth.4303)

Inference of clonal dynamics and tumour evolution has fundamental importance in understanding the major clinical endpoints in cancer: development of treatment resistance, relapse and metastasis. DNA sequencing technology has made measuring clonal dynamics through mutation analysis accessible at scale, facilitating computational inference of informative patterns of interest. However, currently no tools allow for biomedical experts to meaningfully interact with the often complex and voluminous dataset to inject domain knowledge into the inference process. We developed an interactive, web-based visual analytics software suite called E-scape which supports dynamically linked, multi-faceted views of cancer evolution data. Developed using R and javascript d3.js libraries, the suite includes three tools: TimeScape and MapScape for visualizing population dynamics over time and space, respectively, and CellScape for visualizing evolution at single cell resolution. The tool suite integrates phylogenetic, clonal prevalence, mutation and imaging data to generate intuitive, dynamically linked views of data which update in real time as a function of user actions. The system supports visualization of both point mutation and copy number alterations, rendering how mutations distribute in clones in both bulk and single cell experiment data in multiple representations including phylogenies, heatmaps, growth trajectories, spatial distributions and mutation tables. E-scape is open source and is freely available to the community at large.

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