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ClonArch: visualizing the spatial clonal architecture of tumors.
1Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Bioinformatics (Oxford, England)
|July 14, 2020
Summary
ClonArch visualizes tumor clonal architecture, revealing spatial distribution and phylogenetic relationships. This tool aids in understanding intra-tumor heterogeneity and treatment resistance.
Area of Science:
- Oncology
- Computational Biology
- Bioinformatics
Background:
- Cancer arises from accumulated somatic mutations, forming distinct cell clones.
- Tumor clonal architecture drives relapse and treatment resistance.
- Advancements in DNA sequencing yield high-resolution spatial genomics data.
Purpose of the Study:
- To introduce ClonArch, a novel web-based tool for visualizing tumor clonal architecture.
- To enable interactive exploration of phylogenetic trees and spatial clone distribution.
- To address the lack of visual analytics for spatial tumor evolution.
Main Methods:
- ClonArch employs the marching squares algorithm for spatial clone boundary visualization.
- The tool allows examination of clone presence at varying prevalence thresholds.
- It supports analysis across multiple phylogenetic trees and simulated/real tumor data.
Main Results:
- ClonArch successfully visualizes the phylogenetic tree and spatial distribution of tumor clones.
- Demonstrated on simulated tumors and a hepatocellular carcinoma case with extensive biopsies.
- Facilitates interactive examination of spatial clonal architecture.
Conclusions:
- ClonArch provides an automated method for analyzing intra-tumor spatial heterogeneity.
- Enhances clinical and biological interpretation of tumor evolution.
- A valuable resource for cancer genomics research.
