ClonArch

ClonArch visualizes spatial clonal architecture in tumors by mapping phylogenetic relationships and clone prevalence onto biopsy coordinates to elucidate intratumor heterogeneity.

Key Features:

• Interactive visualization: Visualizes phylogenetic trees alongside spatial distributions of clones mapped to biopsy coordinates.
• Marching squares algorithm: Uses the marching squares algorithm to draw closed boundaries representing the presence of different clones.
• Prevalence thresholds and multiple phylogenies: Enables examination of spatial architecture across prevalence thresholds and across multiple phylogenetic trees.
• Application on real and simulated data: Demonstrated on simulated tumors with varying numbers of biopsies and on a hepatocellular carcinoma dataset comprising approximately 280 sequencing biopsies.
• DNA sequencing data support: Operates on high-resolution DNA sequencing data and accommodates large numbers of spatial sequencing samples.

Scientific Applications:

• Clinical interpretation: Supports analysis of how spatial distributions of clones may influence tumor behavior, treatment response, resistance, and relapse.
• Biological insights: Enables study of evolutionary dynamics and spatial coexistence and competition of clones within tumors.

Methodology:

Uses DNA sequencing data mapped to biopsy coordinates, applies the marching squares algorithm to draw closed clone boundaries, and examines spatial architecture across prevalence thresholds and multiple phylogenetic trees, demonstrated on simulated tumors and a hepatocellular carcinoma dataset (~280 sequencing biopsies).