SITH: An R package for visualizing and analyzing a spatial model of intratumor heterogeneity.

Area of Science:

• Computational biology
• Cancer research
• Mathematical modeling

Background:

• Cancer progression is a spatial process, leading to intratumor heterogeneity.
• Mathematical models of tumor evolution can elucidate patterns of heterogeneity.
• Spatial growth models, where tumor cells replicate into neighboring lattice sites, are commonly studied.

Purpose of the Study:

• To introduce the R package SITH for exploring spatial tumor growth models.
• To provide an efficient simulation tool for generating large-scale 3D tumors.
• To facilitate the investigation of the relationship between spatial growth and intratumor heterogeneity.

Main Methods:

• Development of an R package named SITH.
• Implementation of an efficient simulation algorithm for 3D tumor generation (millions of cells in under a minute).
• Inclusion of interactive graphics, summary plots, and synthetic data generation (bulk and single-cell DNA-seq).

Main Results:

• SITH enables rapid generation of large 3D tumors.
• The package offers tools for visualizing mutation distribution.
• Synthetic sequencing data can be produced for further analysis.

Conclusions:

• SITH provides a user-friendly interface for studying spatial tumor growth and intratumor heterogeneity.
• The package is valuable for computational cancer research.
• SITH is available on CRAN for easy installation and use.