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

Abstract

Abstract Cancer progression, including the development of intratumor heterogeneity, is inherently a spatial process. Mathematical models of tumor evolution may be a useful starting point for understanding the patterns of heterogeneity that can emerge in the presence of spatial growth. A commonly studied spatial growth model assumes that tumor cells occupy sites on a lattice and replicate into neighboring sites. Our R package SITH provides a convenient interface for exploring this model. Our efficient simulation algorithm allows for users to generate 3D tumors with millions of cells in under a minute. For the distribution of mutations throughout the tumor, SITH provides interactive graphics and summary plots. Additionally, SITH can produce synthetic bulk and single‐cell DNA‐seq datasets by sampling from the simulated tumor. A streamlined application programming interface (API) makes SITH a useful tool for investigating the relationship between spatial growth and intratumor heterogeneity. SITH is a part of CRAN and can be installed by running install.packages(“SITH”) from the R console. See https://CRAN.R‐project.org/package=SITH for the user manual and package vignette.

Keywords

• sequencing
• simulation
• tumor evolution