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

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.