SISTEM

SISTEM simulates tumor evolution and cell migrations at single-cell resolution under genotype-driven selection, generating realistic DNA sequencing data with ground truth cell lineages and migration graphs.

Key Features:

• Agent-based tumor simulation: SISTEM simulates tumor populations under somatic clonal selection using an agent-based framework rather than neutral coalescent or simple birth-death models.
• Genomic event-driven fitness: Cell fitness is driven by genomic events at multiple scales including single nucleotide variants, segmental gains and losses, whole-chromosomal and chromosome-arm aberrations, and whole-genome duplications.
• Sequencing data generation: SISTEM generates mutation profiles, read counts, and DNA sequencing reads alongside ground truth cell lineages and migration graphs.
• Customizable models: The framework supports easily customizable mutation and selection models.
• Migration models for metastasis: SISTEM includes numerous migration models to simulate metastatic cancers and facilitate exploration and evaluation of diverse migration patterns.

Scientific Applications:

• Tumor evolution research: SISTEM enables simulation of cancer cell populations under somatic clonal selection for studying tumor evolutionary dynamics.
• Metastasis simulation: SISTEM facilitates exploration and evaluation of diverse cancer cell migration patterns in metastatic cancers.
• Method benchmarking: SISTEM provides ground truth cell lineages and migration graphs for evaluating methods that infer tumor phylogenies or migration histories from DNA sequencing data.

Methodology:

SISTEM uses an agent-based mathematical framework to simulate tumor populations under somatic clonal selection with genotype-driven fitness at single-cell resolution.