TimeScape

TimeScape visualizes temporal clonal evolution in cancer by integrating a clonal phylogeny with quantitative clone prevalence measurements across sequential time points to reveal clonal expansions, contractions, and mutation dynamics during disease progression or treatment.

Key Features:

• Input data: Accepts a clonal phylogeny and a table of clonal prevalences measured at multiple sampling times, with optional per-clone targeted mutation data and allele prevalence trajectories.
• Phylogeny–prevalence integration: Integrates clonal phylogenetic relationships with quantitative prevalence estimates across time points to link evolutionary structure and temporal dynamics.
• Continuous timeline plot: Produces a time-series plot mapping clonal prevalence on the vertical axis and time on the horizontal axis with clone heights proportional to observed prevalence.
• Bézier curve interpolation: Connects clone prevalences across sampling times using smooth Bézier curves to represent trajectories of clonal change.
• Tumour volume encoding: Optionally encodes global plot height as tumour volume to represent clonal behavior during shrinkage or regrowth.
• Mutation and allele trajectory visualization: Displays per-clone targeted mutations and allele prevalence trajectories to show mutation dynamics within evolving subclones.
• Clonal dynamics representation: Visualizes expansions, bottlenecks, and shifts in dominance among tumour subpopulations over longitudinal sampling.

Scientific Applications:

• Treatment resistance analysis: Visualizes the emergence and expansion of resistant subclones during and after therapy.
• Metastatic progression tracking: Tracks changes in clonal prevalence over time to infer dissemination and dominance shifts associated with metastasis.
• Tumor evolutionary dynamics: Characterizes clonal expansions, bottlenecks, and lineage relationships across longitudinal datasets.
• Mutation trajectory monitoring: Monitors allele prevalence trajectories and targeted mutation occurrence within subclonal lineages over time.

Methodology:

Requires a clonal phylogeny and a table of clonal prevalences across sampling times (optional per-clone mutation and allele trajectories); maps prevalence vertically and time horizontally, connects prevalences with smooth Bézier curves, integrates phylogenetic structure with temporal prevalence, and can encode global plot height as tumour volume.