METAMATS_SIZE

This software fits models of metastatic development to longitudinal data of metastatic sizes and provides simulation and visualization tools for metastatic modeling.

Language: Matlab

Dependencies: carcinom, metamats_core

How to use it

• Data loaded in
  import_data_<subject_ID>
• Fit launched in
  ./main_fit_separately.m
• Results (including parameter values) are exported in a file /fit.mat
• Birth times and growth curves of the metastases can be computed via manips_birth_times by informing the folder where results where exported
• Example provided is a patient with non-small cell lung cancer developing brain metastases. Additional data for at least two other patients are available in ~/work/brain_metastases (either code/ or B_MATEMATICS)

Features

#### Model and fit * For multiple subjects, fits can be performed either independently or jointly (i.e. with common parameters across subjects) * Fit can be performed on either total number of visible metastases (not tested in details) or cumulative size distributions at possibly multiple time points * Computes standard errors * Allows different mechanistic models including: delay to metastasis, dormancy, secondary dissemination (metastases from metastases), equal or distinct growth functions and/or parameters between primary tumor and metastases * Allows a multistart search for parameters’ estimation (to avoid local minima issues) * Estimates PT growth parameters from size at diagnosis and doubling time (only available for lung ADK or squamous cell carcinoma and gompertz growth)
#### Simulation * Estimation of mets birth times and growth kinetics
./manips_birth_times.m * Movie with primary tumor growth curve and metastatic size distribution. Launched by setting output_s.hist_movie = 1 in
./main_fit_several_subjects_mets.m (for instance) * Movie with primary tumor and metastases sizes represented as disks is launched using
./plot_circles_for_movie.m

Abbreviations: PT = Primary tumor, mets = metastases