MET_PCa: Met-Score for Prostate Cancer Metastasis Risk

This repository includes the analysis scripts used to produce the results reported in the manuscript entitled “A Conserved Metastatic Competence Signature from Primary Prostate Tumors”.

Overview

The code covers the discovery, implementation, and validation of the locked Met-Score classifier, and generation of the manuscript figures and supplementary tables.

Repository structure

• code/ — analysis and figure-generation scripts.
• config/ — locked Met-Score and Decipher-surrogate configuration files.
• setup.sh and environment.yml — software setup.

Setup

bash setup.sh
conda activate metpca

Python dependencies are listed in environment.yml, the R dependencies are installed by setup.sh, and analyses should be run from the repository root.

Main analysis scripts

• code/signature_discovery/MET_PCa_MetaIntegrator.R — signature discovery and Figure 1.
• code/survival_analysis/Met_PCa_Survival.R — frozen scoring and the JHU analysis object.
• code/validation/Durham_MetScore_Validation_BatchCorrected.R — Durham validation.
• code/data_preparation/Calibration_LockedLR_AllCohorts.R and code/figures/Figure2_unified_validation.py — Figure 2.
• code/survival_analysis/Met_PCa_Survival_Multivariate.R and code/figures/Figure3_GS7.py — Figure 3 and multivariable results.
• code/figures/Figure4_Biopsy_Validation.R — Figure 4.
• code/figures/FigureS1_purity_clinical_utility.py through code/figures/FigureS6_sensitivity.py — supplementary figures.
• code/supplementary/generate_supplementary_tables.py — supplementary tables.