Inferring Selective Advantage Relationships to Reconstruct Cancer Progression Models
summary
Algorithms named Capri and Caprese reconstruct cancer progression as directed relations of selective advantage using the Suppes probabilistic causality score and formalisms for mutual exclusivity (patterns taken from tools like Mutex). Implemented in the TRONCO library, the pipeline analyzes TCGA cross‑sectional cohorts (colorectal example), finds a plausible placement of SOX9 downstream of APC/MYC alterations, shows robustness to noise, and yields clinician‑validated models though experimental validation remains pending.
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chapters (12)
- 0:00Intro
- 0:50CRC Standard Progression
- 1:41Cross-sectional Data
- 3:57Ensemble vs. Individual Progression Reconstruction
- 4:49Foundations of the Reconstruction
- 7:56Progression Reconstruction Core Ideas Summarized
- 10:45TRONCO: A Suite of Algorithms
- 10:59Performance comparisons...
- 11:53Picnlc: A Pipeline for Inference А
- 14:55Main Characters
- 15:35Final Acknowledgments
- 19:52CAPRI: A Logic for Complex Patterns
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