Mechanisms of Amplification in Tumor Genomes
summary
Focuses on focal amplifications and tests three mechanisms: breakage–fusion–bridge (BFB), chromothripsis, and episome/double-minute amplification. Presents a linear-time BFB test on copy-number vectors with simulations and additional heuristics that reach about 80% true positive in small synthetic cases but only flags a handful of TCGA tumors (≈3–4) in real data. Shows that progressive rearrangements can mimic chromothripsis signatures in Monte Carlo tests and cites cytogenetics plus sequencing evidence and a glioblastoma case of EGFR double-minute integration with drug-driven oscillation.
AI-written summary · about
chapters (22)
- 0:00Intro
- 0:13Amplification are a hallmark of cancer
- 2:20Episome model of amplification
- 4:18Telomere Loss
- 4:40Fusion bridge
- 5:04Telomere fusions in breast carcinoma
- 6:55The BFB reconstruction problem
- 9:26Properties of BFB trees
- 10:17Finding Longest Palindromes
- 11:43A non-BFB count vector
- 12:04Count vector canonization
- 12:17Layer 1
- 14:59Detecting BFB: conclusions
- 16:14Re-examining the simulation: the input
- 16:33Stephens' simulation
- 17:13Simulation results
- 20:35Critique of our approach
- 22:432 Origin of DMs and Chromothripsis
- 23:40Progressive DMs and copy number states
- 25:03Amplicon dynamics
- 26:15Similarity of DM and HSR structure
- 27:49Acknowledgments
related talks
30mUnlocking the Genome: Exploring the Potential of CRISPR/Cas9
01h 22mTutorial 5: The GCT Chasm II
53mA Commentary on the Collision of Worlds
58mMarkov Chain Mixing Times and Applications III
49mKeynote Address: Everything You Always Wanted to Know about Storage Analysis...
01h 01mThe Gospel According to TCS
58mStrong Generalization from Small Brains and No Training Data
01h 00mMeasure, Then Build