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focal-amplification-ecdna

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

When to use

• structural characterization of focal amplification
• distinguishing ecDNA from chromosomal amplification
• suspecting ecDNA-driven oncogene amplification
• suspecting therapy resistance
• selecting copy-number seeds for amplicon reconstruction
• breakpoint-graph reconstruction
• balanced-flow optimization
• ecDNA classification

When not to use

• depth-only amplification calls

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