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Abstract Here we present AmpliconSuite, a toolkit for focal amplification analysis from cancer whole-genome sequencing that identifies extrachromosomal DNA (ecDNA), breakage–fusion–bridges and other amplification modes. Its ecContext module categorizes ecDNA structures to understand formation mechanisms. Validation across 175 metaphase fluorescence in situ hybridization-probed genes in 72 models demonstrated accurate predictions.
Loading metrics Open Access Peer-reviewed Research Article ? This is an uncorrected proof. Citation: Brennan JW, Spandau S, Xu J, Wang X, Aull H, Wang G, et al. (2026) SARS-CoV-2 defective viral genomes from distinct genomic regions drive divergent interferon responses. PLoS Pathog 22(9): e1014099.
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