Matthew Jones from Stanford University presented at London Calling 2024 a session titled “CoRAL accurately resolves extrachromosomal DNA structures with long-read sequencing.” This toolkit can be used to study extrachromosomal or ecDNA, a form of oncogene amplification in cancers. ecDNA is not found in normal cells, is associated with shorter patient survival, and is large: 100kb to 5 Mb. ecDNA has been studied using short reads by estimating segmental copy number and predicting ecDNA presence and absence. Long-read further permits the detection of breakpoints, phasing together of segment orderings, and deconvolution of structure heterogeneity. Complete Reconstruction of Amplicons with Long Reads (CoRAL) uses long-read sequencing data and detects seed amplification. With this information, copy number is assessed. Jones has tested CoRAL on simulated data and heavily validated cancer cell lines. Jones mentioned they have a pre-print. I did not know about ecDNA and learned from this five-min session!
