King L Hung, Jens Luebeck, Siavash R Dehkordi, Caterina I Colón, Rui Li, Ivy Tsz-Lo Wong, Ceyda Coruh, Prashanthi Dharanipragada, Shirley H Lomeli, Natasha E Weiser, Gatien Moriceau, Xiao Zhang, Chris Bailey, Kathleen E Houlahan, Wenting Yang, Rocío Chamorro González, Charles Swanton, Christina Curtis, Mariam Jamal-Hanjani, Anton G Henssen, Julie A Law, William J Greenleaf, Roger S Lo, Paul S Mischel, Vineet Bafna, Howard Y Chang
Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, to isolate megabase-sized human ecDNAs. We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells and NRAS ecDNA from human metastatic melanoma with acquired therapeutic resistance...
November 2022: Nature Genetics