Siavash Raeisi Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, Jens Luebeck, Kaiyuan Zhu, Gino Prasad, Lena Krockenberger, Guanghui Xu, Biswanath Chowdhury, Utkrisht Rajkumar, Ann Caplin, Daniel Muliaditan, Ceyda Coruh, Qiushi Jin, Kristen Turner, Shu Xian Teo, Andy Wing Chun Pang, Ludmil B Alexandrov, Christelle En Lin Chua, Frank B Furnari, Thomas G Paulson, Julie A Law, Howard Y Chang, Feng Yue, Ramanuj DasGupta, Jean Zhao, Paul S Mischel, Vineet Bafna
Oncogene amplification is a major driver of cancer pathogenesis. Breakage fusion bridge (BFB) cycles, like extrachromosomal DNA (ecDNA), can lead to high copy numbers of oncogenes, but their impact on intratumoral heterogeneity, treatment response, and patient survival are not well understood due to difficulty in detecting them by DNA sequencing. We describe a novel algorithm that detects and reconstructs BFB amplifications using optical genome maps (OGMs), called OM2BFB. OM2BFB showed high precision (>93%) and recall (92%) in detecting BFB amplifications in cancer cell lines, PDX models and primary tumors...
December 13, 2023: bioRxiv