Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples
Fullwood, M.; Animesh, S.; Choudhary, R.; Goh, B. C.; Tay, J.; chong, w.-q.; Ng, X. Y.
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A major challenge in understanding the 3D genome organization of cancer samples is the lack of a method adapted to solid cancer needle biopsy samples. Here we developed Biop-C, a modified in situ Hi-C method, and applied it to characterize three nasopharyngeal cancer patient samples. We identified Topologically-Associated Domains (TADs), chromatin interaction loops, and Frequently Interacting regions (FIREs) at key oncogenes in nasopharyngeal cancer from Biop-C heat maps. Our results demonstrate the utility of our Biop-C method in investigating the 3D genome organization in solid cancers, and the importance of 3D genome organization in regulating oncogenes in nasopharyngeal cancer.
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