Understanding cancer epigenetics, immunogenetics, and energetics

Abstract

We studied human papillomaviruses (HPV) and cervical cancer cell lines and tumors. We used ultra-HMW DNA and full-length direct RNA sequencing to identify HPV integration sites at known super-enhancer hotspots, extrachromosomal DNA, and altered DNA methylation. Pore-C reveals extensive interaction between HPV and the human genome. HLA class I sequencing found extensive deletion of MHC haplotypes and that the HPV E5 protein, an HLA inhibitor, has abundant strong binding peptides. From mitochondrial genomics, we are exploring cancer energetics and mitochondrial variants. In summary, long-read sequencing provides exciting new data to understand the complex phenotypes of cancer cells.

To learn more about other applications of nanopore sequencing in cancer research, click here.