A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease (opens in new tab)

Human endogenous retroviruses (HERVs) are remmants of ancient infections which make up to ~8% of the human genome. Their activity influences development, immunity, and cancer, but studying them has been limited by a key technical challenge: short-read sequencing cannot uniquely assign reads to these highly repetitive elements. Here, we present ERVmancer, a phylogeny-informed method that resolves the read-mapping ambiguity and quantifies HERV expression across scales, from individual loci to e...