A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations

• DOI: 10.1371/journal.pcbi.1006564
• Publication Date: 2019-03-28T17:50:07Z
• Authors: Weiling Li; Lin Lin; Raunaq Malhotra; Lei Yang; Raj Acharya; Mary Poss
• Keywords: Provirus; 1000 Genomes Project

Human Endogenous Retrovirus type K (HERV-K) is the only HERV known to be insertionally polymorphic; not all individuals have a retrovirus at specific genomic location. It possible that HERV-Ks contribute human disease because people differ in both number and location of these retroviruses. Indeed viral transcripts, proteins, antibody against HERV-K are detected cancers, auto-immune, neurodegenerative diseases. However, attempts link polymorphic with any been frustrated part population prevalence provirus each site lacking it challenging identify closely related elements such as from short read sequence data. We present an integrated computationally robust approach uses whole genome data determine occupation status sites reported contain provirus. Our method estimates proportion fixed length (k-mers) matching reference set k-mers unique locus applies mixture model-based clustering values account for low depth analysis 1000 Genomes Project Data (KGP) reveals numerous differences among five KGP super-populations individual co-occurring proviruses; we provide visualization tool easily depict populations combination Further, polymorphic, burden variable humans; this lowest East Asian (EAS) individuals. study identifies population-specific variation proviruses several loci. expect resources will advance research on contributions