ArticlePLoS computational biology2019
A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 40 citations in OpenAlex.
- Analysis of HERV-K (HML2) Expression in Colorectal Cancer Samples.Epigenomes · 2026Article
- The Role of Human Endogenous Retroviruses in the Initiation and Progression of Melanoma.Biomedicines · 2025Review
- High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.Genome research · 2024Article
- GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies.PLoS computational biology · 2024Article
- Limitations of current high-throughput sequencing technologies lead to biased expression estimates of endogenous retroviral elements.NAR genomics and bioinformatics · 2024Article
- Endogenous retroviruses are dysregulated in ALS.iScience · 2024Article
- Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.medRxiv : the preprint server for health sciences · 2024Article
- Mechanistic regulation of HERV activation in tumors and implications for translational research in oncology.Frontiers in cellular and infection microbiology · 2024Review
- TDP-43 Epigenetic Facets and Their Neurodegenerative Implications.International journal of molecular sciences · 2023Review
- A Systems Biology Approach on the Regulatory Footprint of Human Endogenous Retroviruses (HERVs).Diseases (Basel, Switzerland) · 2022Article
- Retroviral Elements in Pathophysiology and as Therapeutic Targets for Amyotrophic Lateral Sclerosis.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2022Review
- Characterizing mobile element insertions in 5675 genomes.Nucleic acids research · 2022Article
- Human endogenous retroviruses and the inflammatory response: A vicious circle associated with health and illness.Frontiers in immunology · 2022Review
- Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus.Molecular biology and evolution · 2021Article
- A plant-based meal reduces postprandial oxidative and dicarbonyl stress in men with diabetes or obesity compared with an energy- and macronutrient-matched conventional meal in a randomized crossover study.Nutrition & metabolism · 2021Article
- Antibodies against human endogenous retrovirus K102 envelope activate neutrophils in systemic lupus erythematosus.The Journal of experimental medicine · 2021Article
- Endogenous retroviruses in the origins and treatment of cancer.Genome biology · 2021Review
- Virus-derived variation in diverse human genomes.PLoS genetics · 2021Article
- Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa.Molecular biology and evolution · 2021Article
- Human endogenous retroviruses in development and disease.Computational and structural biotechnology journal · 2021Review
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human Endogenous Retrovirus type K (HERV-K) is the only HERV known to be insertionally polymorphic; not all individuals have a retrovirus at a specific genomic location. It is possible that HERV-Ks contribute to human disease because people differ in both number and genomic location of these retroviruses. Indeed viral transcripts, proteins, and antibody against HERV-K are detected in cancers, auto-immune, and neurodegenerative diseases. However, attempts to link a polymorphic HERV-K with any disease have been frustrated in part because population prevalence of HERV-K provirus at each polymorphic site is lacking and it is challenging to identify closely related elements such as HERV-K from short read sequence data. We present an integrated and computationally robust approach that uses whole genome short read data to determine the occupation status at all sites reported to contain a HERV-K provirus. Our method estimates the proportion of fixed length genomic sequence (k-mers) from whole genome sequence data matching a reference set of k-mers unique to each HERV-K locus and applies mixture model-based clustering of these values to account for low depth sequence data. Our analysis of 1000 Genomes Project Data (KGP) reveals numerous differences among the five KGP super-populations in the prevalence of individual and co-occurring HERV-K proviruses; we provide a visualization tool to easily depict the proportion of the KGP populations with any combination of polymorphic HERV-K provirus. Further, because HERV-K is insertionally polymorphic, the genome burden of known polymorphic HERV-K is variable in humans; this burden is lowest in East Asian (EAS) individuals. Our study identifies population-specific sequence variation for HERV-K proviruses at several loci. We expect these resources will advance research on HERV-K contributions to human diseases.
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