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A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human
Weiling Li1, Lin Lin2, Raunaq Malhotra1
1The School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, PA, United States of America.
Plos Computational Biology
|March 29, 2019
Summary
Human Endogenous Retrovirus type K (HERV-K) is insertionally polymorphic, varying in presence across individuals. Our study maps HERV-K prevalence in diverse populations, revealing disease-linked variations and population-specific patterns.
Area of Science:
- Genomics
- Human Endogenous Retroviruses
- Population Genetics
Background:
- Human Endogenous Retrovirus type K (HERV-K) is insertionally polymorphic, with variable presence across individuals.
- HERV-K presence and location may influence disease susceptibility, as HERV-K elements are found in various pathologies.
- Previous studies lacked population prevalence data for polymorphic HERV-K sites, hindering disease association research.
Purpose of the Study:
- To develop a robust computational method for determining HERV-K provirus occupation status using whole genome short-read data.
- To analyze the population prevalence of HERV-K proviruses across different human super-populations.
- To identify population-specific sequence variations in HERV-K proviruses.
Main Methods:
- Developed an integrated approach using whole genome short-read data to assess HERV-K provirus occupation.
- Estimated k-mer proportions from sequence data matching unique HERV-K loci.
- Applied mixture model-based clustering to analyze low-depth sequence data and account for variations.
Main Results:
- Analyzed 1000 Genomes Project data, revealing significant differences in HERV-K provirus prevalence among five super-populations.
- Identified variations in the prevalence of individual and co-occurring HERV-K proviruses.
- Found the lowest HERV-K genome burden in East Asian (EAS) individuals and identified population-specific HERV-K sequence variations.
Conclusions:
- The developed method accurately determines HERV-K occupation status and population prevalence.
- HERV-K provirus distribution varies significantly across human populations, with implications for disease research.
- These findings provide valuable resources for investigating HERV-K's role in human diseases.
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