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Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

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Lenz,  Tobias L.
Emmy Noether Research Group Evolutionary Immunogenomics, Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

McLaren, P. J., Coulonges, C., Bartha, I., Lenz, T. L., Deutsch, A. J., Bashirova, A., et al. (2015). Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1514867112.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0029-1A6F-7
Abstract
Previous genome-wide associat ion studies (GWAS) of HIV-1 – infected populations have been underpowered to detect common variants with moderate impact on disease outcome and have not assessed the phenotypic variance explained by genome-wide additive effects. By combining the majority of available genome-wide genotyping data in HIV-infected populations, we tested for association between ∼ 8 million variants and viral load (HIV RNA copies per milliliter of plasma) in 6,315 individuals of Eur opean ancestry. The strongest sig- nal of association was observed in the HLA class I region that was fully explained by independent effects mapping to five variable amino acid positions in the peptide binding grooves of the HLA-B and HLA-A proteins. We observed a second genome-wide significant association signal in the chemokine (C-C motif) receptor (CCR) gene cluster on chromosome 3. Conditional a nalysis showed that this signal could not be fully attributed to the known protective CCR5 Δ 32 allele and the risk P1 haplotype, suggesting further causal variants in this region. Heritability analysis demonstrated that common human ge- netic variation — mostly in the HLA and CCR5 regions — explains 25% of the variability in viral load. This study suggests that analyses in non-European populations and of variant classes not assessed by GWAS should be priorities for the field going forward.