Figure 2. | A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Open accessCopyright infoDownload PDF

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Figure 2.

Affiliation details

École Polytechnique Fédérale de Lausanne, Switzerland; University Hospital and University of Lausanne, Switzerland; Eötvös Loránd University and the Hungarian Academy of Sciences, Hungary; Swiss Institute of Bioinformatics, Switzerland; Microsoft Research, United States; BC Centre for Excellence in HIV/AIDS, Canada; Simon Fraser University, Canada; Murdoch University, Australia; Vanderbilt University Medical Center, United States; Universitat Autònoma de Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain; Instituto de Salud Carlos III, Spain; University of Bern & Inselspital, Switzerland; University Hospital and University of Zürich, Switzerland; Regional Hospital of Lugano, Switzerland; Cantonal Hospital, Switzerland; University of Basel, Switzerland; Geneva University Hospitals, Switzerland; St. Petersburg State University, Russia; Massachusetts General Hospital, United States; University of British Columbia, Canada
Figure 2.
Download figureOpen in new tabFigure 2. Results of the genome-wide association analyses.

(A) Associations between human SNPs and HIV-1 plasma viral load. The dotted line shows the Bonferroni-corrected significance threshold (p-value < 7.25 × 10−9). (B) Associations between human SNPs and HIV-1 amino acid variants, with 3007 GWAS collapsed in a single Manhattan plot. The dotted line shows the Bonferroni-corrected significance threshold (p-value < 2.4 × 10−12). (C) Schematic representation of the HLA class I genes and of the SNPs associated with HIV-1 amino acid variants in the region. (D) Same association results as in panel B, projected on the HIV-1 proteome. Only the strongest association is shown for each amino acid. Significant associations are indicated by a blue dot. The gp120 part of the HIV-1 proteome was not tested. The colored bar below the plot area shows the positions of the optimally defined CD8+ T cell epitopes. An interactive version of this figure can be found at http://g2g.labtelenti.org (which is also available to download from Zenodo, http://dx.doi.org/10.5281/zenodo.7138).

DOI: http://dx.doi.org/10.7554/eLife.01123.004