GWAS Summary statistics - HIV-1 acquisition meta-analysis - Duarte et al. 2022

<strong>Transcriptome-wide association study of HIV-1 acquisition identifies </strong><em><strong>HERC1</strong></em><strong> as a susceptibility gene </strong> <br> <strong>Abstract: </strong>The host genetic factors conferring protection against HIV-1 acquisition, particularly those regulated by common genetic variants, remain elusive. Here, we performed the largest genome-wide association meta-analysis of HIV-1 acquisition, which included 7,303 HIV-1-positive individuals and 587,343 population controls. We identified 25 independent genetic loci with suggestive association, of which one was genome-wide significant within the major histocompatibility complex (MHC) locus. After exclusion of the MHC signal, linkage disequilibrium score regression analyses revealed a SNP heritability of 21%, and genetic correlations with behavioral factors. A transcriptome-wide association study identified 15 susceptibility genes, including <em>HERC1</em>, <em>UEVLD, </em>and<em> HIST1H4K</em>. Convergent evidence from conditional analyses and fine-mapping identified <em>HERC1</em> downregulation in immune cells as a robust mechanism associated with HIV-1 acquisition. Functional studies on <em>HERC1</em> and other identified candidates, as well as larger genetic studies, have the potential to further our understanding of the host mechanisms associated with protection against HIV-1. <br> <strong>Content: </strong>The file in this repository contains GWAS summary statistics for the HIV-1 meta-analysis and a read me file describing the column labels. Studies included in the meta-analysis (see URLs under "References"): 1) McLaren P.J. et al. (2013). Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls. PLOS Pathogens 9, e1003515. 10.1371/journal.ppat.1003515. 2) Johnson E.O. et al. (2015). Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study. PLOS ONE 10, e0118149. 10.1371/journal.pone.0118149. 3) Ben Neale’s group’s UKBB results (data release 3, trait ID 20002_1439 HIV/AIDS). 4) FinnGen (data release 5, trait ID AB1_HIV). <br> <strong>Related content:</strong> Code used in manuscript has also been deposited in Figshare, DOI: 10.18742/20343219. <br> <strong>Disclaimer: </strong>If you choose to download and analyse these data, you acknowledge that: - These data are provided on an “as-is” basis, and no warranty is provided as to their performance or fitness for any purpose - You and your collaborators are in compliance with all applicable local/state/national/international laws or regulations and institutional policies regarding human subjects and genetics research - You will cite Duarte et al. 2022 in any communications or publications arising directly or indirectly from these data - All data here are released for the benefit of the wider biomedical community for use in the investigation of the genetics of susceptibility to infectious agents and wider genetics research.