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

Transcriptome-wide association study of HIV-1 acquisition identifies HERC1 as a susceptibility gene Abstract: 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 HERC1, UEVLD, and HIST1H4K. Convergent evidence from conditional analyses and fine-mapping identified HERC1 downregulation in immune cells as a robust mechanism associated with HIV-1 acquisition. Functional studies on HERC1 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.

Content: 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).

Related content: Code used in manuscript has also been deposited in Figshare, DOI: 10.18742/20343219.

Disclaimer: 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.