Table 1.
Genome-wide association studies on human immunodeficiency virus-1 infection
| First author | Publication date (yyyy-mm-dd) | Journal | Reported trait | Sample number (ancestry) | Cohort used | References |
|---|---|---|---|---|---|---|
| European Ancestry Cohort | ||||||
| Fellay | 2007-07-19 | Science | HIV viral setpoint | 486 European | EuroCHAVI | Fellay et al. (2007) |
| Limou | 2000-01-01 | J Infect Dis | AIDS progression | 1627 European, 86 NR | GRIV | Limou et al. (2009) |
| Le Clerc | 2009-09-15 | J Infect Dis | AIDS | 2134 European | GRIV | Le Clerc et al. (2009) |
| Fellay | 2009-12-24 | PLoS Genet | HIV-1 control | 2362 European | EuroCHAVI | Fellay (2009) |
| Ferreira | 2009-12-31 | AM J Hum Genet |
CD56 positive NK-lymphocyte cell count CD19-positive B-lymphocyte count CD8-positive T-lymphocyte count CD4-positive T-lymphocyte count |
2538 European | Siblings from 1089 Australian families | Ferreira et al. (2010) |
| Shrestha | 2010-01-01 | AIDS | Carotid atherosclerosis in HIV infection | 177 European | FRAM | Shrestha et al. (2010) |
| Herbeck | 2010-02-15 | J Infect Dis | HIV-1 progression | 156 European | MACS | Herbeck et al. (2010) |
| Bol | 2011-02-25 | PLoS One | HIV-1 replication | 191 European | Healthy blood donors | Bol et al. (2011) |
| Troyer | 2011-05-01 | J Infect Dis | AIDS progression | 755 European | GRIV | Troyer et al. (2011) |
| van Manen | 2011-07-21 | PLoS One | HIV-1 progression | 404 European | ACS | van Manen et al. (2011) |
| Irvin | 2011-12-01 | Pharmacogenet Genomics | Fat distribution (HIV) | 192 European | FRAM | Irvin et al. (2011) |
| Lane | 2013-02-10 | Hum Mol Genet | HIV-1 susceptibility | 1195 European | CHAVI014, MHCS | Lane et al. (2013) |
| McLaren | 2013-07-25 | PLoS Pathog | HIV-1 susceptibility | 13,581 European | ACTG; ALIVE; ACS; ANRS CO18; ANRS PRIMO Cohort; CCR; CHAVI; Danish HIV Cohort Study; GISHEAL; GRIV Cohort; HGDS; Hospital Clinic-IDIBAPS Acute/Recent HIV-1 Infection; Icona Foundation Study; International HIV Controllers Study, The IrsiCaixa Foundation Acute/Recent HIV-1 Infection Cohort; Modena Cohort; MACS; MHCS; Pumwani Sex Workers Cohort; SFCCC; The GPC Cohort/ Sanger Institute in Oxford, UK, and in Uganda; SHCS; University Medical Center Utrecht Dutch Controls Cohort; NHS; WTCCC3; Western Australian HIV Cohort Study | McLaren et al. (2013) |
| McLaren | 2015-11-09 | Proc Natl Acad Sci U S A | Setpoint viral load in HIV-1 infection | 6315 European | EuroCHAVI, ALIVE, DCG, HGDS, MHCS, SFCC, GRIV, PRIMO, MACS, ACTG, IHCS, ACS, UHS | McLaren et al. (2015) |
| Ulveling | 2016-07-29 | Hepatology | Liver fibrosis severity in HIV/hepatitis C co-infection | 289 European | French National Agency for Research on AIDS and Viral Hepatitis CO13 HEPAVIH | Ulveling et al. (2016) |
| African Ancestry Cohorts | ||||||
| Pelak | 2010-04-15 | J Infect Dis | HIV-1 viral setpoint | 515 African American or Afro-Caribbean | NHS; MACS | Pelak et al. (2010) |
| Petrovski | 2011-02-20 | AIDS | HIV-1 susceptibility | 1379 Sub-Saharan African | Recruited from the Center for HIV/AIDS Vaccine Immunology Clinical Core in Malawi | Petrovski et al. (2011) |
| Lingappa | 2011-12-12 | PLoS One | HIV-1 susceptibility | 798 Sub-Saharan African, African unspecified | The Partners in Prevention HSV/HIV Transmission Study; The Couples Observational Study | Lingappa et al. (2011) |
| Carr | 2017-01-05 | J Antimicrob Chemother | Nevirapine-induced hypersensitivity in HIV (drug-induced liver injury) | 203 Sub-Saharan African |
Recruited from the Queen Elizabeth Central Hospital, Malawi |
Carr et al. (2017) |
| Nevirapine-induced hypersensitivity in HIV | 333 Sub-Saharan African | |||||
| Nevirapine-induced hypersensitivity in HIV (rash) | 398 Sub-Saharan African | |||||
| Nevirapine-induced hypersensitivity in HIV (hypersensitivity syndrome) | 205 Sub-Saharan African | |||||
| Nevirapine-induced hypersensitivity in HIV (Stevens-Johnson syndrome or toxic epidermal necrosis) | 233 Sub-Saharan African | |||||
| Asian Ancestry Cohorts | ||||||
| Uttayamakul | 2015-06-15 | AIDS Res Hum Retroviruses | Response to stavudine in HIV (lipoatrophy) | 141 Southeast Asian | Bamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand | Uttayamakul et al. (2015) |
| Wei | 2015-06-17 | Sci Rep | HIV-1 viral setpoint | 538 East Asian | Chinese Medical University: HAN, YUN, XIN | Wei et al. (2015) |
| Multiethnic cohorts | ||||||
| Pereyra | 2010-11-04 | Science | HIV-1 control |
1712 European; 1233 African American or Afro-Caribbean; 677 Hispanic or Latin American |
International HIV Controllers Study, ACTG | Pereyra et al. (2010) |
| Moore | 2015-01-09 | Open Forum Infect Dis | Neutrophil count in HIV infection; HDL cholesterol in HI -infection; total bilirubin levels in HIV-1 infection | 2547 European, Hispanic or Latin American, African unspecified | ACTG | Moore et al. (2015) |
| Lehmann | 2015-02-01 | Pharmacogenet Genomics | Response to abacavir-containing treatment in HIV-1 infection (virologic failure) |
346 European; 265 African unspecified; 175 Hispanic or Latin American |
ACTG | Lehmann et al. (2015) |
| Lehmann | 2015-02-01 | Pharmacogenet Genomics | Response to efavirenz-containing treatment in HIV-1 infection (virologic failure) |
737 European; 545 African unspecified; 314 Hispanic or Latin American |
ACTG | Lehmann et al. (2015) |
| Johnson | 2015-03-18 | PLoS One | HIV-1 susceptibility | 2004 African American or Afro-Caribbean; 1132 European | UHS | Johnson et al. (2015) |
| Wanga | 2015-09-01 | Pharmacogenet Genomics | Bilirubin measurement, response to tenofovir, HIV infection, creatinine clearance | 243 European, 149 African American, 100 Hispanic American, 9 UA | ACTG | Wanga et al. (2015) |
| Jia | 2017-04-26 | Am J Med Genet B Neuropsychiatr Genet | Neurocognitive impairment in HIV-1 infection (continuous) |
490 African American or Afro-Caribbean; 443 European; 99 Hispanic or Latin American; 17 NR |
CHARTER | Jia et al. (2017) |
| Jia | 2017-04-26 | Am J Med Genet B Neuropsychiatr Genet | Neurocognitive impairment in HIV-1 infection (dichotomous) |
490 African American or Afro-Caribbean; 443 European; 99 Hispanic or Latin American; 17 NR |
CHARTER | Jia et al. (2017) |
| Ekenberg | 2019-06-13 | J Infect Dis | Pre-treatment viral load in HIV-1 infection |
572 African unspecified; 1398 European; 418 Hispanic or Latin American; 13 Asian unspecified; 39 NR |
START | Ekenberg et al. (2019) |
GWAS were compiled through the NHGRI-EBI GWAS Catalog using the search terms “HIV-1” and “AIDS”. Cohorts used have been abbreviated. All abbreviations are listed below in alphabetical order. ‘NR’ is not reported ancestry, ‘UA’ is unknown ancestry (MacArthur et al. 2018)
ACS Amsterdam Cohort Studies on HIV Infection and AIDS, ACTG AIDS Clinical Trials Group, ALIVE AIDS Linked to the IntroVenous Experience, CCR Center for Cancer Research, National Cancer Institute, CHARTER CNS HIV Antiretroviral Therapy Effects Research, CHAVI Center for HIV/AIDS Vaccine Immunology, EuroCHAVI Consortium Swiss HIV Cohort Study; Icona Foundation Study; IrsiCaixa Foundation; San Raffaele del Monte Tabor Foundation; Danish Cohort; Royal Perth Hospital: Guy's, King's, and St. Thomas' Hospitals; Modena Cohort; Hospital Clinic-IDIBAPS cohort; Multicenter AIDS Cohort Study, FRAM Fat Redistribution and Metabolic Change in HIV Infection, GISHEAL The Genetic and Immunological Studies of European and African HIV-1 Long Term Non-Progressors, HGDS Hemophilia Growth and Development, MACS Multicenter AIDS Cohort Study, MHCS Multicenter Hemophilia Cohort Study, NHS The US Military HIV Natural History Study, SFCCC San Francisco City Clinic Cohort, SHCS Swiss HIV Cohort Study, START Strategic Timing of AntiRetroviral Treatment, UHS Urban Health Study, WTCCC3 The Wellcome Trust Case Control Consortium study of the genetics of host control of HIV-1 infection in the Gambia