Table 2.
Genome wide association studies in HIV/AIDS
| Reference | HIV-1 Outcome tested | Sample Size | Genes/Loci with GW association | Chr. | Platform |
|---|---|---|---|---|---|
| (109) | Viral setpoint | 486 infected | HCP5, HLA-C | 6 | Illumina HumanHap550 |
| Time to CD4<350 | 337 seroconverters | no GW significance | |||
| (114) | Early plasma HIV-RNA | 605 seroconverters | HLA-B, HLA-C | 6 | Illumina HumanHap300 |
| cellular HIV-DNA | 590 seroconverters | no GW significance | |||
| (193) | AIDS non-progression | 275 LTNP, 1352 seronegative controls | HCP5 | 6 | Illumina HumanHap300 |
| (194) | AIDS rapid progression | 85 rapid progressors | no GW significance | Illumina HumanHap300 | |
| 1352 seronegative controls | |||||
| (119) | HIV-1 viral setpoint | 2362 | HCP5, HLA-C | 6 | Illumina HumanHap550, 1M |
| Time to CD4<350 | 1071 seroconverters | HCP5, HLA-C, RNF39, ZNRD1 | 6 | ||
| (111) | Viral setpoint | 515 infected | no GW significance; lowest p-val - SNP linked to B*5703 | Illumina HumanHap550, 1M, 1M-Duo | |
| B*5703 in 285 HLA-typed p=5.6 × 10−10 | |||||
| (195) | Mother-to-child transmission | 100 infant cases | no GW significance | Illumina HumanHap650Y | |
| 126 infant controls | |||||
| (110) | Viral control | 974 controllers | HLA-C, MICA, HCP5, HLA-B, PSORS1C3, HCG22 | 6 | Illumina HumanHap650Y, 1M-Duo |
| 2648 progressors | |||||
| (196) | AIDS non-progression | 186 LTNP (31+59 -2nd) | no GW significance | 3 | Illumina HumanHap300, Affymetrix 500K (MACS) |
| 697 seronegative controls | CXCR6 after the second stage meta-analysis p=2.1×10−8 | ||||
| (197) | AIDS progression | 755 seroconverters | PARD3B | 2 | Affymetrix array 6.0 |
| (198)} | HIV-1 acquisition | 848 high-risk seronegative | no GW significance | Illumina 1M, 1M-Duo | |
| 531 seropositive | |||||
| (199) | AIDS non-progression with low-freq. SNPs | 365 LTNP | HCP5, C6orf48, NOTCH4 | 6 | Illumina HumanHap300 |
| 1394 seronegative controls | RICH2 | 17 | Affymetrix 500K | ||
| AIDS rapid progression with low-freq. SNPs | 147 rapid progressors | no GW significance | |||
| 1394 seronegative controls | |||||
| (200) | AIDS progression | 404 serocoverters | no GW significance | Illumina HumanHap300 | |
| (201) | HIV-1 acquisition | 302 high-risk seronegative | no GW significance | Illumina 1M-Duo | |
| 496 seropositive | |||||
| HIV-1 viral setpoint | 403 infected | no GW significance | |||
| (202) | HIV-1 replication in macrophages in vitro | 96 low replication donors | no GW significance | Illumina 610 Quad | |
| 96 high replication donors | |||||
| (203) | AIDS non-progression | 144 LTNP | HCP5, HLA-B, C6orf48, MICA | 6 | Illumina HumanHap300 |
| 605 seroconverters | |||||
| (204) | HIV-1 acquisition | 764 seropositive (975 - 2nd) | no GW significance; | Illumina HumanHap300 | |
| 1073 seronegative (324 -2nd) | CYP7B1 after the second stage meta-analysis p=7.8 × 10−8 | 8 | |||
| (205) | HIV-1 acquisition | 60 infection resistant | no GW significance | Affymetrix 50K | |
| 48 infected | |||||
| (206) | Development of neutralizing antibodies | 282 infected MSM | no GW significance | Illumina HumanHap300, 370CNV | |
| (207) | HIV-1 acquisition | 431 uninfected hemophiliacs | no GW significance | Illumina 1M, 1M-Duo | |
| 765 infected controls |