Table 1. Candidate study of previously reported variants associated with HIV-1 susceptibility.
Column 1) Reported candidate gene; Column 2) The identical candidate SNPs originally identified and available after passing QC on the 1M-Duo chip; Column 3) The identical candidate SNPs originally identified and available via a proxy found on the 1M-Duo chip; Column 4) The proxy SNP and the corresponding r2 value as identified in the YRI population for the candidate SNP identified in column 3; Column 5) the lowest p-value for the SNPs identified in Column 2, or Column 4, if a proxy SNP; Column 6) the lowest p-value for SNPs linked to the candidate gene; Column 7) The number of SNPs tested in each candidate gene; Column 8) gene-wide corrected p-value for the lowest p-value identified within the candidate gene; Column 9) set-wide corrected p-value for the lowest p-value identified per candidate gene and corrected for all candidate genes investigated; Column 10) genome-wide corrected p-value for the lowest p-value identified per candidate gene; and Column 11) Studies reporting corresponding candidate SNPs and genes
| Gene | previously associated SNPs | previously associated SNPs represented by an LD proxy | Closest proxy (r2 in YRI) | SNP replication P | lowest P in gene | Number of SNPs tested in gene | Gene-Wide correction | Set-wide correction | Genome- wide correction | Reference |
|---|---|---|---|---|---|---|---|---|---|---|
| ABCB1 | rs1045642 | 0.87 | 0.004 | 105 | 0.42 | 1 | 1 | Fellay Jet al.,2002; Lancet, 359:30–36 | ||
| APOBEC3G | 0.26 | 4 | 1 | 1 | 1 | Valcke et al., 2006; AIDS, 20:1984–1986 | ||||
| CCL2 | rs1024610 rs1024611 |
0.54 | 0.0008 | 175 | 0.14 | 0.96 | 1 | Modi et al., 2003; AIDS, 17:2357–2365 | ||
| CCL3 | rs1719134 | rs1719126 (0.43) | 0.41 | 0.1 | 3 | 0.3 | 1 | 1 | Gonzalez et al., 2001; Proc Natl Acad Sci USA, 98: 5199–5204 | |
| CCL4 | 0.15 | 6 | 0.9 | 1 | 1 | Colobran et al., 2005; J Immunol, 174:5655–5664 | ||||
| CCL5 | rs2107538 rs2280789 |
0.68 | 0.04 | 10 | 0.4 | 1 | 1 | McDermott et al., 2000; AIDS, 14:2671–2678 Gonzalez et al., 2001; Proc Natl Acad Sci USA, 98: 5199–5204 An et al., 2002; Proc Natl Acad Sci USA, 99:10002–10007 Fernandez et al., 2003; AIDS Res Hum Retroviruses, 19: 349–352 Liu et al., 2004; J Infect Dis, 190:1055–1058 |
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| CCL7 | 0.11 | 3 | 0.33 | 1 | 1 | Modi et al., 2003; AIDS, 17:2357–2365 | ||||
| CCL11 | 0.2 | 13 | 1 | 1 | 1 | Modi et al., 2003; AIDS, 17:2357–2365 | ||||
| CCR5 | 0.19 | 3 | 1 | 1 | 1 | [3] Dean et al., 1996 [4] Samson et al., 1996 Huang et al.,1996; Nat Med, 2:1240–1243 |
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| CD209 | 0.07 | 19 | 1 | 1 | 1 | Martin et al., 2004; J Virol, 78:14053–14056 | ||||
| CD4 | rs28919570 | 0.21 | 0.007 | 33 | 0.23 | 1 | 1 | Oyugi et al, 2009; J Infect Dis, 199:1327–1334 | ||
| CX3CR1 | rs3732378 rs3732379 |
0.56 | 0.03 | 32 | 0.96 | 1 | 1 | Faure et al., 2000; Science, 287:2274–2277 | ||
| CXCL12 | rs1801157 | rs10900029 (0.22) | 0.8 | 7.07E-05 | 179 | 0.01 | 0.08 | 0.6 | [15] Petersen et al., 2005 Modi et al., 2005; Genes Immun, 6:691–698 |
|
| DARC | rs2814778 | 1 | 0.1 | 8 | 0.8 | 1 | 1 | He et al., 2008; Cell Host Microbe, 4:52–62 | ||
| DEFB1 | 0.03 | 51 | 1 | 1 | 1 | Braida et al., 2004; AIDS, 18:1598–1600 Milanese et al., 2006, AIDS, 20:1673–1675 |
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| IL10 | rs1800872 rs1800896 |
0.2 | 0.007 | 18 | 0.13 | 1 | 1 | Shin et al., 2000; Proc Natl Acad Sci USA, 97:14467–144721 Naicker et al,2009; J Infect Dis, 200:448–452 |
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| IL18 | rs1946518 | 0.004 | 0.004 | 17 | 0.07 | 1 | 1 | [14] Segat et al., 2006 | ||
| IRF1 | rs17848424 | 0.34 | 0.34 | 12 | 1 | 1 | 1 | Ball et al., 2007; AIDS, 21:1091–1101 | ||
| MBL2 | rs5030737 rs1800450 rs1800451 |
0.45 | 0.001 | 297 | 0.3 | 1 | 1 | Garred et al., 1997; Scand J Immunol, 46:204–208 Pastinen et al., 1998; AIDS Res Hum Retroviruses, 14:695–698 Boniotto et al., 2003; AIDS, 17:779–780 Vallinoto et al., 2005; Mol Immunol, 43:1358–1362 |
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| PPIA | 0.03 | 9 | 0.27 | 1 | 1 | An et al., 2007; PLoS Pathog, 3:e88 Rits et al., 2008; PLoS One, 3:e3975 |
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| PTPRC | 0.03 | 188 | 1 | 1 | 1 | Tchilian et al, 2001; AIDS, 15:1892–1894 | ||||
| TRIM5 | rs3740996 | rs10838525 | rs10769175 (0.19) | 0.67 | 0.005 | 23 | 0.12 | 1 | 1 | Javanbakht et al, 2006; Virology, 354:15–27 |