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. Author manuscript; available in PMC: 2010 Dec 1.
Published in final edited form as: Genes Immun. 2009 Aug 20;10(8):673–677. doi: 10.1038/gene.2009.58

Table 2.

(a) HCP5 and 5′ HLA-C SNP genotype frequency and association between HIV RNA at set point and HLA-B*5701 and C*0602; (b) 5′ HLA-C SNP association with HIV RNA at set point and HLA-B*5701; (c) 5′ HLA-C SNP association with HIV RNA at set point and HCP5

Locus rs number SNP Frequency HIV RNA in plasma at
set point, median and
(IQR)		 Mann–Whitney
U-test P-value		 HLA-B*5701
association of given
SNP allele		 HLA-C*0602
association of
given SNP allele
(a)
HCP5 rs2395029 TTa 0.929 18 010 (4456–41 680) TT vs GT or GG 5 of 916 117 of 916
GTa 0.069 graphic file with name nihms-201076-t0001.jpg 3648 (627–11 701) P=7 × 10−7 64 of 69 61 of 69
GGb 0.002 2 of 2 2 of 2
TTa 0.383 21 980 (5104–49 850) TT vs CT P<0.07 2 of 377 1 of 377
5′ HLA-C rs9264942 CTa 0.482 15 480 (3558–37 050) CT vs CC P<0.03 41 of 475 111 of 475
CCb 0.135 7918 (1060–20 780) CC vs TT P<0.002 28 of 133 68 of 133
(b)
Locus rs number SNP HLA-B*5701
association
(+indicates
heterozygosity)c 		Frequency of genotype,
frequency with
set point 		HIV RNA in plasma
at set point, median
and (IQR) 		Mann–Whitney
U-test P-value
against heterozygous
5′ HLA-C rs9264942 TT + 2, 1 20320 0.298
CTa + 41, 14 4920 (732, 12 430)
CCb + 26, 12 773 (300–7443) 0.167
TT − 375, 137 21 980 (4975, 49820) 0.328
CTa − 434, 182 17 000 (4359, 39700)
CCb − 105, 34 11 430 (4464–32 600) 0.341
(c)
Locus rs number SNP HCP5 SNP
associationd 		Frequency of genotype,
frequency with
set point 		HIV RNA in plasma
at set point, median
and (IQR) 		Mann–Whitney
U-test P-value
against heterozygous
5′ HLA-C rs9264942 TT GT 2, 2 17 110 (15 510–18 710) 0.158
CTa GT 41, 22 4920 (720–11 720)
CCb GT 26, 11 708 (300–5295) 0.057
TT TT 379, 137 23 200 (4975, 49890) 0.258
CTa TT 439, 184 17 000 (4346–39 570)
CCb TT 106, 36 11 430 (4935–29 490) 0.324

Abbreviations: HIV, human immunodeficiency virus; HLA, human leukocyte antigen; IQR, interquartile range; SNP, single nucleotide polymorphism.

a

Major SNP alleles.

b

Minor SNP alleles.

c

Two individuals homozygous for HLA-B*5701 were omitted to avoid confounding.

d

Two patients with HCP5 with GG homozygosity were omitted to avoid confounding.

Note: analysis was carried out without correction for multiple comparisons suggested by previous studies.