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. Author manuscript; available in PMC: 2013 Aug 19.
Published in final edited form as: Ann Intern Med. 2013 Feb 19;158(4):235–245. doi: 10.7326/0003-4819-158-4-201302190-00003

Table 1.

Genome-wide association study (GWAS) results and meta-analysis for HCV spontaneous clearance and persistence a) Original GWAS results and meta-analysis b) Replication association results and replication meta-analysis. Ancestry determined by self report in replication cohort which did not undergo GWAS only specific allele testing. OR is the per allele odds ratio. An OR <1 means the SNP is associated with persistence, and OR >1 means the SNP is associated with clearance. MAF is the minor allele frequency. Chromosome 19 SNPs were not included in this replication because the findings in IL28b have previously been reported. All replication SNPs can be seen in Appendix Table 6.

a.
SNP Chr Position European Ancestry (N=1,581) African Ancestry (N=447) Mixed/Other Ancestry (N=373) Meta-Analysis
MAF OR P MAF OR P MAF OR P OR P
rs12979860 19 39738787 0.31(T) 0.45 1.90E-18 0.45 (C) 1.841 1.26E-05 0.34 (T) 0.29 6.81E-11 0.45 2.17E-30
rs12980275 19 39731783 0.31 (G) 0.46 3.45E-18 0.50 (G) 0.58 8.43E-05 0.32 (G) 0.31 2.82E-10 0.46 1.32E-28
rs11881222 19 39734923 0.29 (G) 0.46 2.83E-17 0.30 (G) 0.63 2.54E-03 0.28 (G) 0.29 5.41E-10 0.46 1.07E-25
rs8099917 19 39743165 0.19 (C) 0.40 6.30E-17 0.06 (C) 0.70 2.71E-01 0.19 (C) 0.29 7.49E-08 0.40 1.90E-22
rs4273729 6 32678597 0.39 (C) 0.61 3.42E-10 0.42 (C) 0.55 3.37E-05 0.34 (C) 0.56 5.76E-04 0.59 1.71E-16
rs2647051 6 32670897 0.36 (A) 0.60 2.12E-10 0.34 (A) 0.56 1.57E-04 0.26 (A) 0.54 7.37E-04 0.59 5.35E-16
rs9275224 6 32659878 0.47 (A) 0.63 4.82E-10 0.46 (A) 0.72 1.71E-02 0.39 (A) 0.57 4.24E-04 0.64 9.46E-14
rs2395522 6 32664722 0.47 (T) 0.63 5.59E-10 0.46 (T) 0.73 2.01E-02 0.39 (T) 0.57 3.63E-04 0.64 1.22E-13
rs9469220 6 32658310 0.46 (G) 0.63 9.35E-10 0.42 (G) 0.58 1.60E-04 0.43 (G) 0.73 3.75E-02 0.63 1.30E-13
b.
SNP Chr Position European Ancestry (N=292) African Ancestry (N=284) Egyptian Ancestry (N=169) Meta-analysis I2 I2 P
MAF OR P MAF OR P MAF OR P OR P
rs4273729 6 32678597 0.40 (C) 0.85 0.337 0.44(C) 0.61 0.006 0.39 (C) 0.92 0.693 0.77 0.015 23.2 0.27
rs2647051 6 32670897 0.38 (T) 0.89 0.501 0.35 (T) 0.58 0.007 0.37 (T) 0.87 0.524 0.77 0.022 29.5 0.24
rs9275224 6 32659878 0.48 (A) 0.88 0.464 0.46 (A) 0.59 0.005 0.49 (G) 1.27 0.260 0.75 0.007 24.6 0.27
rs2395522 6 32664722 0.48 (T) 0.88 0.464 0.47 (T) 0.61 0.007 0.48 (A) 1.39 0.112 0.74 0.004 5.79 0.35
rs9469220 6 32658310 0.48 (G) 0.75 0.111 0.43 (G) 0.71 0.071 0.50 (G) 0.82 0.338 0.75 0.011 0 0.88
1

In African Americans the C alleles in the minor allele; the allele frequency for the T allele is 0.54 and the per-allele OR for the T allele is 0.54. I2 is a meta-analysis heterogeneity factor and I2P is the associated p-value