Table 2.
Definition of the C21orf91 Haplotypes and Their Possible Effects on Cold Sore Frequency. PLINK Identified 5 Major Haplotypes Among 6 SNPs Spanning the C21orf91 Gene Region.
| Haplotypea | SNP genotypesb (5′ – 3′) | Haplotype frequency in unaffected (N = 186) | Haplotype frequency in frequently affected (N = 188) | Mean cold sore frequencyc (N = 604) | Interpretationd |
| H1 | GCCCTA | 26% | 27% | 1.49 | Neutral |
| H2 | GCCGTG | 36% | 27% | 1.30 | Protected |
| H3 | GCCCTG | 11% | 10% | 1.16 | Neutral |
| H4 | GTGCCA | 21% | 29% | 1.79 | Susceptible |
| H5 | TCCCCA | 0% | 5% | 2.03 | Susceptible |
The frequency of each haplotype among the participants who are “unaffected” (no cold sores) vs “frequently affected” (≥2 cold sores per y) are shown. N refers to the number of haplotypes observed in each group (2 chromosomes, therefore 2 haplotypes per person). Mean annual cold sore frequencies are reported among the 302 herpes simplex virus type 1 seropositive individuals genotyped from the 43 Utah Genetic Reference Project families. Statistical comparison of the mean cold sore frequencies could not be employed because of the relatedness of the participants.
Abbreviations: SNP, single nucleotide polymorphism; H1, haplotype 1; H2, haplotype 2; H3, haplotype 3; H4, haplotype 4; H5, haplotype 5.
Definition of haplotypes: H1 = Ancestral genotype. H2 = D136E (rs1047978) + 3'-Tag SNP (rs243588). H3 = 3'-Tag SNP only (rs243588). H4 = Intron 2 (rs2824499) + N115K (rs2824495) + 3'-UTR (rs1062202). H5 = 5′ of gene (rs10446073) + 3'-UTR (rs1062202).
The following SNPs (5′ – 3′) were used to derive these haplotypes: rs10446073, rs2824499, rs2824495, rs1047978, rs1062202, rs243588. See also Figure 3.
All herpes simplex virus type 1-302 seropositive individuals contributed their reported cold sore frequency twice—once for each haplotype—for calculation of these estimated frequencies.
As defined by the haplotype frequency differences between the unaffected and frequently affected groups.