Table 10.
Association of Psoriasis with Alleles of HLA-C and CDSN
| Gene and Haplotype Number |
Corresponding Allele(s)a | Haplotype Sequenceb | Frequencyc | T:NT (%T)d | TDT Pe | FBAT S*f | FBAT Pe |
| HLA-C: | |||||||
| 1 | *01(0201–04, 06–11), *02(05), *08(12), *12(0301–07, 11–13,15), *14(0202), and *16(01–0401) | GCCTCCG | .1116 | 108:115 (48.4) | .69 | −.020 | .66 |
| 2 | *01(05), *02(0201–04, 06–12), *03(14), *05(01–11), *07(07, 16), *08(0101–11), *12(0201–0203, 08, and 14), *15(0201–14), *16(06–07), and *17(01–03) | GCCACCG | .1814 | 127:190 (40.1) | 4.8 × 10−4 | −.134 | 9.6 × 10−4 |
| 3 | *03(0201–13, 16, and 18–19) | GCCACTG | .1151 | 76:133 (36.4) | 9.8 × 10−5 | −.195 | 1.1 × 10−5 |
| 5 | *03(17), *14(0201, and 0203–07N) | GCCTCTG | .0116 | 10:14 (41.7) | .54 | .115 | .54 |
| 6 | *04(010101–0103, 0401, 05, 08–10, 12–14, and 16–17) | GAAAGTG | .0961 | 84:96 (46.7) | .41 | −.072 | .14 |
| 11 | *06(02–13) | CCATCCG | .2140 | 295:97 (75.3) | 2.5 × 10−24 | .403 | 3.8 × 10−25 |
| 12 | *07(0101–03, 05–06, 08–10, 13–15, and 17–29) | GCAACCG | .2509 | 169:223 (43.1) | .0074 | −.131 | 3.3 × 10−4 |
| 13 | *07(0401–0402 and 11–12) | CCAACCC | .0182 | 17:17 (50.0) | 1.00 | −.007 | .95 |
| 15 | *18(01–02) | CCAAGTG | .0011 | 0:5 (.0) | .50 | … | … |
| CDSN: | |||||||
| 1 | 1.21 | ACG(AAG)TGTCG | .0658 | 88:45 (66.2) | 2.4 × 10−4 | .237 | 8.6 × 10−5 |
| 2 | 2.21–2.25 | ACA(AAG)TATTA | .2216 | 158:201 (44.0) | .027 | −.123 | .0031 |
| 3 | 1.31–1.32 | ATG(AAG)TATCG | .0179 | 23:11 (67.6) | .058 | .281 | .015 |
| 4 | 1.41–1.44 and 1.61 | ACG(AAG)CATCG | .1845 | 131:180 (42.1) | .0064 | −.117 | .0013 |
| 5 | 2.102 | TCG(—)TATTG | .1775 | 141:177 (44.3) | .050 | −.127 | .0049 |
| 6 | 1.51–1.52 | ACG(AAG)TAGCG | .1709 | 131:175 (42.8) | .014 | −.082 | .034 |
| 7 | 1.11–1.14 | ACG(AAG)TATCG | .1485 | 199:77 (72.1) | 1.3 × 10−13 | .336 | 1.6 × 10−15 |
| 8 | 2.101, 2.103–2.104, and 2.107–2.111 | ACG(—)TATTG | .0119 | 10:15 (40.0) | .42 | −.095 | .43 |
| 9 | … | TCG(—)CATTG | .0004 | 0:1 (.00) | 1.00 | … | … |
| 10 | … | ACG(AAG)TGGCG | .0004 | 1:0 (100.0) | 1.00 | … | … |
| 11 | … | TCG(—)TATTA | .0004 | 0:1 (.0) | 1.00 | −.500 | … |
| 12 | … | ATG(AAG)CATCG | .0004 | 1:0 (100.0) | 1.00 | .500 | … |
| 1, 3, and 7 | 1.21, 1.31–1.32, and 1.11–1.14 | AYG(AAG)TRTCG | .2297 | 289:112 (72.1) | 3.9 × 10−19 | .363 | 5.9 × 10−23 |
HLA-C allele designations follow the classification scheme of release 2.10.0 (July 2005) of the IMGT/HLA Sequence Database maintained by the HLA Informatics Group of the Anthony Nolan Research Institute.20 CDSN allele designations follow the classification scheme of Romphruk et al.,71 which is an extension of the system proposed by Guerrin et al.45 and Hui et al.69 Previously unpublished alleles are denoted with ellipses (…).
Haplotype for seven coding SNPs of HLA-C (mRNA positions 213, 218, 341, 361, 387, 459, and 540) and nine missense polymorphisms of CDSN (mRNA positions 52, 166, 428, 447–449, 605, 1201, 1229, and 1579), in 5′→3′ orientation. The TTC signature common to all three CDSN risk haplotypes is shown in bold italics.
Haplotype frequency, based on 2,850 founder chromosomes in 670 pedigrees for HLA-C and 2,856 founder chromosomes in 678 pedigrees for CDSN.
For the biallelic TDT.
All P values are uncorrected for multiple testing. P values for FBAT were computed only when there are at least 10 families informative for the allele.
Modified S statistic for the FBAT (see the “Subjects and Methods” section for details).