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. 2006 Mar 31;78(5):827–851. doi: 10.1086/503821

Table 12.

Association of Psoriasis with Haplotypes Carrying a Recombination between the Risk Alleles of HLA-C and CDSN

TDT
 PDT
P
 Power
 P
Recombinant Haplotype
and Test Regiona 		Map Bounds (kb)b Haplotype Frequencyc T:NT (%T)e Uncorrectedf Correctedg Uncorrectedh Correctedi Inline graphicj Uncorrectedf Correctedg Excluded as Risk?d
HLA-Cw6+/CDSN*TTC−:
 CDSN 590.5–595.4 .0056 11:2 (84.6) .023 .076 … … .643 .0042 .014 Yes
 M6S190–M6S224 583.3–658.1 .0049 9:1 (90.0) .022 .071 … … .667 .0074 .029 Yes
 M6S111–M6S224 528.9–658.1 .0028 5:0 (100.0) .033 .19 … … .750 .037 .18 No
HLA-Cw6−/CDSN*TTC+:
 CDSN 590.5–595.4 .0209 15:26 (36.6) .12 .33 .995 .983 −.248 .19 .70 Yes
 CDSN-M6S162 590.5–655.7 .0122 9:18 (33.3) .12 .34 .938 .861 −.295 .22 .77 No
 CDSN-M6S224 590.5–658.1 .0066 5:9 (35.7) .42 .86 .700 .527 −.283 .39 .95 No
 M6S190-CDSN 583.3–595.4 .0199 15:24 (38.5) .20 .52 .994 .980 −.212 .36 .93 Yes
 M6S198-CDSN 566.7–595.4 .0105 8:13 (38.1) .38 .81 .899 .790 −.261 .42 .96 No
 M6S200-CDSN 561.7–595.4 .0063 5:8 (38.5) .58 .95 .677 .498 −.214 .66 1.00 No
 HCR-CDSN 551.1–595.4 .0049 4:7 (36.4) .55 .94 .553 .363 −.250 .62 .97 No
a

Bounds of the test region with use of the markers and genes of figure 2. To be conservative, the smallest possible portion of the extended HLA-Cw6+/CDSN*TTC+ risk haplotype not carried by HLA-Cw6+/CDSN*TTC− recombinant haplotypes and the smallest possible portion of the extended risk haplotype carried by HLA-Cw6−/CDSN*TTC+ recombinant haplotypes were used to determine whether a recombinant haplotype qualified for assessing the exclusion of the test region from the PSORS1 candidate interval.

b

Map bounds refer to the map coordinate system of figure 2.

c

Frequency of HLA-Cw6+/CDSN*TTC− recombinant haplotypes not carrying the test region or the frequency of HLA-Cw6−/CDSN*TTC+ recombinants carrying the test region; results are based on 2,867 founder chromosomes in 678 pedigrees.

d

The test region is considered excluded from the PSORS1 candidate interval if the corrected TDT or PDT P value is <.05 for the positively associated HLA-Cw6+/CDSN*TTC− haplotypes or if the corrected TDT power was at least 95% for the unassociated HLA-Cw6−/CDSN*TTC+ haplotypes.

e

For the biallelic TDT.

f

Nominal P value uncorrected for multiple testing.

g

P value corrected for multiple testing (see the “Subjects and Methods” section for details of correction procedure).

h

Nominal power of the TDT on the basis of a type I error rate of 0.05, an additive model with a GRR2 of 5, and a disease prevalence of 0.02.

i

Corrected power of the TDT based on a type I error rate of 0.016, which ensures an experimentwide type I error rate of 0.05 for all tests in the table, an additive model with a GRR2 of 5, and a disease prevalence of 0.02.

j

Inline graphic is a standardized measure of disequilibrium for the PDT (see the “Subjects and Methods” section).