Supplement to publication:
Sequence and Haplotype Analysis Supports HLA-C as the Psoriasis Susceptibility 1 Gene
Rajan P. Nair, Philip E. Stuart, Ioana Nistor, Ravi Hiremagalore, Nicholas V.C. Chia, Stefan Jenisch, Michael Weichenthal, Gonçalo R. Abecasis, Henry W. Lim, Enno Christophers, John
J.Voorhees, and James T. ElderAmerican Journal of Human Genetics 78:827-851, 2006.
PSORS1 haplotype clusters: consensus alleles and family-based tests of association with psoriasis
ALLELE AT
New
Old
clustera Clusterb Freqc
D
6
S
2
7
3
M
6
S
1
2
4
7
T
N
F
B
M
6
S
1
2
5
M
6
M S
I 1
C 6
A 6
H
L
A
B
M
6
S
1
0
1
M
6
S
1
5
1
H
L
A
C
M
6
S
1
6
7
M M M M M M M M M M M M M
M M M M M M M M M M M M
6 6 6 6 6 6 6 6 6 6 6 6 6
6 6 6 6 6 6 6 6 6 6 6 6
S S S S S S S S S S S S S C S S S S S S S S S S S S
1 1 1 1 1 1 1 1 1 1 2 1 1 D 1 1 1 1 2 1 1 1 1 1 1 2
0 6 7 0 7 7 4 4 1 6 0 9 9 S 6 6 5 6 2 7 8 8 6 6 6 0
5 8 8 2 2 6 5 3 1 9 0 8 0 N 1 0 9 2 4 9 1 7 4 3 5 1
4
6
T:NT (% T)d
TDT Pe
PDT D f
Number
inform.
pedigrees
for PDTg
PDT Ph
1
61
.0059
2
3
2
3
65
2
8
8
8 13 1
1
1
3
1
1
5
2
5
4
4
5 15 6
4 17 13
1
2
6
6 13 8
–
4:8 (33.3)
.39
–.377
14
.15
2
60
.0030
6 13 13 4
4
1
52 13 2
12
6
4
1
5
1
6
2
1
1
8
2
2
4
4
8 12 4
4 19 19
1
2
7
6 14 8
5
2:3 (40.0)
1.00
–.167
6
—
3
—
.0026
7 14 13 4
4
1
52 13 2
12
8
4
1
5
1
6
2
1
1
7
2
2
4
4
8 12 4
4 19 –
1
2
7
6 13 8 10
4:2 (66.7)
.69
.036
7
—
4
59
.0044
5
5
4 11 51 10 2
14 20 4
2
5
64
.0104
5
9 10 10 1 12 18 14 3
6
65
.0063
6 10 13 4
5
3
7
66
.0219
5 10 10 17 5
3
8
57
.0033
3
5
7 14 4
1
–
–
9
—
.0022
6
6
4
4
3 14 44
5
10
62
.0078
6
6
4
4
3
44
11
63
.0256
5 10 6
3
3 15 44
12
42
.0022
6
6
4
4
3 15 44
13
38
.0074
5
5
6
3
1
7
14
37
.0030
5
–
6
3
1
7
27 15 2
15
39
.0163
5
5 11 14 4 11 51
8
2
16
40
.0052
6 10 2 14 4 11 51
8
2
17
41
.0026
6 10 2 10 4 11 nd 6
18
27
.0081
6
4
4
3 15 44
2 704 8
19
35
.0067
5 10 6
4
2 11 35 13 2
4
20
34
.0019
5 10 6
3
4 11 nd 14 2
4
21
33
.0026
4
6
6
3
4 11 35 15 2
4
22
30
.0167
5
6
5 12 5 13 35 19 2
23
31
.0093
6 11 2 10 5 14 35 17 2
24
32
.0081
6 11 2
25
—
.0019
5
5 13 4
26
—
.0022
2
7
6
6
4
4
6
1
3
1
1
6
2
5
4
5
6 12 8
4 22 –
1
2
4
3
6
1 10
3:4 (42.9)
1.00
–.167
9
—
12
2
3 13 7
2
3
1
2
5
9
5
5
3
9
6 18 9
4 14 10
1
2
6
3
8
3 11
8:10 (44.4)
.82
–.106
22
.58
39 14 3
12
2
3 12 7
2
3
1
2
6
9
5
5
3
8
6 17 8
4 16 –
1
2
6
3
8
3
–
7:9 (43.8)
.80
–.063
16
.77
38 14 3
12
2
3 12 7
2
3
1
2
6
9
5
5
3
8
6 21 8
4 16 8
1
2
6
3
6
8
–
24:25 (49.0)
1.00
–.060
50
.95
3 ≠6 1
8
4
6
3
1
1
1
2
4
5
4
7
5 16 11 4
1 24
1
2
6
1
4
4
–
2:3 (40.0)
1.00
–.133
6
—
2
5
8
3 13 7
3
3
1
1
1
2
4
5
4
8
5 15 11 4
1 27
1
2
7
3
6
1 12
2:2 (50.0)
1.00
.188
4
—
5
2
5
8
3 13 7
3
3
1
1
1
2
4
5
4
8
5 14 –
4
1
–
1
2
6
3
6
–
–
9:11 (45.0)
.82
–.035
19
.64
4
2
5
10 3 13 7
3
3
1
1
1
2
4
5
4
8
5 14 13 4
1
–
1
2
4
3
6
1
–
18:35 (34.0)
.027
–.265
57
.085
5
2
5
16 3
1
4
6
4
1
2
2
4
2
6
3
7
6 15 8
1 13
1
1
8
4
8
3 11
1:2 (33.3)
1.00
–.167
4
—
27 15 2
1
12 3
1
3
6
4
1
2
2
4
2
6
3
7
6 13 10 4
1
–
1
1
8
3
6
1 10
9:5 (64.3)
.42
.289
16
.43
1
12 3
1
3
6
2
1
2
2
4
2
6
3
7
6 13 11 4
1 13
1
1
7
7 13 8 13
3:2 (60.0)
1.00
.167
7
—
15 12 3
1
3
6
4
1
2
2
5
2
6
3
4
6 13 8
4
1 13
1
1
9
3
6
1 13
2:6 (25.0)
.29
–.500
8
—
15 10 3
1
3
6
4
1
2
2
5
2
6
3
7
6 13 8
4
1 13
1
1
8
3
6
1
8
2:5 (28.6)
.45
–.447
12
.069
2 ≠6 10 3
1
3
6
4
1
2
2
4
2
6
3
7
6 13 8
4
1
5
1
2
4
9 11 7
–
1:4 (20.0)
.38
–.429
7
—
3
1
3
6
4
1
2
2
7
2
5
3
4
6 17 10 1 14 –
1
2
7
6 14 1
–
7:9 (43.8)
.80
–.098
18
.82
12 3
1
3
6
5
2
2
2
2
4
4
3
6
2 15 8
4
1 25
1
1
8
3
6
1
–
5:9 (35.7)
.42
–.278
18
.20
10 3
1
3
6
5
2
2
2
2
4
4
3
6
2 13 10 4
1 16
1
1
9
3
6
8
9
2:0 (100.0)
.50
.000
4
—
10 3
1
3
6
5
2
2
2
2
4
4
3
6
2 15 10 4
1 19
1
1
6
6 13 8
5
3:3 (50.0)
1.00
–.286
7
—
4
10 3
1
3
6
5
2
2
2
2
4
4
3
6
2 15 8
4
1 19
1
1
6
3
6
1 10
11:18 (37.9)
.27
–.290
33
.11
4
10 3
1
3
6
5
2
2
2
2
4
4
3
7
2 17 9
4
1 19
1
1
8
3
6
1 13
11:7 (61.1)
.27
.121
22
.77
5 13 35 16 2
4
10 3
1
3
6
5
2
2
2
2
4
4
3
6
2 15 9
4
1 19
1
1
7
3
6
1 13
8:9 (47.1)
1.00
.000
19
1.00
2
1 nd 12 2
4
6
3
1
3
6
5
2
2
2
2
4
4
3
5
2
4
1 16
1
2
9
3
5
4 10
2:2 (50.0)
1.00
.250
4
—
5 19 2 12 nd 12 2
4
4
3
1
3
6
5
2
2
2
2
4
4
3
6
2 13 10 4
1 13
1
2
6
3
5
3
2:1 (66.7)
1.00
.667
3
—
9
–
9
1
–
8
4
5
27
36
.0056
5 10 5 17 2 12 35 12 2
6
3
1
3
6
5
2
2
2
2
4
4
3
7
2 13 13 4
1 19
1
2
7
6 13 8
–
3:7 (30.0)
.34
–.361
13
.24
28
—
.0026
4
–
7
3
4
1 nd 18 3 ≠6 1
8
1
4
6
4
1
2
2
7
2
5
3
1
7 12 –
4 14 –
2
2
8
7
9
2
6
2:2 (50.0)
1.00
–.200
5
—
29
58
.0133
4
5
7
7
4
5
44 11 2
4
8
8
1
3
6
5
2
1
1
4
4
6
4
6
6
7
8
4 16 18
1
2
5
3
6
3 15
10:15 (40.0)
.42
–.205
29
.24
30
4
.0022
3 10 11 3
1 12 18 15 4
7
12 11 13 1
2
6
2
1
1
5
2
6
4
5
6
7
8
4 20 –
1
2
6
3
7
4 10
3:1 (75.0)
1.00
.250
4
—
31
5
.0078
5 10 10 17 1 12 18 16 3
7
12 11 14 1
2
5
2
1
1
5
2
6
4
8
6 13 9
4
2
–
1
2
6
3
6
1 13
4:10 (28.9)
.18
–.423
14
.10
32
2
.0019
3
6 10 13 4
5 nd 19 3
7
3 11
8
1
2
4
2
2
2
2
4
6
4
7
4
2
2
2
4 21
1
2
7
3
8
3
9
4:1 (80.0)
.38
.600
5
—
33
1
.0063
6
–
–
–
4
5 nd 17 3
7
3 11
8
1
2
4
2
2
2
2
4
6
4
8
4
2
2
2
4 21
1
2
7
3
8
3
9
3:11 (21.4)
.057
–.600
16
.037
34
3
.0059
3
5
1
3
1
1
18
5
2
5
4 10
8
1
2
4
2
2
2
2
4
6
4 10
6 16 10 4 13 10
1
2
9
4
6
5
2
5:7 (41.7)
.77
–.115
13
.63
35
16
.0037
5
5
6
6
5
3
39
7
3 702 3
5 15 5
1
3
3
1
1
4
4
6
3
6
2 15 10 4
1 16
1
1
8
3
5
4
–
6:3 (66.7)
.51
.222
9
.34
36
–
.0019
4
– 11 6
3
5
7
9
3 702 1
7 15 5
1
3
3
1
1
4
4
6
3
2
2
2
2
2
4 26
2
2
6
3
–
4 10
2:3 (40.0)
1.00
–.400
5
.53
37
14
.0926
6
6 11 6
3
5
7
9
3 702 1
7
–
5
1
3
3
1
1
4
4
6
3
2
2
2
2
2
4 23
2
2
5
3
5
3
5
66:104 (38.8)
.0044
–.228
171
3.0 × 10-4
38
13
.0056
– 10 –
–
3
5 nd 9
3 702 1
7
–
5
1
3
3
1
1
4
4
6
3
2
2
2
2
2
4 23
2
2
5
3
5
3
5
5:5 (50.0)
1.00
.091
12
.85
39
15
.0041
4
5 11 6
5
3
39
3 702 2
40
18
.0048
5 10 11 6
4
8
45 16 3
6
41
19
.0141
2
4
6
42
—
.0019
6 13 2 12 5
43
23
.0204
6
44
24+25
.0881
6 13 2 12 5
9
57 15 3
45
—
.0026
6 13 2 12 5
9
46
20
.0022
4 14 10 8
6
6
5
9
3
9
7
4
5
–
5
1
3
3
1
1
4
4
6
3
2
2
2
2
2
4 23
2
2
4
6 13 4 10
6:2 (75.0)
.29
.563
8
—
17 3
2
3
6
1
3
1
1
4
4
6
4
3
7
2
2
2
4
20 1
2
6
6 13 3
–
5:2 (71.4)
.45
.476
7
—
50 16 3
6
9
3
2
3
6
1
3
1
1
9
3
4
3
1
3
2
2
2
4
8
2
1
4
3
3
9
20:8 (71.4)
.036
.427
32
.027
9 nd 18 3
7
13 3
4
3
6
1
3
1
1
9
2
4
3
6
5
2
2
2
4 16
2
1
6
6 13 8
5
2:3 (40.0)
1.00
–.200
5
—
3 10 37 15 3
6
13 3
2
3
6
1
3
1
1
8
2
4
3
1
7
2
2
2
4
26 1
2
4
6 13 8
5
28:12 (70.0)
.017
.348
44
.010
6
13 3
2
3
6
1
3
1
1
8
2
4
3
1
7
2
2
2
4
20 1
2
4
6 13 8
5
138:38 (78.4)
1.6 × 10-14
.574
173
1.7 × 10-15
57 15 3
6
13 3
2
3
6
1
3
1
1
8
2
4
3
1
7
2
1
2
4
1
1
2
7
3
6
3 16
4:1 (80.0)
.38
.400
7
—
3 13 nd 15 3
6
17 3
2
3
6
1
3
1
1
9
2
4
3
1
7
2
2
2
4
13 1
2
6
4
7
6
3:2 (60.0)
1.00
.333
6
—
.406
122
.45
–.250
8
—
5
47
21+22
.0615
3
6
7
7
3
5
13 16 3
6
15 3
2
3
6
1
3
1
1
2
4
3
1
1
2
2
2
4
16 1
2
7
9
9
3
3
84:37 (69.4)
48
—
.0030
2
5
2
3
4
3
65
5
2
8
15 3
5
3
6
1
3
1
1 12 2
4
3
6
5
2
1
2
4
1
1
2
7
3
6
3 16
2:5 (28.6)
49
26
.0904
8
4
2 16 3 12
8
7
3 701 15 3
2
1
2
4
50
—
.0019
4
6
6
4
5 11 nd 11 2
51
17
.0189
4
6
2
3
4
3
65
5
52
28
.0026
6
– 11 19 3
4
7
53
55
.0022
4
5
1
62
54
29
.0026
6 10 4
4
3 15 44
55
43
.0019
4
5
3
2
56
45
.0093
5
5 11 8
57
44
.0148
3
5
58
—
.0022
5 10 6
3
3 13 60 12 2 304 15 3
59
46
.0019
4
3
3 12 62 14 2
60
47+48
.0252
6 10 2 10 2
61
53
.0022
4 15 10 6
1 10 nd 9
2
62
54
.0085
4
– 10 6
1 10 55
9
63
—
.0026
4 15 10 6
1 10 55
9
2 303 –
64
52
.0096
5
5
6
3
2
1
62
9
65
49
.0033
5
–
6
3
3
1
62
9
2 303 13 3
5
2 10 2
6
9
5
2.3 × 10
-5
6.6 × 10-7
5
3
6
1
3
1
1 10 2
4
3
6
5
1
1
2
7
3
6
3 16
69:80 (46.3)
.41
–.073
161
.30
4
12 3
1
3
6
1
3
1
1
5
2
2
2
6
4 14 10 4 14 –
1
2
7
5
5
3 10
3:1 (75.0)
1.00
.200
5
—
2
8
13 3
2
3
6
1
3
1
1
9
2
4
3
8
4
3 10 4 16 –
1
2
6
4
6
2 21
26:13 (65.0)
.053
.268
43
.0048
10 2
15
8
3
1
3
6
5
1
1
2
5
2
5
3
5
6
2
2
2
4 23
2
2
4
7
9
3
–
2:4 (33.3)
.69
–.306
6
—
9
2 303 –
3
9
7
6
6
2
2
2
8
2
5
3
7
4
2
2
2
4 14
2
1
6
6 13 8
6
3:3 (50.0)
1.00
–.037
6
—
8
2 704 8
3
1
3
6
4
1
2
2
8
2
5
3
7
4
2
2
2
4 14
2
1
6
4
8
3
–
1:3 (25.0)
.63
.000
6
—
1 nd 16 2 ≠6 15 3
5
2
6
1
3
2
4
2
1
5
3
7
4
2
2
2
4
9
2
1
6
3
6
1
–
4:0 (100.0)
.13
.800
5
—
3 12 60 12 2 304 15 3
7
6
6
2
2
2
4
2
1
6
3
9
4
2
2
2
4 11
2
1
6
3
6
4
–
3:13 (18.8)
.021
–.571
20
.011
4 16 3 13 60 12 2 304 15 3
7
6
6
5
2
2
4
2
1
6
3
8
4
2
3
2
4 11
2
1
6
3
8
4
9
6:19 (24.0)
.015
–.435
27
.015
8
6
6
5
2
2
4
2
1
6
3
8
4
2
2
2
4 11
2
1
7
3
6
7 13
2:3 (40.0)
1.00
–.333
6
—
15 3
8
6
6
5
2
2
4
2
1
6
3
–
4
2
2
2
4 11
2
1
6
3
6
4
–
3:1 (75.0)
.63
.600
5
—
62 14 2 304 15 3
8
6
6
5
2
2
4
2
1
6
3
8
4
2
2
2
4 11
2
1
6
3
6
4 11
20:33 (37.7)
.098
–.244
56
.032
13 3
9
7
6
7
2
2
4
2
1
6
3
8
4
2
2
2
4 11
2
1
8
6 13 1
5
3:2 (60.0)
1.00
.000
6
—
2 303 13 3
9
7
6
7
2
2
4
2
1
6
3
8
4
2
2
2
4 11
2
1
8
3
6
2
–
11:10 (52.4)
1.00
.024
22
.64
9
7
6
–
2
2
4
2
1
6
3
8
4
2
2
2
4 11
2
1
7
3
6
7
6
2:3 (40.0)
1.00
–.467
5
—
2 303 13 3 11 7
6
7
2
2
4
2
1
6
3
2
2
2
2
2
4 17
2
1
6
3
6
8
–
9:10 (47.4)
1.00
–.053
19
.36
6
7
2
2
4
2
1
6
3
2
2
2
2
2
4
1
2
6
3
6
3
–
3:6 (33.3)
.51
–.370
9
—
6
1
3
3
3
9
7
–
66
50
.0059
4
2 10 2
1
62
9
2 303 13 3
9
7
6
7
2
2
4
2
1
6
3
2
2
2
2
2
4
–
1
2
6
3
3
6
2:10 (16.7)
.039
–.594
15
.020
67
51
.0026
5 10 2 10 2
5
1
62
9
2 303 13 3
9
7
6
7
2
2
4
2
1
6
3
2
2
2
2
2
4 23
2
2
4
6 13 –
–
2:2 (50.0)
1.00
.000
4
—
68
56
.0204
4
7
4
5
44
3
2
16 15 3
9
6
6
5
2
2
4
2
1
5
3
6
4
2
1
2
3 20
2
1
6
4
3
3
5
21:27 (43.8)
.47
–.119
51
.53
69
11
.0041
5 10 10 4
2
8 nd 1
3
2
8
3
6
4
3
5
2
1
1
5
2
2
2
7
4
2
2
2
4 17
2
1
5
6
6
1
–
2:6 (25.0)
.29
–.500
8
—
70
10
.0044
5
3
1
7
27
1
3
2
8
3
6
4
3
5
2
1
1
5
2
2
2
6
4
2
2
2
4 17
2
1
6
3
6
1
5
6:4 (60.0)
.75
.200
11
.24
71
8
.0041
5 10 10 3
1
7
27
1
3
2
6
3
4
4
3
5
2
1
1
5
2
2
2
–
4
2
2
2
4 14
2
1
6
3
6
1 11
3:4 (42.9)
1.00
–.111
9
—
72
9
.0022
5 10 10 6
3 15 nd 1
3 ≠6 6
3
4
5
3
5
2
1
1
5
2
2
2
9
4
2
2
2
4 14
2
1
6
3
6
1
–
0:5 (0.00)
.063
–1.000
5
—
73
7
.0030
6
1
1
3
2
8
3
6
4
3
4
2
1
1
5
2
2
2
7
6 13 10 4
1 13
1
1
8
3
6
1 10
4:3 (57.1 )
1.00
.143
7
—
74
12
.0037
5 10 10 3
4 11 nd 1
3
2
8
3
6
4
3
5
2
1
1
2
1
6
3
2
2
2
2
2
4 26
2
2
4
3
6
1 11
6:1 (85.7)
.13
.500
8
—
75
6
.0030
7
3
63 15 3
7
10 2
8
1
2
5
2
1
1 10 2
4
3
5
5
2
2
2
4 14
2
1
6
3
6
3
5:2 (71.4)
.45
.429
7
—
5
5
5
7
6
9
3
8 10 9
7
1
27
6
5
NOTE—The table displays all 36 markers subjected to haplotype clustering, along with HLA-B, in centromeric to telomeric order from left to right. Dashes (–) indicate that no allele occurred
in at least 50% of the founder haplotypes comprising the cluster. Italicized numbers indicate that the allele shown occurred in between 50 to 80% of the founder haplotypes comprising the
cluster. Non-italicized numbers indicate that the allele shown occurred in at least 80% of the founder haplotypes comprising the cluster. The symbol ‘nd’ denotes no data. Alleles at the three
gene loci (HLA-B, HLA-C, and CDSN) are shown in boldface type. Alleles are shaded when they differ among HLA-Cw6 haplotypes for a marker or gene but are not indicative of a
significant difference in the underlying sequence of the region. The dashed boxes shows the minimum region of conserved or shaded marker alleles shared in common by all HLA-Cw6
haplotypes.
a
Cluster numbers for current 36-marker clustering of haplotypes of 2700 founder chromosomes in 620 pedigrees are shown. All clusters with a frequency of at least 0.2% (5 occurrences) are
shown.
b
Cluster numbers for previous 34-marker clustering of haplotypes of 2156 founder chromosomes in 491 pedigrees (Nair et al., 2000, AJHG 66:1833-1844), which represent a subset of the
pedigrees and founders used for this table.
c
Frequency of haplotypes in cluster.
d
Ratio of transmissions (T) to nontransmissions (NT) and percent transmission (% T) of the haplotye cluster for the biallelic TDT.
e
Uncorrected exact binomial p-value for TDT.
f
The number of families that are informative for the haplotype cluster being tested by the PDT.
g
D is a standardized measure of disequilibrium for the PDT with a range of [-1.00,1.00].
h
Uncorrected p-value for the PDT-avg test using all trios and discordant sibpairs.