Detailed genetic characterization of the psoriasis-associated gene IL23R
S. J. Schrodi1, M. Chang1, V. E. Garcia1, N. Matsunami2, M. F. Leppert1, G. G. Krueger2, A. B. Begovich1
1. Celera, Alameda, CA, USA 2. University of Utah, Salt Lake City, UT, USA
INTRODUCTION
SINGLE SNP ANALYSES
HAPLOTYPE ANALYSES
Figure 2 shows a plot of the allelic association P-values as a function of position for the 61 SNPs selected to interrogate the
IL23R region. Results for the three sample sets are plotted separately. The peak of psoriasis association occurs over the
IL23R coding region.
Figure 2. IL23R Single SNP Analysis: 61 SNPs Genotyped
Figure 6
Using a sliding window of haplotype association on 3 adjacent SNPs, we identified two
neighboring windows composed of rs10789229, rs10889671, rs11209026 and
rs10889674 yielding the peak global association with psoriasis when analyses are
combined across the three independent sample sets (window 1 combined P-value =
1.28E-04 and window 2 combined P-value = 6.42E-05). Both windows were significant
(P<0.05) in each of the three studies. These four SNPs reside within a 12kbp region
within IL23R.
Figure 6. IL23R region sliding window Haplotype association
IL23R Region
3-SNP Windows
10
EXPERIMENTAL DESIGN
25,215 SNPs
Discovery UPI Sample Set
40 Orthogonal Pools (465 cases / 460 controls)
Replication GCI Sample Set
42 Orthogonal Pools (494 cases / 495 controls)
Confirmation: Individual Genotype
C1orf141
IL23R
IL12RB2
Table 1. Genotype frequencies for significantly associated SNPs across sample sets
Figure 1. Physical map of 338kb around IL23R on human chromosome 1
Discovery
Sample Set
dbSNP ID
rs7530511
Gene
IL23R
rs11465804
IL23R
rs10889671
Chr1 (p31.3)
IL23R
rs11209026
IL23R
rs10889674
IL23R
B36 Position
Genes
C1orf141
SERBP1
IL12RB2
IL23R
LD Regions
rs1857292
Genotyped Markers
Frequency in
Cases Controls
Type
Position (kbp) Genotype (n=465) (n=460)
CC
L310P
97.357
0.801
0.723
CT
0.190
0.262
TT
0.009
0.015
TT
Intron
114.496
0.924
0.889
GT
0.074
0.107
GG
0.002
0.004
GG
Intron
117.696
0.805
0.728
AG
0.186
0.259
AA
0.009
0.013
GG
Q381R
117.928
0.918
0.885
AG
0.078
0.111
AA
0.004
0.004
TT
Intron
129.498
0.316
0.370
GT
0.492
0.475
GG
0.192
0.155
AA
3' of IL23R
150.292
0.795
0.736
AT
0.196
0.248
TT
0.009
0.015
Replication
Sample Set 1
Replication
Sample Set 2
Frequency in
Frequency in
Cases Controls Cases Controls
(n=481)
(n=494) (n=495)
(n=424)
0.810
0.788
0.793
0.762
0.180
0.196
0.199
0.214
0.010
0.016
0.008
0.024
0.887
0.846
0.929
0.871
0.109
0.144
0.068
0.124
0.004
0.010
0.002
0.005
0.808
0.788
0.794
0.760
0.180
0.198
0.195
0.214
0.012
0.014
0.010
0.026
0.888
0.832
0.932
0.873
0.105
0.158
0.066
0.122
0.006
0.010
0.002
0.005
0.340
0.362
0.318
0.359
0.454
0.467
0.476
0.472
0.206
0.171
0.206
0.169
0.800
0.762
0.805
0.768
0.190
0.228
0.183
0.204
0.010
0.010
0.012
0.028
Combined
Analysis
Pcomb
0.012572595
0.000415864
0.031240837
0.019748711
LINKAGE DISEQUILIBRIUM
2
Cases and Controls
rs7530511
1
rs11209026
r2
0
61
1
60
Pairwise linkage disequilibrium was calculated across
cases and controls combined as an exploratory analysis
to better understand the detailed structure in the IL23R
region (Abecasis et al, 2000). The correlation statistic r2
was employed. Results are displayed in the Figure 3
heat-map. As much of the association signal was being
driven by rs11209026, we specifically sought to elucidate
the decay of rs11209026-LD in a positional fashion as
shown in Figure 4. Only a single SNP attained a r2 value
greater than 0.20 in our sample sets: rs11465804, located
in an IL23R intron. A genotypic-based squared correlation
coefficient was calculated between the two sites:
Discovery cases g2 = 0.902, Discovery controls g2 = 0.888,
Repl 1 cases g2 = 0.705, Repl 1 controls g2 = 0.870, Repl
2 cases g2 = 0.914, and Repl 2 controls g2 = 0.872. TwoSNP analyses of rs11209026 and rs11465804 appear to
indicate that recombinants between the two SNPs are
reasonably rare in our samples. Figure 5 shows the decay
of statistical association with psoriasis as a function of LD
with Q381R (rs11209026).
Figure 4. LD with rs11209026: 61
follow-up IL23R SNPs genotyped
Table 2. Effect sizes for haplotypes at rs7530511-rs11209026-rs10889674
Discovery
Sample Set
Replication
Sample Set 1
Counts in
0.01667346
Figure 5. Psoriasis association
decay with rs11209026 LD
IL12RB2
SERBP1
150
200
250
300
350
Position (kb)
Table 2
SNPs significantly associated using a Fisher’s combined P-value across all three studies (6
SNPs from Table 1) were examined and partitioned into three groups on the basis of LD
structure and significance.
Group1: rs7530511, rs10889671, rs1857292; Group2:
rs11465804 and rs11209026; Group3: rs10889674. One representative SNP from each
group was used in a haplotype analysis where phase was estimated through a pseudoGibbs sampling algorithm (SNPAnalyzer program). Haplotypes segregating at rs7530511rs11209026-rs10889674 were then evaluated for statistical association. One psoriasispredisposing haplotype (C-G-G), one neutral haplotype (C-G-T) and two protective
haplotypes (T-G-T and C-A-T) were found.
0.000799398
rs7530511 rs11209026
Figure 3. Pairwise LD between the 61 IL23R-region
SNPs as measured by r2 in the cases & controls of
all three sample sets combined
0.01
1
IL23R
C1ORF141
0
50
100
GENOTYPE ANALYSES
SNP SELECTION
We undertook a multifaceted approach to identify SNPs to genotype individually in a fine-scale mapping effort in the
IL23R region. A 336 kbp region was selected across a portion of C1orf141 through SERBP1. SNPs in moderate to
high LD (r2>0.20) with the two originally-identified missense SNPs from Cargill et al (2007), rs7530511 and
rs11209026, were initially selected and reduced so that those pairs within this group in extremely high LD (r2>0.97)
were represented by one or two SNPs. Next, we ran the tagging SNP program Redigo (Hu et al, 2004) to select a
set of tagging SNPs among those in weak LD (r2<0.20) with the original two SNPs. Further, any SNP with putative
function annotation were selected to be genotyped. In all, 61 SNPs were identified to cover the IL23R region.
0.001
0.1
Six individual SNPs with combined P-values below 0.05 are presented in detail showing genotype frequencies in cases and
controls across the three sample sets. Notably, the Q381R SNP (rs11209026) yielded the most significant combined
association results.
Fine-scale mapping
Haplotypes/Diplotypes
Sliding Window Haplotype Association
3-SNP windows
SERBP1
P<0.05
Comb P
< 0.05
Replication #2 GCI/BCW sample set
(481 cases / 424 controls)
-5
0.0001
Global P-Value
Using a multi-tiered, case-control association design, scanning over 25,000 gene-centric SNPs,
we recently identified two psoriasis susceptibility genes: IL12B and IL23R (Cargill et al, 2007).
One of the IL23R missense SNPs implicated in psoriasis has also been strongly associated with
predisposition to inflammatory bowel disease (Duerr et al, 2006; Van Limbergen et al, 2007;
Rioux et al, 2007; Libioulle et al, 2007; Dubinsky et al, 2007). To refine our initial association
results and further investigate the region involved in psoriasis risk, we extended our genetic
analysis by resequencing this gene in 96 psoriatic individuals. Twelve novel IL23R SNPs were
discovered including one missense, two synonymous and three 3’ UTR SNPs. Using a series of
selection criteria, we identified 58 additional IL23R–linked SNPs which were genotyped in our
three independent, white North American sample sets (>2800 individuals in toto). Single marker
and preliminary haplotype analyses have been performed on the full set of interrogated SNPs. A
sliding window of haplotype association demonstrates co-localization of psoriasis susceptibility
within the boundaries of IL23R across all sample sets, thereby decreasing the likelihood that
neighboring genes, particularly IL12RB2 which lies directly adjacent to IL23R, are driving the
association of this region with psoriasis. The refinement of disease association patterns within
IL23R to specific predisposing and protective genetic variants will play an important role in the
elucidation of the causes of psoriasis and possibly additional autoimmune phenotypes as well as
the role of IL23R genetic variants in response to therapy and dosage.
Haplotype
CGG
CGT
TGT
CAT
Others
Cases Controls
(n=465) (n=460) OR
404
385
95
40
0
360
376
133
55
2
1.22
1.04
0.68
0.72
N/A
Counts in
Cases Controls
(n=494) (n=495) OR
425
407
93
56
5
403
390
113
88
0
1.11
1.09
0.81
0.62
N/A
Replication
Sample Set 2
Counts in
Cases Controls
(n=481) (n=424)
424
398
104
34
0
344
338
110
56
0
OR
1.16
1.07
0.82
0.52
N/A
CONCLUSIONS
Fine-scale mapping of the IL23R region across three independent psoriasis case-control
sample sets shows variants segregating at IL23R that are significantly associated with disease.
This observation, in conjunction with many immunology and clinical results in the literature (e.g.
Park et al, 2005; Ivanov et al, 2006; Krueger et al, 2007), substantially aids our understanding
of the role of IL-23 pathobiology underlying chronic inflammatory conditions.
As with several other inflammation disease susceptibility genes exhibiting pleiotropy, variants
at IL23R now appear to confer risk/protection for psoriasis and IBD.
A novel SNP-selection procedure to fine-scale map regions with initial association data is
discussed.
Single marker analysis produces little evidence that the IL23R-neighboring gene IL12RB2
(also a functional candidate) is generating the patterns of psoriasis-association in the region.
Three-SNP haplotype sliding window analysis yields a peak association of 6.42E-05 located
at IL23R with the adjacent SNPs rs10889671-rs11209026-rs10889674.
Additional haplotype analyses with representative SNPs derived from LD groups,
demonstrate that haplotypes segregating at rs7530511-rs11209026-rs10889674 (L310P –
Q381R – putative transcription factor binding site) generate susceptible, neutral and protective
effects with regard to psoriasis.
REFERENCES
C1orf141
IL23R
IL12RB2 SERBP1
Cargill et al (2007) AJHG 80:273-290.
Duerr et al (2006) Science 314:1461-1463.
Van Limbergen (2007) Gut Epub Mar 2.
Rioux et al (2007) Nat Genet 39:596-604.
Libioulle et al (2007) PLoS Genet 3:e58 Epub Apr 20.
Dubinsky et al (2007) Inflamm Bowel Dis 13:511-515.
Hu et al (2004) Hum Hered 57:156-170.
Abecasis et al (2000) Bioinformatics 16:182-183.
Yoo et al (2005) Nucleic Acids Res 33:W483-W488.
Park et al (2005) Nat Immunol 6:1133-1141.
Ivanov et al (2006) Cell 126:1121-1133.
Krueger et al (2007) N Engl J Med 356:580-592.