Overview

A meta-analysis of 3 genome-wide association studies (GWAS) and 2 independant datasets genetopyed on the Immunochip using a total of 10,588 individuals with Psoriasis and 22,806 controls.  Overall the anlysis included 111,236 SNPs that were genotyped in both Immunochip datasets and had good imputation quality in at least 2 of the 3 GWAS.  The meta-analysis confirmed genome-wide associations (p < 5x10-8) at 19 of the 21 known loci and identified 15 new significant risk loci, bringing the total number to 36 in European individuals.

Pairwise comparison were perfromed using the genome function in PLINK to identify duplicate pairs or highly related individuals among the data sets. Principal component analysis was able to seperate samples by country of origin therefore a a linear mixed-model method (EMMAX) was used for the association analysis.

Imputation on cases and controls was performed using the CEU reference haplotypes to increase the number of overlapping SNPs between the datasets.  SNPs with a low imputation quality (r2 ≤ 0.3 for minimac and info score < 0.5 for IMPUTE2) were removed.

Study Type
Case-Control Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryPSO1058822806--
Exclusion Criteria

Samples were excluded due to :-

  • Low call rate(<98%).
  • Non-European ancestry
  • Exterme inbreeding co-efficients or heterozygosity values computed by PLINK
  • Related sample pairs, most due to duplication

Markers were excluded due to :-

  • Low call rate (<95%).
  • Deviation from Hardy-Weinberg equilibrium in controls (p<1x10-06

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p31.3chr1:67130418-67302310IL23R  rs9988642T > C0.0711.10e-26C1.52D
1p36.11chr1:24134948-24201326IFNLR1  rs7552167G > A0.1428.50e-12C1.2D
1p36.11chr1:24898466-24981785RUNX3  rs7536201C > T0.4942.30e-12C1.13D
1p36.23chr1:8140630-8245971TNFRSF9  SLC45A1  rs11121129G > A0.2871.70e-08C1.13D
1q21.3chr1:152564308-152813337LCE3B  LCE3D  rs6677595T > C0.3602.10e-33C1.27D
2p15chr2:62256286-62420888B3GNT2  rs10865331G > A0.3744.70e-10C1.12D
2p16.1chr2:60694033-61571694LINC01185  REL  rs62149416T > C0.3651.80e-17C1.18D
2q24.2chr2:162136981-162536251KCNH7  IFIH1  rs17716942T > C0.1373.30e-18C1.27D
5q15chr5:96647765-97039314ERAP1  rs27432G > A0.2741.90e-20C1.20D
5q31.1chr5:132447521-132799680IL13  IL4  rs1295685G > A0.2023.40e-10C1.18D
5q33.1chr5:151035777-151110563TNIP1  rs2233278G > C0.0582.20e-42C1.59D
5q33.3chr5:159398209-159480008IL12B  rs12188300A > T0.0953.20e-53C1.58D
6p25.3chr6:496761-661714EXOC2  IRF4  rs9504361A > G0.4542.10e-11C1.12D
6q21chr6:111086030-111648145TRAF3IP2  rs33980500C > T0.0744.20e-45C1.52D
6q23.3chr6:137707015-137957868TNFAIP3  rs582757T > C0.2732.20e-25C1.23D
6q25.3chr6:158907321-159123547TAGAP  rs2451258T > C0.3483.40e-08C1.12D
7p14.1chr7:37319353-37399609ELMO1  rs2700987A > C0.4364.30e-09C1.11D
9p21.1chr9:32425912-32581661DDX58  rs11795343T > C0.4038.40e-11C1.11D
9q31.2chr9:107981292-108105810KLF4  rs10979182A > G0.4092.30e-08C1.12D
10q22.3chr10:79237086-79312766ZMIZ1  rs1250546A > G0.4216.80e-07C1.1D
11q13.1chr11:64077883-64456055RPS6KA4  PRDX5  rs645078A > C0.3912.20e-06C1.09D
11q22.3chr11:110026038-110323530ZC3H12C  rs4561177A > G0.4197.70e-13C1.14D
11q24.3chr11:128502273-128623452ETS1  rs3802826G > A0.4841.00e-09C1.12D
12q13.3chr12:55958153-56408728STAT2  IL23A  rs2066819C > T0.0665.40e-17C1.39D
14q13.2chr14:34900397-35394209NFKBIA  rs8016947G > T0.4362.50e-17C1.16D
16p11.2chr16:30520539-31368034PRSS53  FBXL19  rs12445568T > C0.3681.20e-16C1.16D
16p13.13chr16:11198022-11372654PRM3  SOCS1  rs367569C > T0.2914.90e-08C1.14D
17q11.2chr17:27548316-27947963NOS2  rs28998802G > A0.1453.30e-16C1.22D
17q21.2chr17:42166716-42824441STAT5A  STAT3  PTRF  STAT5B  rs963986G > C0.1545.30e-09C1.15D
17q25.3chr17:80130413-80261661CARD14  rs11652075T > C0.4983.40e-08C1.11D
18q21.2chr18:53952661-54742246MBD2  STARD6  POLI  rs545979C > T0.2913.50e-10C1.12D
19p13.2chr19:10280033-10517872TYK2  rs34536443G > C0.0479.10e-31C1.89D
19p13.2chr19:10523588-11054105ILF3  CARM1  rs892085A > G0.4423.00e-17C1.18D
20q13.13chr20:49792078-50046045RNF114  rs1056198C > T0.4271.50e-14C1.16D
22q11.21chr22:21454896-21649639UBE2L3  rs4821124T > C0.1893.80e-08C1.13D
MHCchr6:31239202-31359557HLA-B  HLA-C  rs4406273G > A0.0920.00e+00C4.32D

Criteria

GDXHsS00016 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date