Overview

A genome-wide association study (GWAS) comprising 2,178 affected individuals (cases) and 5,175 controls of self-reported European ancestry, post QC. Individuals with psoriasis (cases) were genotyped on the Illumina Human660W-Quad, and controls were genotyped on the Illumina custom Human1.2M-Duo. Imputation was performed using IMPUTE2. GENECLUSTER was used to investigate possible secondary signals within GWAS associated regions

Of the 9 previously reported loci, 3 reached genome-wide significance in the discovery part of this study. Sixteen previously unreported regions were identified and taken forward for replication with the most strongly associated SNP for each loci being genotyped using the Sequenom iPlex platform. The replication datasets were obtained from across Europe, incorporating 3,174 cases and 5,464 controls. This identified 8 new significant loci of which 6 reached genome-wide significance (P<5x10-8), with multiple signals being detected in 2 of those regions.

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryPSO21785175--
ReplicationPSO31745464--
Exclusion Criteria

Samples

  • Reported gender and genotyping gender mismatch
  • Call rate & Heterozygosity QC
  • Relatedness > 5% identity by descent (IBD)

SNPs

  • MAF < 0.0001
  • HWE deviation P < 1 x 10-20

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p31.3chr1:67128876-67302310IL23R  rs11209026G > A0.0707.13e-07D1.49 (1.75-1.27)D
1p36.11chr1:24144798-24201903IFNLR1  rs4649203A > G0.2706.89e-08C1.22 (1.12-1.32)D
1q21.3chr1:152564308-152813337LCE3D  rs4112788C > T0.4303.32e-10D1.28 (1.41-1.19)D
2p16.1chr2:60694033-61571694REL  rs702873C > T0.4403.59e-09C1.23 (1.14-1.32)D
2q24.2chr2:162136981-162536251IFIH1  rs17716942T > C0.1401.06e-13C1.39 (1.23-1.54)D
3p24.3chr3:18566300-18815368rs6809854A > G0.1901.12e-07C1.24 (1.14-1.36)D
5q15chr5:96639288-97038254ERAP1  rs27524G > A0.3602.56e-11C1.27 (1.18-1.38)D
5q31.1chr5:132444463-132796955IL13  rs20541G > A0.2102.32e-02D1.12 (1.02-1.23)D
5q33.1chr5:151049891-151115398TNIP1  rs1024995T > C3.92e-05D 
5q33.3chr5:159088191-159399302IL12B  rs3213094C > T4.93e-11D 
6q21chr6:111072574-111647042TRAF3IP2  rs240993G > A0.2505.29e-20C1.36 (1.25-1.48)D
6q21chr6:111072574-111647042rs458017A > G0.0602.16e-16C1.62 (1.40-1.88)D
6q23.3chr6:137707015-137959884TNFAIP3  rs610604T > G0.3206.54e-07D1.22 (1.13-1.32)D
12q13.3chr12:55958153-56408728IL23A  rs2066808A > G0.0702.49e-07D1.49 (1.28-1.72)D
14q13.2chr14:34900397-35394209NFKBIA  rs8016947G > T0.4301.52e-11C1.19 (1.11-1.28)D
19p13.2chr19:10284572-10517872rs280519G > A0.4704.42e-09C1.20 (1.12-1.30)D
19p13.2chr19:10280033-10517872TYK2  rs12720356A > C0.1004.04e-11C1.33 (1.18-1.52)D
20q13.13chr20:49792078-50046045RNF114  rs2235617C > G1.65e-06D 
MHCchr6:31253891-31375450HLA-C  rs10484554C > T4.06e-214D 

Criteria

GDXHsS00013 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date