Overview

High-density genotyping study involving 10,619 individuals with ankylosing spondylitis and 15,145 controls of European, East Asian and Latin American ancestry using the Illumina ImmunoChip platform. A total of 128,935 SNPs were available for analysis after the QC process. For relatedness analysis, PLINK (v1.07) was used to calculate identity-by-descent. Association analysis and population stratification control was perfomed using linear mixed models as implemented in FaST-LMM(v1.05). Imputation was carried out with MACH and Minimac. Association at genome-wide significance (P < 5x10-8) was observed for 25 loci, including the MHC, out of which 13 were novel. 
 
Study Type
Case-Control Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryAS1061915145--
Exclusion Criteria
Samples were excluded due to:-
  • Low call rate (<95%) - before merging data sets
  • Low call rate (<98%) - after merging data sets
  • Duplication
 
Markers were excluded due to:-
  • Low call rate(<95%) - before merging data sets
  • Low call rate(<98%) - after merging data sets
  • Deviation from Hardy-Weinberg equilibrium in controls (P < 1x10-6)
  • Differential missingness between collections (P < 1x10-7)

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p31.3chr1:67130418-67302310IL23R  rs12141575G > A0.3309.40e-11C1.15C
1p31.3chr1:67128876-67302310IL23R  rs11209026G > A0.0662.00e-27C1.61C
1p36.11chr1:24901186-24981785RUNX3  rs6600247C > T0.4992.60e-15C1.16C
1q21.3chr1:154332714-154679688IL6R  rs4129267C > T0.4083.40e-13C1.18C
1q23.3chr1:161419627-161668253FCGR2A  rs1801274C > T0.4761.40e-09C1.11C
1q32.1chr1:200892467-201069559KIF21B  GPR25  rs41299637T > G0.2851.90e-15C1.19C
2p15chr2:62258716-62420888rs6759298G > C0.3784.90e-47C1.29C
2q31.3chr2:180946221-181404099UBE2E3  rs12615545T > C0.4211.00e-09C1.12C
2q37.3chr2:240619922-240712978GPR35  rs4676410C > T0.2099.90e-09C1.13C
5p13.1chr5:40287627-40841639PTGER4  rs12186979A > G0.4984.30e-06C1.08C
5q15chr5:96743698-97141497ERAP1  ERAP2  rs2910686T > C0.4404.50e-17C1.17C
5q15chr5:96647765-97039314ERAP1  rs30187C > T0.3384.40e-45C1.29C
5q15chr5:96647765-97039314ERAP1  ERAP2  rs10045403A > G0.2705.80e-14C1.2C
5q33.3chr5:159397971-159460964IL12B  rs6871626C > A0.3373.10e-08C1.10C
6q15chr6:89927785-89989043BACH2  rs17765610A > G0.1185.30e-08C1.15C
9q34.3chr9:136243135-136513440CARD9  rs1128905C > T0.4977.00e-09C1.1C
10q22.3chr10:79258505-79313758ZMIZ1  rs1250550G > T0.3481.50e-09C1.11C
10q24.2chr10:99508770-99570210NKX2-3  rs11190133C > T0.2934.90e-14C1.16C
12p13.31chr12:6315411-6354696TNFRSF1A  LTBR  rs1860545C > T0.3952.80e-10C1.14C
12q24.12chr12:111278572-112592683SH2B3  rs11065898C > T0.2164.70e-08C1.11C
14q31.3chr14:87865031-88175959GPR65  rs11624293T > C0.0871.50e-10C1.20C
16p11.2chr16:28283985-29016486SULT1A1  IL27  rs75301646G > A0.3932.60e-09C1.11C
17q11.2chr17:27647591-27952572NOS2  rs2531875T > G0.3671.20e-10C1.12C
17q21.32chr17:47231738-47798656NPEPPS  TBKBP1  TBX21  rs9901869A > G0.4846.00e-15C1.14C
19p13.2chr19:10299117-10520699TYK2  rs35164067G > A0.2043.40e-10C1.15C
21q22.2chr21:39081110-39111851rs2836883G > A0.2666.50e-17C1.18C
21q22.3chr21:44152485-44266077CH507-9B2.1  ICOSLG  rs7282490A > G0.3906.20e-09C1.11C

Criteria

GDXHsS00026 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date