Overview

Fine mapping on a Immunochip (Illumina Infinium) custom SNP array, in 2816 individuals (cases) with juvenile idiopathic arthritis (JIA) and 13056 controls of European ancestry for 123003 markers. The Illumina GenomeStudio GenTrain2.0 algorithm was used to recluster all 15,872 samples. Principal-component analysis (PCA) was performed using EIGENSOFT v4.2 on the samples merged with HapMap phase 2 individuals (CEU, YRI and CHB). Statistical analyses were performed using PLINK v1.07 and SNPGWA v4.0.  SHAPEIT (version unknown) was used to prephase the Immunochip data and IMPUTE2 to impute the SNP genotypes. SNPTEST (version unknown) was used for testing association, to account for phase uncertainty. This study has reported 14 new JIA (oligoarticular and rheumatoid factor-negative polyarticular subtype) regions reaching genome-wide significance level of P < 5 x 10-8.
Study Type
Case-Control Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryJIA281613056--
Exclusion Criteria

Samples were excluded due to :-

Low call frequency (<98%) and autosomal heterozygosity
Fail IBD (identity-by descent)
Fail HapMap PCA
Fail outlier PCA
Duplication and first- or second-degreee relatives
Additional exclusions due to gender mismatches or misdiagnosis of cases
 
Markers were excluded due to :-
 
Low call rate (<98%) or low cluster seperation score (< 0.4)
Duplication
Monomorphic
MAF < 0.01
Deviation from Hardy-Weinberg equilibrium in controls (P < 0.001)
Differential missingness between cases and controls (P < 0.05)

 

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p13.2chr1:113288123-114002809PTPN22  rs6679677C > A0.1003.19e-25D1.59 (1.45-1.73)D
1p36.11chr1:24688318-24938167RUNX3  rs4648881A > G0.4904.66e-07D1.16 (1.10-1.23)D
1q21.3chr1:153855143-154540234IL6R  ATP8B2  rs11265608G > A0.1002.75e-08D1.33 (1.20-1.47)D
2q11.2chr2:99928492-100431688AFF3  LONRF2  rs10194635A > T0.4308.10e-07D1.24 (1.14-1.36)D
2q11.2chr2:99928492-100425222AFF3  LONRF2  rs6740838C > A0.4308.83e-07D1.25 (1.14-1.37)D
2q32.3chr2:191008827-191144926STAT4  rs10174238A > G0.2301.28e-13D1.29 (1.20-1.37)D
3p21.31chr3:45869583-46467579CCR3  CCR1  rs79893749G > A0.1501.88e-07D1.28 (1.16-1.39)D
3q13.33chr3:119384793-119581808TIMMDC1  CD80  rs4688013G > A0.1906.30e-07D1.20 (1.12-1.29)D
3q13.33chr3:119384793-119581808TIMMDC1  CD80  rs11714843T > A0.1803.64e-07D1.22 (1.13-1.31)D
4q27chr4:122041679-122644147IL21  IL2  rs1479924A > G0.2906.24e-11D1.27 (1.18-1.35)D
5q11.2chr5:56122309-56161300ANKRD55  rs71624119G > A0.2504.40e-11D1.28 (1.19-1.37)D
5q15chr5:96744764-97141497LNPEP  ERAP2  rs27290A > G0.4407.50e-09D1.32 (1.20-1.45)D
5q31.1chr5:132225629-132670364IRF1  rs4705862A > T0.4401.02e-08D1.19 (1.12-1.27)D
7p15.1chr7:28080094-28222707JAZF1  rs10280937A > G0.1106.60e-07D1.25 (1.15-1.37)D
7p15.1chr7:28080094-28222707JAZF1  rs73300638A > C0.1101.12e-07D1.28 (1.17-1.41)D
7p15.3chr7:22658847-22772705IL6  rs7808122G > A0.4405.80e-08D1.19 (1.11-1.25)D
7p15.3chr7:22667223-22772705IL6  rs6946509C > T0.4503.36e-08D1.19 (1.12-1.26)D
10p15.1chr10:5988231-6125916IL2RA  rs7909519A > C0.1108.00e-10D1.39 (1.25-1.56)D
10q23.31chr10:88976642-89029704FAS  rs7069750A > C0.4402.93e-08D1.18 (1.11-1.25)D
11p13chr11:36260041-36375878PRR5L  rs4755450G > A0.3503.35e-07D1.25 (1.15-1.35)D
11p13chr11:36258300-36375878PRR5L  rs7127214C > G0.3501.90e-08D1.28 (1.18-1.41)D
12p13.31chr12:6373620-6414083LTBR  rs2364480A > C0.2505.10e-08D1.20 (1.12-1.28)D
12p13.31chr12:6373620-6414083LTBR  rs10849448G > A0.2404.54e-09D1.24 (1.55-1.33)D
12q24.12chr12:111278572-112592683ATXN2  SH2B3  rs3184504G > A0.4902.60e-09D1.20 (1.13-1.27)D
13q14.11chr13:39618079-39887654COG6  rs7993214G > A0.3501.61e-07D1.19 (1.11-1.27)D
13q14.11chr13:39618079-39887654COG6  rs9532434C > T0.3604.52e-08D1.19 (1.12-1.27)D
13q14.11chr13:42249799-42527627rs34132030G > A0.3201.77e-07D1.18 (1.11-1.26)D
14q24.1chr14:68696033-68851345ZFP36L1  rs12434551T > A0.4701.59e-08D1.3 (1.18-1.41)D
16p13.13chr16:11276759-11405845RMI2  PRM1  rs11074967C > G0.4202.40e-07D1.18 (1.1-1.25)D
16p13.13chr16:11225188-11390934RMI2  PRM1  rs66718203G > C0.1804.46e-07D1.23 (1.14-1.35)D
18p11.21chr18:12738414-12925254PTPN2  rs2847293T > A0.1701.44e-12D1.31 (1.22-1.41)D
19p13.2chr19:10280033-10517872TYK2  rs34536443C > G0.0501.00e-10D1.79 (1.49-2.13)D
21q22.12chr21:35316472-35449600RUNX1  rs9979383A > G0.3701.06e-08D1.28 (1.18-1.39)D
22q11.21chr22:21454896-21649639UBE2L3  rs2266959C > A0.1906.20e-09D1.24 (1.15-1.33)D
22q12.3chr22:37106383-37148205IL2RB  rs2284033G > A0.4401.55e-08D1.19 (1.12-1.27)D
MHCchr6:32463515-32718045HLA-DQB1  HLA-DQA2  rs7775055A > G0.0203.14e-174D6.01 (5.30-6.81)D

Criteria

GDXHsS00023 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date