Overview

A meta-analysis of SLE was carried out. Firstly a multi-cohort GWAS was conducted for 4,036 cases and 6,959 controls resulting in 644,674 markers typed on both HumanOmni1-Quad and HumanOmni2.5 genotyping platforms. This identified 25 loci of which three were novel. The results from this meta-analysis were combined with an additional cohort of 1,165 cases and 2,107 controls, which validated the original loci identified. Loci which achieved significance (P<2.5 x 10-5 for potential novel loci and P<1x10-4 for previously reported loci) were included in a replication step in 6,925 cases and 2,018 controls . Finally a post replication analysis was carried out using all available datasets, on a custom chip, this uncovered an additional 18 loci. All association analyses were performed using SNPTEST.   The final Meta analysis was imputed to 1000 genomes using SHAPEIT to prephase the data and IMPUTE (v2.2.3) to impute. 

Study Type
Case-Control Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoverySLENULL52019066--
ReplicationSLENULL20186925--
Exclusion Criteria

Samples

  • Individual missingness > 3%.
  • Identity by descent (IBD > 0.125).
  • Population structure.

SNPs

  • SNP missingness > 3%
  • MAF < 0.2 %
  • Heterozygosity
  • HWE

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p13.2chr1:113296527-114009223PTPN22  rs2476601G > A0.0911.10e-28C1.39 (1.34-1.53)D
1q23.3chr1:161419627-161668253FCGR2A  rs1801274A > G0.4971.04e-12C1.21 (1.11-1.21)D
1q25.1chr1:173128850-173331701TNFSF4  rs704840T > G0.2863.12e-19C1.26 (1.17-1.27)D
1q25.3chr1:183277955-183610838NCF2  SMG7  rs17849501C > T0.0513.45e-88C2.24 (1.95-2.26)D
1q32.1chr1:206709013-206867232IL10  rs3024505G > A0.1564.64e-09C1.12 (1.11-1.24)D
1q42.3chr1:235651207-235928298LYST  rs9782955C > T0.2521.25e-09C1.2 (1.22-1.11)D
2p14chr2:65250869-65490608SPRED2  rs6740462A > C0.2652.67e-05C1.2 (1.16-1.05)D
2q24.2chr2:162104363-162502867IFIH1  rs2111485G > A0.4041.27e-11C1.15 (1.2-1.11)D
2q32.2chr2:190990148-191143008STAT4  rs11889341C > T0.2165.59e-122C1.75 (1.65-1.81)D
2q34chr2:212899279-213151021IKZF2  rs3768792A > G0.1291.21e-13C1.26 (1.17-1.31)D
3p14.3chr3:58172132-58566602ABHD6  PXK  rs9311676C > T0.4243.06e-14C1.14 (1.22-1.14)D
3q25.33chr3:159973324-160104880IL12A  rs564799C > T0.4071.54e-09C1.15 (1.18-1.09)D
4q24chr4:101780701-102172329BANK1  rs10028805G > A0.3754.31e-17C1.2 (1.25-1.15)D
5q31.1chr5:134055825-134440162SKP1  TCF7  rs7726414C > T0.0444.44e-16C1.46 (1.32-1.58)D
5q33.1chr5:151012930-151104264TNIP1  rs10036748C > T0.2521.27e-45C1.32 (1.32-1.45)D
5q33.3chr5:160397457-160540930MIR146A  MIR3142HG  rs2431697T > C0.4428.01e-28C1.25 (1.32-1.2)D
6p21.31chr6:34537417-35395071UHRF1BP1  rs9462027G > A0.2867.55e-09C1.14 (1.09-1.19)D
6q21chr6:106100256-106180825PRDM1  ATG5  rs6568431C > A0.3765.04e-14C1.22 (1.15-1.27)D
6q23.3chr6:137718634-137974695TNFAIP3  rs6932056T > C0.0311.97e-31C1.82 (1.65-2.02)D
7p12.2chr7:50206640-50325467IKZF1  rs4917014T > G0.3286.39e-14C1.14 (1.23-1.14)D
7p15.1chr7:28080094-28222707JAZF1  rs849142C > T0.4948.61e-11C1.13 (1.10-1.19)D
7q32.1chr7:128911686-129137466IRF5  rs10488631T > C0.1089.37e-110C1.79 (1.81-2.03)D
8p23.1chr8:11426026-11546260BLK  rs2736340C > T0.2546.28e-20C1.30 (1.22-1.37)D
10q11.23chr10:48742291-48932543WDFY4  rs2663052G > A0.4795.25e-09C1.18 (1.10-1.22)D
10q21.2chr10:62002144-62170402ARID5B  rs4948496T > C0.4691.04e-10C1.15 (1.10-1.19)D
11p13chr11:34998708-35142427CD44  rs2732549A > G0.4451.20e-23C1.2 (1.28-1.19)D
11p15.5chr11:406483-715420IRF7  rs12802200C > A0.1978.81e-10C1.23 (1.15-1.31)D
11q13.4chr11:71400136-71530651DHCR7  NADSYN1  rs3794060T > C0.2561.32e-20C1.13 (1.18-1.29)D
11q24.3chr11:128558890-128692203FLI1  ETS1  rs7941765C > T0.4921.35e-10C1.15 (1.19-1.1)D
12q24.12chr12:111281256-112592683SH2B3  rs10774625G > A0.4994.09e-09C1.17 (1.08-1.18)D
12q24.33chr12:128772462-128861985SLC15A4  rs1059312A > G0.3911.48e-13C1.14 (1.12-1.21)D
14q24.1chr14:68071518-68480615RAD51B  rs4902562G > A0.4176.15e-10C1.13 (1.09-1.19)D
15q24.2chr15:74435612-75197474CSK  rs2289583C > A0.2816.22e-15C1.20 (1.14-1.24)D
16p11.2chr16:30754926-31373327ITGAM  rs34572943G > A0.1173.39e-76C1.78 (1.61-1.81)D
16p13.13chr16:10923201-11215894CIITA  SOCS1  rs9652601G > A0.3327.42e-17C1.18 (1.27-1.15)D
16q24.1chr16:85927444-85950409IRF8  rs11644034G > A0.2169.58e-18C1.33 (1.32-1.19)D
17p13.2chr17:4788077-4894010PLD2  rs2286672C > T0.0712.93e-09C1.24 (1.16-1.35)D
17q12chr17:39219977-40074859IKZF3  rs2941509C > T0.0327.98e-09C1.41 (1.22-1.49)D
19p13.2chr19:10285007-10517872TYK2  rs2304256C > A0.2853.50e-13C1.27 (1.17-1.31)D
22q11.21chr22:21454896-21649639UBE2L3  rs7444T > C0.2041.84e-22C1.28 (1.21-1.33)D
MHCchr6:31600692-32218019rs1270942A > G0.0932.25e-165C2.52 (2.15-2.42)D
Xp21.2chrX:30513441-30624914CXorf21  rs887369C > A0.2535.26e-10C1.16 (1.2-1.1)D
Xq28chrX:153906725-154125011MECP2  IRAK1  rs1734787A > C0.1541.78e-15C1.57 (1.22-1.40)D

Criteria

GDXHsS00047 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date