Whole Genome Association Study:CEL:Dubois PCA:2010:20190752

Overview

A genome-wide association study meta-analysis of 4,533 individuals with celiac disease (cases) and 10,750 controls of European descent. Genotyping of the studies were performed on Illumina Infinium HumanHap300 beadchip. A further 231,362 additional non-HLA markers from Illumina Hap550 marker set were tested for association in 3,796 cases and 8,154 controls. Genotype imputation using BEAGLE software and HapMap3 reference samples for samples typed on HumanHap300 chip was performed. After QC SNPs from 113 loci were selected for replication in 4,918 cases and 5,684 controls. All tests for association were conducted using PLINK v1.07 allowing the discovery of 13 novel celiac disease susceptibility loci.

Study Paper

Multiple common variants for celiac disease influencing immune gene expression. 2010-02-28

Study Type

Whole Genome Association Study

Samples

Group	Phenotype	Population	Cases	Controls	Families	Trios
Discovery	CEL	NULL	4533	10750	-	-
Replication	CEL	NULL	4918	5684	-	-

Exclusion Criteria

SNPs

Call rate >95%.
HWE (P<0.0001).
Manual checking of discovery SNP signal clouds for artefacts.

Sample

Call rate >98%
Non-european descent via EIGENSTRAT analysis.
Duplicates and first degree relatives.
Incompatible recorded gender.

Study Association

Region	Location	Gene(s)	Marker	Allele	MAF	P Value	Odds Ratio
1p31.3	chr1:61287283-61384764	NFIA	rs6691768	A > G	0.378	1.19e-07^C	1.11 (1.06-1.15)^C
1p36.11	chr1:24901186-24981785	RUNX3	rs10903122	G > A	0.480	1.73e-10^C	1.12 (1.09-1.18)^C
1p36.23	chr1:7858046-8146070	PARK7 TNFRSF9	rs12727642	C > A	0.185	9.11e-08^C	1.14 (1.09-1.20)^C
1p36.32	chr1:2431888-2879054	TNFRSF14 MMEL1	rs3748816	A > G	0.339	3.28e-09^C	1.12 (1.09-1.18)^C
1q24.2	chr1:167197279-167474186	CD247	rs864537	A > G	0.391	3.80e-07^C	1.1 (1.06-1.15)^C
1q24.3	chr1:172681545-172912687	TNFSF4 FASLG TNFSF18	rs859637	G > A	0.486	1.75e-06^C	1.10 (1.06-1.14)^C
1q31.2	chr1:192500477-192579099	RGS1	rs2816316	A > C	0.160	2.20e-17^C	1.25 (1.19-1.32)^C
1q32.1	chr1:200893429-201069559		rs296547	G > A	0.357	4.11e-09^C	1.12 (1.09-1.16)^C
2p14	chr2:68309121-68455124	PLEK	rs17035378	A > G	0.278	7.79e-09^C	1.14 (1.09-1.19)^C
2p16.1	chr2:60701232-61642429	REL AHSA2	rs13003464	A > G	0.401	3.71e-13^C	1.15 (1.11-1.20)^C
2q12.1	chr2:102238781-102651983	IL1RL1 IL18R1 IL1RL2 IL18RAP	rs917997	G > A	0.236	1.11e-15^C	1.19 (1.14-1.25)^C
2q31.3	chr2:180933651-181404099	ITGA4 UBE2E3	rs13010713	A > G	0.448	4.74e-11^C	1.13 (1.09-1.18)^C
2q33.2	chr2:203813694-203952558	CD28 ICOS CTLA4	rs4675374	G > A	0.223	5.79e-09^C	1.14 (1.09-1.19)^C
3p21.31	chr3:45866656-46467034	CCR2 CCR5 CCRL2 CCR9 CCR1 CCR3	rs13098911	G > A	0.097	3.26e-17^C	1.30 (1.23-1.39)^C
3p22.3	chr3:32872212-33057492	CCR4	rs13314993	A > C	0.464	3.27e-09^C	1.13 (1.08-1.17)^C
3q13.33	chr3:119383611-119581808	POGLUT1 CD80	rs11712165	A > C	0.394	8.03e-09^C	1.13 (1.08-1.17)^C
3q25.33	chr3:159857988-160002484	IL12A	rs17810546	A > G	0.125	3.98e-28^C	1.36 (1.29-1.44)^C
3q26.2	chr3:169635396-169886565		rs10936599	G > A	0.252	4.57e-07^C	1.12 (1.07-1.16)^C
3q28	chr3:188351572-188422865	LPP	rs1464510	C > A	0.485	2.98e-40^C	1.29 (1.25-1.34)^C
4q27	chr4:122017479-122644147	IL21 IL2	rs13151961	A > G	0.142	2.18e-27^C	1.35 (1.28-1.43)^C
6p25.3	chr6:375936-427152	IRF4	rs1033180	G > A	0.080	5.58e-08^C	1.21 (1.13-1.29)^C
6q15	chr6:90097116-90316707	MAP3K7 BACH2	rs10806425	C > A	0.397	3.89e-10^C	1.13 (1.09-1.17)^C
6q22.33	chr6:127633469-128020756	PTPRK THEMIS	rs802734	A > G	0.311	2.62e-14^C	1.17 (1.12-1.22)^C
6q23.3	chr6:137552553-137804198	TNFAIP3	rs2327832	A > G	0.216	4.46e-19^C	1.23 (1.17-1.28)^C
6q25.3	chr6:158897742-159119181	TAGAP	rs1738074	G > A	0.434	2.94e-15^C	1.16 (1.12-1.21)^C
7p14.1	chr7:37318708-37399609	ELMO1	rs6974491	G > A	0.170	1.56e-07^C	1.14 (1.09-1.20)^C
8q24.21	chr8:128130288-128286991		rs9792269	A > G	0.238	3.28e-09^C	1.14 (1.1-1.19)^C
10q22.3	chr10:79256182-79313071	ZMIZ1	rs1250552	A > G	0.466	9.09e-10^C	1.12 (1.09-1.16)^C
11q24.3	chr11:128468236-128555266	ETS1	rs11221332	G > A	0.237	5.28e-16^C	1.21 (1.16-1.27)^C
12q24.12	chr12:111284392-112592683	SH2B3	rs653178	A > G	0.495	7.15e-21^C	1.20 (1.15-1.24)^C
13q14.2	chr13:50160568-50490165		rs2762051	G > A	0.184	6.64e-07^C	1.13 (1.08-1.18)^C
14q24.1	chr14:68698241-68851345	ZFP36L1	rs4899260	G > A	0.263	3.92e-07^C	1.12 (1.07-1.16)^C
16p13.13	chr16:11213167-11383900	CLEC16A CIITA SOCS1	rs12928822	G > A	0.161	3.12e-08^C	1.16 (1.1-1.22)^C
17q21.31	chr17:45998697-46810843		rs2074404	A > C	0.250	1.23e-06^C	1.11 (1.06-1.16)^C
18p11.21	chr18:12738414-12925254	PTPN2	rs1893217	A > G	0.165	2.52e-10^C	1.17 (1.12-1.23)^C
21q22.3	chr21:44177696-44284761	ICOSLG CH507-9B2.1	rs4819388	G > A	0.280	2.46e-09^C	1.14 (1.09-1.19)^C
22q11.21	chr22:21454896-21649639	YDJC UBE2L3	rs2298428	G > A	0.201	1.84e-07^C	1.13 (1.08-1.19)^C
MHC	chr6:32414162-32714887	HLA-DQA1 HLA-DQA2 HLA-DQB1	rs2187668	G > A	0.258	1.00e-50^C	6.23 (5.95-6.52)^C
Xp22.2	chrX:12892402-13005960	TLR8 TLR7	rs5979785	A > G	0.263	6.36e-08^C	1.14 (1.09-1.19)^C

Criteria

GDXHsS00038 meets the following criteria:

Criteria Name

Details

Disease Tags

Study for a Disease

CEL

Publications

PMID	Title	First Author	Journal	Disease(s)	Date