Overview

Genome-wide association study in T1DGC (3983 cases and 3999 controls) and meta-analysis with Wellcome Trust Case Control Consortium (WTCCC) and Genetics of Kidneys in Diabetes (GoKinD) study of diabetic nephropathy (Total in meta-analysis 7514 cases and 9045 controls). A total of 841622 SNPs where available for analysis of which 437739 where typed on the Illumina platform, 328044 on the Affymetrix platform and 75839 on both platforms. Imputation was performed by linear regression using data from 1422 controls genotyped on both plat-forms. 41 regions was identified in the meta-analysis and 27 potential novel regions were chosen for replication in additional British and Danish cases 4267 and controls 4463 and 2,319 affected sib-pair (ASP) families. 18 novel T1D regions was confirmed by this study.

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryT1D75149045--
ReplicationT1D42674670-4342
Exclusion Criteria

Samples were excluded using the following criteria(Totals): Non-European ancestry(236),duplications(21),close relatives(29).

SNPs were excluded from analysis using the following criteria: Minor allele frequency below 1%, Hardy-Weinberg equilibrium above 25, call rate below 95%.

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p13.2chr1:113296527-114009223PTPN22  rs2476601G > A0.1178.50e-85D 
1q31.2chr1:192500477-192579099RGS1  rs2816316A > C0.1993.10e-05D 
1q32.1chr1:206709013-206867232IL10  rs3024505C > T0.1691.90e-09C1.19 (1.1-1.3)C
2q24.2chr2:162104363-162504293IFIH1  rs1990760T > C0.3816.60e-09D 
2q33.2chr2:203750711-203951852CTLA4  rs3087243G > A0.4601.20e-15D 
3p21.31chr3:45921450-46556887CCR5  rs11711054A > G0.3051.70e-05D 
4p15.2chr4:26026175-26130530rs10517086G > A0.2994.60e-10C1.09 (1.02-1.17)C
4q27chr4:122017479-122644147IL2  rs4505848A > G0.3814.70e-13D 
6q15chr6:90097116-90317592BACH2  rs11755527C > G0.4295.40e-08D 
6q22.32chr6:126136349-127098552CENPW  rs9388489A > G0.4524.20e-13C1.17 (1.10-1.24)C
6q23.3chr6:137552553-137804198TNFAIP3  rs2327832A > G0.1553.00e-04D 
6q25.3chr6:158897742-159119181TAGAP  rs1738074C > T0.4656.00e-03D 
7p12.1chr7:50833203-51066332COBL  rs4948088C > A0.0474.40e-08C1.3 (1.11-1.49)C
7p15.2chr7:26618343-27162670rs7804356T > C0.2385.30e-09C1.14 (1.06-1.22)C
9p24.2chr9:4238265-4315101GLIS3  rs7020673G > C0.4985.40e-12C1.14 (1.08-1.20)C
10p15.1chr10:6388017-6503142PRKCQ  rs11258747G > T0.2631.20e-07D 
10p15.1chr10:5988280-6136651IL2RA  rs12251307C > T0.1021.30e-13D 
10q23.31chr10:88245291-88476640RNLS  rs10509540T > C0.2851.30e-28C1.33 (1.25-1.43)C
11p15.5chr11:2157710-2260001INS  rs7111341C > T0.3144.40e-48D 
12p13.31chr12:9430620-9820167CD69  rs4763879G > A0.3681.90e-11C1.09 (1.02-1.16)C
12q13.2chr12:55958153-56404651ERBB3  rs2292239G > T0.3302.20e-25D 
12q24.12chr12:111278572-112592683SH2B3  rs3184504C > T0.4422.80e-27D 
14q24.1chr14:68696738-68851345rs1465788G > A0.2871.80e-12C1.16 (1.1-1.25)C
14q32.2chr14:97897175-98138364rs4900384A > G0.2883.70e-09C1.09 (1.02-1.16)C
15q25.1chr15:78728401-78968794CTSH  rs3825932C > T0.3057.70e-08D 
16p11.2chr16:28283985-29014657IL27  rs4788084G > A0.4242.60e-13C1.16 (1.1-1.23)C
16p13.13chr16:10923201-11218316CLEC16A  rs12708716A > G0.3192.20e-16D 
16q23.1chr16:75182342-75487132rs7202877T > G0.0963.10e-15C1.28 (1.17-1.41)C
17q12chr17:39226421-40084508ORMDL3  rs2290400A > G0.4955.50e-13C1.15 (1.08-1.22)C
17q21.2chr17:40563547-40722575rs7221109C > T0.3531.30e-09C1.05 (0.99-1.12)C
18p11.21chr18:12738414-12925254PTPN2  rs1893217A > G0.1153.60e-15D 
18q22.2chr18:69831437-69902924CD226  rs763361C > T0.4961.20e-05D 
19q13.32chr19:46648121-46811943rs425105A > G0.1622.70e-11C1.16 (1.08-1.27)C
20p13chr20:1508984-1739154rs2281808C > T0.3621.20e-11C1.11 (1.05-1.19)C
21q22.3chr21:42389309-42458550UBASH3A  rs11203203G > A0.3231.70e-09D 
22q12.2chr22:29677916-30273198rs5753037C > T0.3912.60e-16C1.10 (1.04-1.17)C
MHCchr6:32350867-32661068rs9268645C > G0.3981.00e-100D 
Xq28chrX:154425779-155057576rs2664170A > G0.3167.80e-09C1.16 (1.07-1.24)C

Criteria

GDXHsS00004 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date