Overview

A genome-wide association study (GWAS) genotyped on a combination of Illumina 610K and 550K arrays using 1,054 individuals affected with Alopecia Areata and 3278 controls. After SNP quality control a total of 463,301 SNPs were available for analysis.

Analysis of samples identified 139 SNPs that exceed the threshold for genome-wide significance (p<5x10-7),  and a total of 302 SNPs that exceed nominal significance  (p<1x10-4). Quality control was performed with Helix Tree software (Golden Helix) or PLINK. Statistically significant SNPs implicate 8 novel loci within the genome.

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryAA10543278--
Exclusion Criteria

Samples were excluded due to :-

  • Low call rate in cases or controls (<95%).
  • Non-European ancestry
  • More than 10% missing genotype data
  • Closely related samples with >25% inferred identity by descent

Markers were excluded due to :-

  • Lacked more than 5% data
  • Deviation from Hardy-Weinberg equilibrium in controls (P<1x10-4)
  • Not present on both Illumina 550Kv2 and Illumina 610K
  • Discordant clustering between platforms by Illumina

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
2q33.2chr2:203746472-203951852CTLA4  rs1024161G > A0.4003.55e-13D1.44 (1.30-1.59)D
2q33.2chr2:203775181-203952558ICOS  rs3096851A > C0.3103.58e-08D1.32 (1.19-1.46)D
4q27chr4:122061159-122684373IL21  IL2  rs7682241C > A0.3304.27e-08D1.34 (1.21-1.48)D
6q25.1chr6:149982265-150130556ULBP3  rs2009345A > G0.3904.43e-17D1.52 (1.38-1.68)D
6q25.1chr6:149981913-150128692RAET1L  rs9479482A > G0.4304.49e-19D1.64 (1.47-1.82)D
9q31.1chr9:99518831-100406715STX17  rs10760706A > G0.3103.60e-07D1.32 (1.19-1.47)D
10p15.1chr10:5988280-6132638IL2RA  rs4147359G > A0.3302.22e-08D1.30 (1.17-1.44)D
10p15.1chr10:5988280-6131453IL2RA  rs3118470A > G0.3001.74e-12D1.41 (1.27-1.56)D
11q13.1chr11:64076473-64456055PRDX5  rs694739A > G0.3704.14e-07D1.33 (1.19-1.47)D
12q13.2chr12:55958153-56404651ERBB3  rs705708G > A0.4701.27e-07D1.32 (1.19-1.46)D
12q13.2chr12:55958153-56397446IKZF4  rs1701704A > C0.3303.21e-08D1.34 (1.21-1.48)D
MHCchr6:32611966-32771535rs9275572G > A0.4101.38e-35D2.22 (1.96-2.5)D

Criteria

GDXHsS00027 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date