Genetic Variants in IgAN and LN

The IgAN susceptibility loci discovered in genome-wide association studies (GWAS) were primarily from five genomic regions: the MHC region at 6p21, the DEFA locus at 8p23, the TNFSF13 locus at 17p23, the HORMAD2 locus at 22q12 and the CFH/CFHR locus at 1q32 (10 (link), 11 (link)). Thus all of the SNPs reported as top association signals in GWASs of IgAN were selected for further testing in LN. In total, 15 SNPs, including 8 SNPs within the MHC loci and seven SNPs outside the MHC region, were genotyped. In the discovery cohort from Beijing, genotyping in LN patients was performed with an Illumina Solexa HiSeq 2000 platform, and selected SNPs checked in the SLE patients without LN were genotyped using TaqMan allele discrimination assays (Applied Biosystems, Foster City, California, USA). For replicates, genotypes were determined using TaqMan allele discrimination assays (Beijing and Shanghai) or were directly retrieved from the original GWAS data (Hong Kong) (9 (link)).

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Zhou X.J., Nath S.K., Qi Y.Y., Cheng F.J., Yang H.Z., Zhang Y., Yang W., Ma J.Y., Zhao M.H., Shen N, & Zhang H. (2014). Identification of MTMR3 as a novel susceptibility gene for lupus nephritis in northern Han Chinese by shared-gene analysis with IgA nephropathy. Arthritis & rheumatology (Hoboken, N.J.), 66(10), 2842-2848.

Publication 2014

Solexa HiSeq 2000 platform TaqMan allele discrimination assays

Allele Assays Discrimination Genome wide association studies Genomic Genotypes Igan Patients Snps Susceptibility Tnfsf13

Corresponding Organization :

Other organizations : Peking University, Peking University First Hospital, University of Oklahoma Health Sciences Center, University of Hong Kong, Renji Hospital, Shanghai Jiao Tong University, Chinese Academy of Sciences, Shanghai Institutes for Biological Sciences, Cincinnati Children's Hospital Medical Center

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Variable analysis

independent variables

Genetic variants (SNPs) in the following genomic regions: MHC region at 6p21, DEFA locus at 8p23, TNFSF13 locus at 17p23, HORMAD2 locus at 22q12, and CFH/CFHR locus at 1q32

dependent variables

Susceptibility to lupus nephritis (LN) in patients

control variables

Patients with systemic lupus erythematosus (SLE) without lupus nephritis (LN) used as controls

controls

Positive control: Genotyping of the selected SNPs in the discovery cohort of LN patients from Beijing.
Negative control: Genotyping of the selected SNPs in SLE patients without LN

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