GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region

Abstract

In a genome-wide association study (GWAS) of individuals of European ancestry afflicted with systemic lupus erythematosus (SLE) the extensive utilization of imputation, step-wise multiple regression, lasso regularization and increasing study power by utilizing false discovery rate instead of a Bonferroni multiple test correction enabled us to identify 13 novel non-human leukocyte antigen (HLA) genes and confirmed the association of four genes previously reported to be associated. Novel genes associated with SLE susceptibility included two transcription factors (EHF and MED1), two components of the NF-κB pathway (RASSF2 and RNF114), one gene involved in adhesion and endothelial migration (CNTN6) and two genes involved in antigen presentation (BIN1 and SEC61G). In addition, the strongly significant association of multiple single-nucleotide polymorphisms (SNPs) in the HLA region was assigned to HLA alleles and serotypes and deconvoluted into four primary signals. The novel SLE-associated genes point to new directions for both the diagnosis and treatment of this debilitating autoimmune disease.

Figure 1

Manhattan plot of genome wide association data. Significant SNPs (FDR ≤ 0.05) are shown as circles in dark green ( ), non-significant SNPs (FDR > 0.05) are shown as goldenrod asterisks ( ). The blue horizontal line is an estimate of the p value where FDR = 0.05 for non-HLA regions.

Figure 2

Step-wise multiple regression of the IRF5 and TNPO3 region. Panel A shows all SNPs in the IRF5 and TNPO3 region. Each subsequent panel (B–C) shows the same SNPs after accounting for the most significant remaining SNP in the model, with SNPs more significant than the FDR (BH−Rq/m) threshold for this region (a blue horizontal line) shown in dark green circles ( ); those less significant than the threshold are shown as goldenrod Xs ( ). Panel B accounted for rs10488631 and panel C, for rs4728142 and rs10488631. Genes are depicted below the figure, with the starting positions of IRF5 and TNPO3 indicated.

Figure 3

Imputation in the LAMC1, EDEM3, and NCF2 region. Panel A shows the imputation results. Significant imputed SNPs are shown as dark green circles ( ), significant genotyped SNPs are shown as cyan triangles ( ), non-significant SNPs (FDR > 0.05) are shown as goldenrod asterisks ( ) The blue horizontal line is an estimate of the p value where FDR = 0.05. The spiky gold line depicts the recombination rate in centimorgans per megabase. Panel B shows the LD (D′) of significant SNPs and rs17849502. SNPs in LD (D′ near 100) are red; those not in LD (D′ near 0) are blue, intermediate LD are on the red-orange-yellow-green-blue color continuum.

Figure 4

Step-wise multiple regression of the HLA region. Panel A shows all significant SNPs in the HLA region. Each subsequent panel (B–E) shows the same SNPs after accounting for of the most significant remaining SNP in the model, with SNPs more significant than the genome-wide FDR threshold for this study shown in dark green circles ( ); those less significant than the threshold are shown as goldenrod Xs ( ). Panel B accounted for rs558702, panel C accounted for rs9275572 and rs558702, panel D accounted for rs2764208, rs9275572 and rs558702. After accounting for rs10946940, rs2764208, rs9275572 and rs558702 (panel E), there were no SNPs meeting the genome-wide FDR threshold.