Genomic convergence of locus-based GWAS meta-analysis identifies DDX11 as a novel Systemic Lupus Erythematosus gene

Mohammad Saeed; Alejandro Ibáñez-Costa; Alejandra María Patiño-Trives; Eduardo Collantes Estevez; María Ángeles Aguirre; Chary López-Pedrera

SNIPPER located 410 genes (Table S1) in 30 SLE loci identified by OASIS (Saeed 2017b) and these were tested in 3 GEO expression datasets. This search identified over 1000 expression probe sets in GEO datasets GSE30153, GSE13887 and more than 500 probe sets in GEO dataset GSE10325 for the reference gene list. Significant T-tests for these probe tests identified, 103 probes in dataset 4193 (GSE30153), 141 probes in dataset 4719 (GSE13887) and 66 probes in dataset 4185 (GSE10325). Additional 215 probes were found to be significant in GSE10325: Tcells, B-cells and Monocytes datasets. Hence, a total of 525 statistically significant probe sets in six (3+3) GEO datasets were finalized. This composite probe list was matched against the SNIPPER reference gene list of 410 genes, to remove those that the GEO query included, however, were not found in the OASIS SLE loci. Hence, 187 unique genes in the 6 GEO datasets were identified that had significant change in expression and were located in the 30 SLE loci (Table S2) .