Identification of diagnostic biomarker in patients with gestational diabetes mellitus based on transcriptome-wide...

Gestational diabetes mellitus (GDM) is becoming a growing threat for all pregnancies. In this study, we set up an automatic screening method combining both transcriptomic databases and support vector machine (SVM)-based pattern recognition to select biomarkers that can be used in predicting and preventing GDM for gravidas. We screened 63 samples (32 GDM samples and 31 normal controls) in GEO database for the GDM-specific biomarkers. Differentially expressed genes between patients with GDM and normal controls were picked out using edgeR package. Enrichment analysis was performed using database for annotation, visualization, and integrated discovery. The regulatory gene network was constructed based on the KEGG pathway database. Genes in the hub of the network were selected as specific biomarkers of GDM and further validated through document investigation. Finally, the GDM prediction model was verified using the SVMs. In total, 189 probes corresponding to 69 genes that differentially expressed between GDM and controls were screened out by edgeR package. Nineteen pathways were clustered by KEGG enrichment analysis and were integrated into a regulatory network containing 572 nodes and 1874 edges. The intersection of 50 hub genes extracted from the network and 69 differential genes picked out by edgeR was a collection of six genes, including members of HLA superfamily. In the SVM model, the six genes had a good capacity of predicting GDM in both the training data set (area under curve [AUC] is 0.781) and the testing data set (AUC is 0.710) and had been reported to be associated with GDM. We found that the collection of six genes can be potentially applied as a biomarker for GDM diagnosis.