Combining computational approaches and functional analysis for characterizing the deleterious effect of RHD gene...

Previous studies have shown that both intronic and exonic variants in RHD, the gene encoding the D antigen in the Rh blood group system, can alter mRNA splicing at the qualitative and/or quantitative level(s), thus resulting in a D variant phenotype. Here, we sought to further document this mechanism by analyzing extensively RHD variants found in the Chinese population.

From an in-house database of whole exome sequencing of over 27,000 gDNA samples from Chinese individuals, as well as from ten Chinese individuals presenting with a D variant phenotype, RHD variants were selected in a first round of in silico approaches previously used (i.e., Alamut suite splicing module and ΔtESRseq score) for functional analysis by minigene splicing assay. All variants were further reevaluated subsequently by two contemporary bioinformatics tools, that is, SpliceAI and SPiP.

From the 269 single nucleotide variants (SNVs) included in the study, the 34 top-score SNVs were selected as potential candidates for altering RHD splicing and comprehensively analyzed at the functional level. We demonstrated that eight SNVs, including three located within the consensus splice sites (c.336-1G>C, c.801+2T>G, and c.940-2delA), four in proximal intronic regulatory regions (c.149-6G>A, c.939+5G>T, c.1154-8T>G, and c.1227+5G>C), and one in exon (c.318G>A) alter splicing with a moderate to severe effect.

Our findings suggest that combining computational prediction with SpliceAI and/or SPiP using specific settings is an efficient approach (accuracy = 0.941) for selecting candidate SNVs that are prone to disrupt RHD splicing and alter D phenotype subsequently.