Fig. 1

Evaluation of variant-induced splicing alterations by using a cell-based minigene assay. a Structure of pCAS2 minigenes used in the splicing reporter assay. The bent arrow indicates the CMV promoter, boxes represent exons, lines in between the boxes indicate introns, and arrows below the exons represent primers used in RT-PCR reactions. The minigenes were generated by inserting a genomic fragment containing the exon of interest together with its flanking intronic sequences into the intron of pCAS2, as described under Materials and Methods. b Analysis of the splicing pattern of pCAS2 minigenes carrying variants identified in this study. Wild-type (WT) and mutant constructs, as indicated, were introduced into HeLa cells and the transcripts of the minigenes were analyzed by RT-PCR 24 h post-transfection. The image shows the results of a representative experiment in which the RT-PCR products were separated on a 2.5% agarose gel stained with EtBr and visualized by exposure to ultraviolet light. M, 100 bp DNA ladder (New England Biolabs). c Quantification of splicing events observed in the minigene splicing assay. The relative levels of exon inclusion indicated under the gel are based on RT-PCR experiments equivalent to those shown in B but performed with a fluorescent forward primer and then separated on an automated sequencer. Quantification results were obtained by using the GeneMapper v5.0 software (Applied Biosystems) and correspond to the average of two independent fluorescent-RT-PCR experiments. d Representative fluorescent RT-PCR experiment. The panel shows superposed peaks corresponding to the WT and mutant products (in blue and red, respectively), as indicated