Figure 1. PCR annotation of alternative splicing. A complete dataset can be viewed at http://palace.lgfus.ca. (a) Alternative splicing (AS) events are identified from transcript databases or datasets, and PCR primers are designed to flank each event. A screenshot from the database for two transcripts of the fibroblast growth factor receptor 2 (FGFR2) is shown. Schematic detail of the AS event is shown, indicating the relative positions of the forward (green) and reverse (red) primers; (b) Electropherogram obtained following endpoint PCR amplification. Microcapillary electrophoresis is performed on each reaction to detect expected short (205 bp) and long (472 bp) amplicons. Size and concentration are measured for each amplicon signal, and these are used to calculate the Ψ value, as indicated at the right. Marker peaks at 15 and 5000 bp are labeled M, residual primers are detectable immediately to the left of the M15 peak, and a heterodimer peak is detectable to the left of the long amplicon; (c) Graphic display of the Ψ values. Left, Ψ value heatmap for seven AS events (rows) in eight samples (columns). The top row of the heatmap shows an AS event depicted in panel (a) for FGFR2. Right, amplicon ratio representation for the FGFR2 AS event in eight samples. Relative concentrations of the short (red bars) and long (green bars) amplicons; each row represents a different RNA source. Total detected molarity is shown to the right of each row; values greater than 5 nM are generally considered acceptable; (d) Scaled heatmap representation of Ψ values for 656 AS events (columns) in 25 normal human ovary tissues and 21 serous ovarian cancer specimens. See Ref. [ 6] for full details of the clustering methods used.