Figure 3: Standardized gene analysis procedure for GIST. (1) DNA samples extracted from macrodissected tissues are subjected to PCR with the best primer sets; group D primer set for exon 9 and group A primer sets for the other exons. (2) The best primer set-negative samples are recommended to amplify with the second or third choice of primer sets shown in the flow chart separately for each exon. (3) and (4) Single band samples on electrophoresis after successful PCR are first subjected to direct sequencing. (5) Single-band samples with consecutive single peak on direct sequencing suggest no mutation (wild type) in the corresponding exon. (6) Single-band samples with single base-pair double peaks suggest a point mutation in the exon. (7) Single-band samples with superimposed consecutive double peaks on direct sequencing suggest deletion-or insertion-type mutation in the exon. (8) and (9) The exact mutation profile of single-band samples with superimposed consecutive double peaks on direct sequencing should be further analyzed using a subcloning approach. (10) and (11) Double-band samples on PCR electrophoresis of KIT exon 11, which always carried a mutation of the gene, should be further analyzed using a subcloning approach because direct sequencing for such samples always presents consecutive superimposed double peaks.