Exon 9 Exon 11 Exon 13 Primer set group *Case No Overall amplification % with corresponding primers Primer set group Case No. Overall amplification % Primer set group Case No. Overall amplification %  with corresponding primers with corresponding primers   7 10 17     2     28                         A PS NG NG 77% B PS 57% B PS 42% B NG PS PS 57% C NG 65% C PS 61% C NG NG NG 31% D NG 35% D PS 65% E NG NG NG 15% E PS 92% E NG 57% **Rank of primers D →B →A Rank of primers A →E →B Rank of primers A →D →C Exon 17 Exon 12 Exon 18 Primer set group Case No. Overall amplification % with corresponding primers Primer set group Case No. Overall amplification % with corresponding primers Primer set group Case No. Overall amplification % with corresponding primers   28     28     2 17                       B PS 19% B PS 88% B PS NG 80% C PS 46% C PS 58% C NG NG 35% D PS 73% D PS 50% D NG NG 69% E NG 38% E PS 53% E NG PS 69% Rank of primers A →D →C Rank of primers A →B →C Rank of primers A →B →E NG: Negative with corresponding primer set; PS: Positive with corresponding primer set. *Case number of the best primer set- negative samples. **Rank of second and third choice of primer set was determined according to the frequency of successful amplification of best primer negative samples with corresponding primer sets and comparison of overall percentage of positive samples in 26 GISTs. For example, in exon 9, three samples (Cases 7, 10, and 17) were negative on electrophoresis for the best primer sets (group D), but two of them were positive for the group B primer set and one was positive for the group A primer set. Based on this result, the group D primer sets (exon 9D) were recommended as the first choice for exon 9, and primers of groups B and A (exon 9B and exon 9A) were ranked as the second and third choices, respectively. In exon 11, one sample was negative for the best primer sets (group A), but positive for groups B and E with overall percentages of 58% for B and 92% for group E. So in exon 11, primer sets of group A were recommended as the best, and groups E and B (exon 11E and exon 11B) were ranked as the second and third choices, respectively. The same evaluation method was used for the other exons and ranking of the three choices for each exon was as follows: exon 9: D>B>A, exon 11: A>E>B, exons 13 and 17: A>D>C in the KIT gene, exon 12: A>B>C, exon 18: A>B>E in the PDGFRA gene.

Table 4: PCR results of best primer negative samples with other primer sets.