DNA ploidy and c-Kit mutation in gastrointestinal stromal tumors

Table 1 Primer sequence for c-Kit exons 9, 11, 13, and 17 and the corresponding annealing temperature (T_A) and the size of expected PCR size products

c-Kit exon No.	Primers	Primer sequence 5’->3’	TA (°C)	Product size (bp)
9	hEx9-F	TTCCTAGAGTAAGCCAGGG	53	298
	hEx9-R	AATCATGACTGATATGGT
11	hEx11-F	CAGGTAACCATTTATTTGT	53	326
	hEx11-R	TCATTGTTTCAGGTGGAAC
13	hEx13-F	ATCAGTTTGCCAGTTGTGCT	53	250
	hEx13-R	TTTATAATCTAGCATTGCC
17	hEx17-F	GTTTTCACTCTTTACAAGT	53	277
	hEx17-R	TTACATTATGAAAGTCACAGGAAAC

Table 2 Comparison of clinicopathologic parameters accord-ing to the risk groups of gastrointestinal stromal tumors

Parameter\Risk group		Very low and low (n = 36)	Intermediate and high (n = 19)	P
Cellularity	Low	11	0
	Intermediate	22	15	0.019
	High	3	4
Nuclear atypia	Mild	22	5
	Moderate	12	9	0.019
	Severe	2	5
Necrosis	Absent	34	10	0.000
	Present	2	9
Hemorrhage	Absent	28	10	0.055
	Present	8	9
Infiltrative	Absent	22	8	0.178
Growth pattern	Present	14	11
Tumor cell type	Spindle	29	11	0.001
Epithelioid		7	8

Table 3 Comparison of clinicopathologic parameters accord-ing to c-Kit mutations

Parameter	Mutations		P
	Negative (n = 20)	Positive (n = 35)
Sex (M:F)	11:9	14:21	0.283
Age (mean, yr)	58.2	61.0	0.360
Mean tumor size (cm)	3.8	6.2	0.020
Mean mitoses counts	7.8	13.4	0.360
Risk group: Very low/low	14	22	0.592
Intermediate/high	6	13
Cellularity: Low	5	6	0.741
Intermediate	13	24
High	2	5
Nuclear atypia Mild	10	17	0.898
Moderate	7	14
Severe	3	4
Necrosis Absent	18	26	0.161
Present	2	9
Hemorrhage Absent	17	21	0.054
Present	3	14
Infiltrative growth Absent	12	18	0.539
Present	8	17
Tumor cell type Spindle	13	27	0.330
Epithelioid	7	8

Table 4 Comparison of clinicopathologic parameters accord-ing to DNA ploidy

Parameter	Diploid (n = 45)	Aneuploid (n = 10)	P
Sex (M:F)	21:24	4:6	0.702
Age (mean, yr)	60.8	56.1	0.225
Mean tumor size (cm)	4.1	10.5	0.007
Mean mitoses counts	5.0	40.0	0.022
Risk group: Very low/low	34	2	0.001
Intermediate/high	11	8
Cellularity: Low	11	0	0.008
Intermediate	31	6
High	3	4
Nuclear atypia Mild	24	3	0.016
Moderate	18	3
Severe	3	4
Necrosis Absent	38	6	0.080
Present	7	4
Hemorrhage Absent	33	5	0.149
Present	12	5
Infiltrative growth Absent	27	3	0.085
Present	18	7
Tumor cell type Spindle	36	4	0.010
Epithelioid	9	6

Table 5 Correlation of c-Kit mutation and DNA ploidy

DNA ploidy1	c-Kit mutation
	Negative	Positive
Diploid	19	26
Aneuploid	1	9

¹P = 0.063.