Characterizing gastrointestinal stromal tumors and evaluating neoadjuvant imatinib by sequencing of endoscopic ultrasound-biopsies

Table 1 Baseline characteristics, follow-up, and clinical outcome n (%)

Parameter	Baseline period	Study period	P value
Age, median (range)	75 (23-89)	68 (49-89)	0.07
Gender (M/F)	11/9	19/25	0.43
Study patients (n)	20	44
Tumor location (n)
Stomach	18	40
Duodenum	2	4
Tumor size (mm), median (range)	60 (12-200)	38 (13-220)	0.29
Tumor endosonographic appearance
Homogenous (solid)	8	17
Heterogeneous (necrotic)	12	27
EUS-FNA (n)	16	38
Needle (22 G/25 G)	12/4	26/12	0.75
Passes (n), median (range)	2 (1-3)	3 (1-4)	0.10
EUS-FNB (n)	7	44
Needle (TCB 19 G/FNB 19 G/FNB 22 G)	7/0/0	0/5/39	< 0.001
Passes (n), median (range)	1 (1-4)	2 (1-4)	0.15
ROSE1	9 (56)	26 (68)	0.53
Study cytologist	5 (31)	32 (84)	< 0.001
Study pathologist	2 (29)	38 (86)	0.003
Resected cases	15 (75)	27 (61)	0.40
Resection margin (R0/R1/R2)	13/1/1	24/3/0
Follow-up time2, mo (range)	72 (16-105)	19 (1-45)
Overall survival (OS)3, 12 mo	20/20 (100)	31/31 (100)	1.00
OS, 24 mo	19/20 (95)	17/18 (94)	1.00
OS, 36 mo	18/20 (90)	10/11 (91)	1.00
Patients deceased	9/20 (45)	2/44 (5)

¹Rapid on-site cytology evaluation by a cytotechnician;

²From the date of EUS until death or until end of follow-up;

³From the date of EUS until 12, 24 and 36 mo post-EUS. EUS: Endoscopic ultrasound; FNA: Fine needle aspiration; FNB: Fine needle biopsy.

Table 2 Parameters with potential influence on the sensitivity of Endoscopic ultrasound-fine needle aspiration n (%)

Parameter			P value
Tumor echogenicity	Homogenous (solid)	Heterogeneous (necrotic)
EUS-FNA-sensitivity	11/20 (55)	18/32 (56)	1.0
Tumor size	< 30 mm	≥ 30 mm
EUS-FNA-sensitivity	10/18 (56)	19/34 (56)	1.0
ROSE	ROSE	non-ROSE
EUS-FNA-sensitivity	21/34 (62)	8/18 (44)	0.26
FNA-needle	22 gauge	25 gauge
EUS-FNA-sensitivity	20/37 (54)	9/15 (60)	0.77
FNA-passes	< 3 passes	≥ 3 passes
EUS-FNA-sensitivity	9/17 (53)	20/35 (57)	1.0
Sampling order1	EUS-FNA first	EUS-FNB first
EUS-FNA-sensitivity	12/19 (61)	10/19 (53)	0.63

¹Only the GISTs (n = 38) sampled during the Study Period (2012-2015). All study GISTs examined by EUS-FNA (n = 52) from 2006 to 2015. GIST: Gastrointestinal stromal tumor; EUS: Endoscopic ultrasound; FNA: Fine needle aspiration; FNB: Fine needle biopsy.

Table 3 Individual case data on the mutation profile, treatment, and Ki-67-index

Case	Mutation gene and exon	Mutation	Treatment neoadj1	Surgery	Group	EUS-surgery (mo)	Ki67EUS	Ki67SURG	Ki67RED
1	KIT exon 11	p.V560del	No	Yes	Neo-	2	2.2	2.8	26
2	PDGFRA exon 18	p.D842V2	No	No	NA	-	NC	-	-
3	Wild Type	Wild Type	Yes	Yes	Neo + r	2	2.1	1.7	-19
4	KIT exon 11	p.V559D	Yes	Yes	Neo + s	6	4.2	0.7	-82
5	KIT exon 11	p.Y553-Q556del	Yes	Yes	Neo + s	13	1.5	0.2	-84
6	Unknown	Unknown	No	No	NA	-	NC	-	-
7	KIT exon 11	V559D	No	No	NA	-	2.4	-	-
8	KIT exon 11	p.P577-R586dupl	No	Yes	Neo-	2	6.3	7.4	17
9	KIT exon 11	V559del	Yes	Yes	Neo + s	9	2.5	0.1	-96
10	KIT exon 11	p.V560D	No	Yes	Neo-	1	1.5	1.8	17
11	KIT exon 11	p.V560D	No	Yes	Neo-	2	0.8	1.2	47
12	KIT exon 11	p.V560del	Yes	No	NA	-	19.3	-	-
13	KIT exon 11	p.V559D	No	Yes	Neo-	3	1.9	0.9	-52
14	KIT exon 11	V559G	Yes	Yes	Neo + s	16	1.6	0.9	-43
15	PDGFRA exon 18	p.D842V	Yes	Yes	Neo + r	2	9.1	9.0	-1
16	KIT exon 11	p.W557G	Yes	Yes	Neo + s	12	0.6	0.1	-93
17	KIT exon 11	p551-W557delinsR	Yes	Yes	Neo + s	12	3.4	0.2	-94
18	KIT exon 11	D579del	No	Yes	Neo-	2	6.7	6.3	-6
19	PDGFRA exon 12	E556-I565dupl	Yes	Yes	Neo + s	2	0.9	0.1	-89
20	KIT exon 13	p K642E	Yes	Yes	Neo + r	4	20.1	15.3	-24
21	KIT exon 11	p.W557R	No	Yes	Neo-	2	7.2	7.8	9
22	KIT exon 11	V559D	Yes	Yes	Neo + s	2	5.6	0.3	-95
23	KIT exon 11	P551-E554delinsQ	Yes	Yes	Neo + s	12	5.8	0.1	-98
24	KIT exon 11	K558-G565delinsR	Yes	No	NA	-	21.5	-	-
25	PDGFRA exon 18	p.D842V	No	No	NA	-	1.5	-	-
26	PDGFRA exon 18	p.D842V	Yes	Yes	Neo + r	1	2.7	2.5	-10
27	KIT exon 11	V559D	No	Yes	Neo-	3	2.8	3.1	13
28	KIT exon 11	p.V559D	No	Yes	Neo-	2	1.1	0.8	-25
29	KIT exon 11	p.V559D	Yes	Yes	Neo + s	17	2.5	0.2	-90
30	KIT exon 11	pQ575-L576dupl	No	No	NA	-	2.7	-	-
	KIT exon 13	V654A
31	KIT exon 11	V559D	No	No	NA	-	1.4	-	-
32	KIT exon 11	p.L576P	No	No	NA	-	1.8	-	-
33	PDGFRA exon 18	p.D842V	No	Yes	Neo-	2	6.6	8.9	35
34	PDGFRA exon 18	p.D846Y	No	Yes	Neo-	2	2.6	2.0	-22
35	KIT exon 11	p P551-W560del	No	No	NA	-	3.0	-	-
36	KIT exon 11	V560E	Yes	No	NA	-	NC	-	-
37	Wild type	Wild type	Yes	Yes	Neo + r	3	9.2	12.0	31
38	KIT exon 11	pL567del	Yes	No	NA	-	10.1	-	-
39	PDGFRA exon 12	M578-S584del	Yes	No	NA	-	11.0	-	-
40	KIT exon 11	p.P551-Q556del	Yes	No	NA	-	4.6	-	-
41	KIT exon 11	p.N567-T574del	No	Yes	Neo-	1	8.3	6.8	-18
42	KIT exon 11	57-E561del	Yes	No	NA	-	4.6	-	-
43	Wild type	Wild type	No	No	NA	-	0.1	-	-
44	KIT exon 9	A502-Y503dupl	Yes	No	NA	-	0.7	-	-

¹Neoadjuvant treatment with imatinib;

²For comparison, the sequencing was performed on an endoscopy biopsy. The 44 GIST study cases sampled with EUS-FNB and ordered by the date of study enrollment. Ki-67_EUS: The Ki-67_index (%) of the EUS-biopsies; Ki-67_SURG: The Ki-67_index (%) of the resected specimens; Ki-67_RED: The percentage of the reduction in the Ki-67_index, comparison of the Ki-67_EUS with the Ki-67_SURG (see Methods); NA: Not annotated; NC: Not countable; KIT: KIT proto-oncogene receptor tyrosine kinase; PDGFRA: Platelet-derived growth factor receptor alpha.