Detection of a novel panel of 24 genes with high frequencies of mutation in gastric cancer based on next-generation sequencing

Table 1 Cancer genes targeted in the custom panel

24-gene panel
ATR	ATM	AR	BRCA2	BMPR1A	CHD4
CDKN2A	ERBB2	ERBB3	FBXW7	FGFR2	KRAS
KDR	KIT	MET	MSH2	MTOR	NF1
PTEN	PDGFRA	PIK3CA	PTPN11	STK11	TP53

Table 2 Clinicopathological features of the custom panel and cBioPortal database

Clinical information	Custom panel, n (%)	cBioPortal database, n (%)
Total	64	258
Age median (range)	64 (25-83)	68 (34-90)
Sex
Male	50 (78.1)	156 (60.5)
Famale	14 (21.9)	102 (39.5)
T classification
T1	20 (31.2)	11 (4.3)
T2	33 (51.6)	43 (16.7)
T3	10 (15.6)	133 (51.5)
T4	1 (1.6)	63 (24.4)
Unknown	0 (0)	8 (3.1)
N classification
N0	24 (37.5)	87 (33.7)
N1	18 (28.1)	54 (20.9)
N2	6 (9.4)	52 (20.2)
N3	16 (25.0)	54 (20.9)
Unknown	0 (0)	11 (4.3)
M classification
M0	58 (90.6)	238 (92.2)
M1	6 (9.4)	18 (7)
Unknown	0 (0)	2 (0.8)
Clinical stage
Stage I	10 (15.6)	32 (12.4)
Stage II	28 (43.8)	102 (39.5)
Stage III	23 (35.9)	92 (35.7)
Stage IV	3 (4.7)	18 (7)
Unknown	0 (0)	14 (5.4)
Lauren class
Diffuse	22 (34.4)	62 (24.0)
Intestinal	40 (62.5)	169 (65.5)
Mixed	2 (3.1)	16 (6.2)
Unknown	0 (0)	11 (4.3)

Table 3 Correlation of TP53 mutations with the clinicopathological features of the custom panel and the cBioPortal database

Clinicalinformation	Custom panel		P value	cBioPortal database		P value
	Wild	Mutated		Wild	Mutated
Age
≤ 65	16	19	0.530	60	48	0.878
> 65	11	18		79	68
Unknown	0	0		2	1
Sex
Male	19	31	0.200	86	70	0.849
Female	8	6		55	47
T classification
T1	10	10	0.716	6	5	0.451
T2	13	20		23	20
T3	4	6		67	66
T4	0	1		39	24
Unknown	0	0		6	2
N classification
N0	7	17	0.310	45	42	0.929
N1	10	8		29	25
N2	2	4		29	23
N3	8	8		31	23
Unknown	0	0		7	4
M classification
M0	25	33	0.645	127	111	0.040
M1	2	4		14	4
Unknown	0	0		0	2
clinical stage
Stage I	6	4	0.414	17	15	0.255
Stage II	9	19		51	51
Stage III	11	12		50	42
Stage IV	1	2		14	4
Unknown	0	0		9	5
Lauren class
Diffuse	12	10	0.059	44	18	0.017
Intestinal	13	27		81	88
Mixed	2	0		10	6
Unknown	0	0		6	5

Table 4 Treatment options based on gene mutations according to the OncokB database

Gene	Variation type	Variable area	Associated drug	Level of evidence
ERBB2	CNV	Amplification	Trastuzumab, Pembrolizumab	1
NF1	Mutation	Oncogenic variants	Trametinib, Cobimetinib	4
PIK3CA	Mutation	C420R, E542, E545, Q546, H1047	Alpelisib + Fulvestrant	3B
BRCA2	Mutation	Oncogenic variants	Olaparib, Talazoparib, Niraparib, Rucaparib	3B
FGFR2	Fusions/Mutation	Fusions, Oncogenic variants	Infigratinib, Erdafitinib, Debio1347, AZD4547	4
PTEN	Mutation	Oncogenic variants	GSK2636771, AZD8186	4
MET	CNV, exon 14-skipping	Exon 14-skipping, Amplification	Crizotinib	4
KRAS	Mutation/CNV	G12C, Oncogenic Mutations	Adagrasib, Sotorasib, Trametinb, Cobimetinib, Binimetinib	3B, 4
KIT	Mutation/CNV	Exon 8, 9, 11, 13, 14, 17, 18	Imatinib, Sunitinib, Regorafenib	4
MTOR	Mutation	Oncogenic variants	Everolimus, Temsirolimus	4
CDKN2A	Mutation	Oncogenic variants	Palbociclib, Ribociclib, Abemaciclib	4
PDGFRA	Mutation/CNV	Exon 12, 14, 18	Imatinib, Sunitinib, Regorafenib	4