Table 1

Focal regions of CNA regions in gastric cancer

CNA	Chr	Start	End	Length (kb)	Cytoband	Q value	Genes in peak
Amplification
1	10	123 336 181	123 337 713	1.5	10q26.13	3.9561E-99	*FGFR2*
2	8	128 628 340	128 670 251	41.9	8q24.21	7.984E-27	*[MYC]*
3	19	34 982 652	35 002 397	19.7	19q12	3.1439E-23	*CCNE1*
4	12	25 213 920	25 336 398	122.5	12p12.1	1.5713E-14	*KRAS, CASC1, LYRM5*
5	18	17 947 474	18 040 783	93.3	18q11.2	1.0616E-13	GATA6
6	5	21 377 838	21 406 308	28.5	5p14.3	9.501E-12	*[CDH12]*
7	7	91 921 079	92 111 471	190.4	7q21.2	2.0612E-10	*CDK6, PEX1, GATAD1, DKFZP564O0523, FAM133B*
8	8	11 346 688	11 659 701	313.0	8p23.1	9.0544E-10	BLK, GATA4, C8orf13
9	7	55 237 447	55 373 693	136.2	7p11.2	2.4109E-09	*EGFR*
10	17	35 102 118	35 136 335	34.2	17q12	3.8268E-09	*ERBB2*
11	13	72 528 937	72 770 614	241.7	13q22.1	1.4729E-07	KLF5
12	11	69 161 019	69 306 967	145.9	11q13.2	9.1737E-07	*CCND1, FGF4, FGF19, ORAOV1*
13	7	115 987 034	116 178 774	191.7	7q31.2	0.00012527	CAV1, *MET*
Deletion
1	3	60 447 451	60 472 964	25.5	3p14.2	3.4002E-41	*FHIT*
2	8	4 182 635	4 182 916	0.3	8p23.2	1.0797E-18	CSMD1
3	9	21 953 419	21 995 192	41.8	9p21.3	1.0299E-17	*CDKN2A, CDKN2B*
4	6	2 019 538	2 068 880	49.3	6p25.3	1.7756E-14	GMDS
5	16	77 269 209	77 293 232	24.0	16q23.1	5.4871E-12	WWOX
6	6	162 551 244	162 610 874	59.6	6q26	2.1056E-11	PARK2
7	13	47 806 677	47 809 375	2.7	13q14.2	3.3682E-11	*RB1*
8	5	58 436 441	58 569 237	132.8	5q11.2	1.6661E-10	PDE4D
9	9	9 524 063	9 675 303	151.2	9p23	1.2287E-09	PTPRD

Focal recurrent CNA (amplifications and deletions) identified by genomic identification of significant targets in cancer (GISTIC). Genes previously reported as oncogenes or tumour suppressor genes are highlighted in bold. Start and end indicates the boundary of the region identified. Length indicates size of each region identified. Q value represents the significance of the recurrent CNA region across all the gastric tumours. Genes in peak, genes covered by the corresponding region, a square bracket indicates that the gene lies immediately adjacent to the peak.