Cost-effective low-coverage whole-genome sequencing assay for the risk stratification of gastric cancer

Table 1 Clinical features of the 40 study patients diagnosed with gastric cancer

	EBV+	H. Pylori+	ERBB2+	KRAS+	P value
Age (yr), mean ± SD	62.2 ± 6.4				No significance
Sex, n					No significance
Male	3	13	8	5
Female	2	2	1	2
Tumor location, n					P = 0.013 (H. Pylori associated with antrum)
Cardia/fundus	5	2	3	1
Polyrus/antrum	0	13	5	6
Other	0	0	1	0
Borrmann, n					P = 0.013 (H. Pylori associated with ulcerative)
Type I	1	1	2	2
Type II	1	7	4	1
Type III	1	7	2	2
Type IV	2	0	1	1
Gastritis, n					No significance
Yes	0	4	2	2
No	5	11	7	5
Vascular invasion, n					No significance
Yes	2	9	1	2
No	3	6	8	5

H. Pylori: Helicobacter pylori.

Table 2 Copy number variation segments identified in gastric cancer patients

Chrom	Loc.start	Loc.end	Seg.mean	LogP	Key genes
Chr04	0	190800000	-1.63	-100.00	FHIT
Chr05	45800000	131000000	-1.49	-100.00
Chr13	19000000	110000000	0.87	-88.38
Chr18	30800000	77800000	-1.86	-86.67
Chr03	0	66200000	-1.23	-80.98
Chr07	0	55600000	1.28	-75.03	EGFR
Chr20	30200000	62800000	2.54	-74.06
Chr16	0	76200000	-0.93	-67.73
Chr08	90600000	122000000	1.84	-59.87
Chr05	0	45600000	1.29	-56.55	TERT
Chr01	170000000	240000000	0.78	-55.86
Chr21	9400000	47800000	-1.33	-54.61
Chr09	0	29800000	-1.56	-50.52	CDKN2A
Chr08	47800000	90400000	1.02	-49.62
Chr08	122200000	146000000	2.42	-49.24	MYC
Chr01	29600000	98400000	-0.69	-47.14
Chr19	0	28800000	-2.03	-43.15
Chr10	50800000	111400000	-0.77	-41.27
Chr03	165800000	197800000	1.19	-40.36
Chr22	16000000	51000000	-1.11	-38.57
Chr14	19000000	107000000	-0.57	-37.54
Chr12	107600000	133600000	-1.44	-36.53
Chr15	20000000	88200000	-0.60	-34.61
Chr01	151200000	169800000	1.47	-32.21
Chr17	0	21800000	-1.75	-31.78	TP53
Chr03	96200000	165600000	0.48	-30.10
Chr19	32200000	58800000	-1.15	-29.94
Chr07	76400000	117800000	0.66	-28.48
Chr05	131200000	180600000	-0.70	-28.10
Chr17	49200000	80800000	-0.85	-26.77
Chr06	26000000	57000000	0.80	-25.75
Chr12	73400000	107400000	-0.64	-23.98
Chr06	57200000	104200000	-0.63	-22.49
Chr20	0	17000000	1.09	-22.19
Chr20	17200000	30000000	1.73	-18.89
Chr01	98600000	109600000	-1.31	-18.38
Chr11	67000000	96000000	0.58	-17.22
Chr08	20200000	47600000	-0.82	-16.59
Chr03	66400000	96000000	-0.54	-16.41
Chr01	19800000	29400000	-1.60	-15.48
Chr02	92200000	122200000	0.51	-14.89
Chr11	37000000	66800000	-0.69	-14.39
Chr02	153200000	193600000	0.37	-14.32
Chr09	30000000	115400000	-0.36	-13.72
Chr01	0	19600000	-0.77	-12.44
Chr10	200000	5600000	1.32	-10.20
Chr02	62400000	76000000	0.58	-9.30
Chr12	7400000	31200000	-0.40	-9.25
Chr13	110200000	113800000	3.69	-8.57
Chr06	104400000	170800000	0.24	-8.31
hr18	23000000	30600000	-0.85	-7.70
Chr12	31400000	38200000	-1.65	-7.02
Chr15	88400000	95200000	0.80	-6.84
Chr16	76400000	90000000	-0.45	-6.61
Chr12	52200000	58200000	0.72	-6.00
Chr19	29000000	32000000	1.50	-6.00
Chr08	0	6200000	-0.65	-5.82
Chr10	123000000	126800000	1.09	-5.72
Chr11	96200000	134800000	-0.26	-5.51
Chr17	37600000	39600000	4.54	-5.50
Chr02	122400000	153000000	-0.28	-5.38
Chr07	55800000	76200000	-0.63	-5.35
Chr15	99200000	102200000	1.24	-5.04
Chr11	0	4000000	-1.16	-4.92
Chr12	38400000	52000000	-0.46	-4.85
Chr01	109800000	119800000	-0.44	-4.03
Chr01	120000000	151000000	0.52	-4.01
Chr07	118000000	158800000	-0.21	-3.77
Chr17	22000000	37400000	0.44	-3.48
Chr08	6400000	20000000	0.27	-3.01