Integrated Genome-Wide Analysis of Gene Expression and DNA Copy Number Variations Highlights Stem Cell-Related Pathways in Small Cell Esophageal Carcinoma

Table 3

Minimal common regions of recurrent copy number amplification and deletion ().

Chromosomal aberration	Positon (Mb)	Size (Mb)	(%)	Samples	Possible cancer-associated genes
Gains
14q11.2	20.22–23.91	3.69	3 (100%)	1, 2, 3	—
3q25.31-q29	155.59–197.83	42.25	2 (67%)	1, 3	TCTEX1D2, YEATS2, PIGX, LRCH3, RFC4, LSG1, CAMK2N2
5p15.31-15.2	8.87–10.99	2.12	2 (67%)	1, 2	PAIP1
8q21.11-24.3	74.51–146.28	71.76	2 (67%)	1, 3	ZNF704, PTP4A3, ZNF7
9p23-13.1	9.38–39.07	29.7	2 (67%)	1, 2	EXOSC3
14q11.2-32.33	19.38–20.22	0.84	2 (67%)	1, 2	—
	23.91–107.29	83.37	2 (67%)	1, 3	—
Losses
4q22.3-23	98.14–99.10	0.96	3 (100%)	1, 2, 3	—
3p26.3-25.3	0.07–90.25	90.07	2 (67%)	1, 2	IP6K2, APEH, TMEM42, WNT5A, UQCRC1, C3orf38, RPL29, PRKAR2A, MAP4, AZI2, ALAS1, GOLGA4, FBLN2, SHQ1, ATG7
4p16.3-11	0.72–49.06	48.99	2 (67%)	2, 3	GBA3, SH3TC1
4q11-22.3	52.69–98.14	45.45	2 (67%)	2, 3	STAP1, GNRHR, REST
4q23-25	99.10–107.92	8.22	2 (67%)	2, 3
8p23.3	0.18–0.50	0.33	2 (67%)	2, 3	—
16p13.3	5.50–5.61	0.12	2 (67%)	1, 3	—
	6.75–6.82	0.06	2 (67%)	1, 3	—