Characterization of genetic rearrangements in esophageal squamous carcinoma cell lines by a combination of M-FISH and array-CGH: further confirmation of some split genomic regions in primary tumors

Jia-Jie Hao; Zhi-Zhou Shi; Zhi-Xin Zhao; Yu Zhang; Ting Gong; Chun-Xiang Li; Ting Zhan; Yan Cai; Jin-Tang Dong; Song-Bin Fu; Qi-Min Zhan; Ming-Rong Wang

doi:10.1186/1471-2407-12-367

Table 4 Recurrent breakpoint regions analyzed by array-CGH in ESCC cell lines

From: Characterization of genetic rearrangements in esophageal squamous carcinoma cell lines by a combination of M-FISH and array-CGH: further confirmation of some split genomic regions in primary tumors

Region	Cell line	CN status^a	BP Intervals (hg 18) in array-CGH	Distance between cell lines^b	Genes^c	CFSs
9p21.3 a	KYSE180	Neutral/Del	21958099-21968346	115.1 kb	C9orf53 ^§ , CDKN2A ^* , CDKN2B ^† , CDKN2B-AS1 ^†	FRA9C
	KYSE450	Neutral/Del	21853263-21968346		MTAP ^§ , C9orf53 ^§ , CDKN2A ^*
	KYSE510	Loss/Del	21958099-21968346		C9orf53 ^§ , CDKN2A ^* , CDKN2B ^† , CDKN2B-AS1 ^†
	YES2	Neutral/Del	21853263-21957548		MTAP ^§ , C9orf53 ^† , CDKN2A ^†
15q25.3	KYSE450	Neutral/Gain	86361096-86429254	154.2 kb	LINC00052 ^§ , NTRK3 ^* , MRPL46 ^† , MRPS11 ^†
	KYSE510	Neutral/Gain	86275066-86429254		LINC00052 ^§ , NTRK3 ^* , MRPL46 ^† , MRPS11 ^†
11q13.4	KYSE30	Amp/Loss	70964483-71305189	340.1 kb	KRTAP5-11 ^§ , FAM86C1, DEFB108B, RNF121 ^†	FRA11H
	KYSE510	Amp/Neutral	70964483-71305189		KRTAP5-11 ^§ , FAM86C1, DEFB108B, RNF121 ^†
3q28	KYSE180	Gain/Gain	191171376-191222891	517.0 kb	TP63 ^§ , LEPREL1 ^* , CLDN1 ^†
	KYSE510	Neutral/Gain	191610761-191688399		CLDN1 ^§ , CLDN16, TMEM207 ^† , IL1RAP ^†
10q26.3	KYSE30	Neutral/Gain	133045086-133476780	801.8 kb	TCERG1L ^§ , PPP2R2D ^†
	YES2	Neutral/Gain	133795639-133846905		BNIP3 ^§ , JAKMIP3 ^* , DPYSL4 ^†
11q13.3	KYSE30	Amp/Amp	69339391-69569221	1.05 Mb	FGF3 ^§ , ANO1 ^† , FADD ^†	FRA11H
	KYSE180	Amp/Amp	70182767-70386856		CTTN ^§ , SHANK2 ^* , DHCR7 ^†
4p13	KYSE150	Amp/Loss	41832777-42109513	1.15 Mb	SLC30A9 ^§ , BEND4, SHISA3 ^† , ATP8A1 ^†
	KYSE510	Neutral/Loss	40955943-41226036		UCHL1 ^§ , LIMCH1 ^* , PHOX2B ^†
11p13	KYSE510	Neutral/Gain	33107818-33136537	1.2 Mb	TCP11L1 ^§ , PIGCP1 ^§ , CSTF3 ^* , HIPK3 ^†
	YES2	Neutral/Gain	34278741-34307224		NAT10 ^§ , ABTB2 ^* , CAT ^†
8q24.21	KYSE450	Amp/Neutral	129216964-129574570	1.23 Mb	FAM84B ^§ , POU5F1B, MYC ^† , PVT1 ^†
	KYSE510	Amp/Loss	129972316-130159085		FAM84B ^§ , POU5F1B, MYC ^† , PVT1 ^†
	YES2	Amp/Neutral	130159144-130451718		far from genes, PVT1 ^§ , GSDMC ^†
2q35	KYSE30	Loss/Neutral	217432472-218386863	1.37 Mb	DIRC3 ^§ , TNS1, CXCR2P1 ^†
	KYSE150	Loss/Gain	218517852-218801703		TNS1 ^§ , CXCR2P1, CXCR2, CXCR1, HMGB1P9, ARPC2 ^†
1q31.1	KYSE150	Gain/Loss	186080345-186315797	1.40 Mb	PLA2G4A ^§, FAM5C ^†	FRA1K
	KYSE450	Gain/Neutral	184912220-185051701		PTGS2 ^§ , PLA2G4A ^†
21q21.1	KYSE30	Gain/Neutral	17060792-17145790	1.48 Mb	USP25 ^§ , C21orf34 ^§ , CXADR ^†
	YES2	Gain/Neutral	18435266-18540695		CHODL-AS1 ^§ , CHODL ^† , TMPRSS15 ^†
9p21.3 b	KYSE180	Del/Neutral	21999029-22136626	1.45 Mb	CDKN2A ^* , CDKN2B, CDKN2B-AS1, DMRTA1 ^†	FRA9C
	KYSE450	Del/Neutral	21980581-21993651		CDKN2A ^* , CDKN2B, CDKN2B-AS1 ^* , DMRTA1 ^†
	KYSE510	Del/Loss	22992377-23425976		DMRTA1 ^* , ELAVL2 ^†
	YES2	Del/Neutral	21999029-22136626		CDKN2B, CDKN2B-AS1, DMRTA1 ^†
18q12.2	KYSE450	Gain/Loss	33583906-33747373	1.64 Mb	CELF4 ^§ , LOC647946 ^†	FRA18A
	KYSE510	Amp/Loss	32107441-32200063		MOCOS ^§ , FHOD3, C18orf10 ^†
3p14.2	KYSE150	Gain/Loss	58573676-58887412	1.69 Mb	FAM107A ^§ , FAM3D, C3orf67, FHIT ^†	FRA3B
	KYSE450	Neutral/Del	59933661-60267262		FHIT ^#
3q12.1-q12.2	KYSE180	Neutral/Amp	100190484-100877203	1.86 Mb	TFG ^§ , ABI3BP ^* , IMPG2 ^†
	KYSE450	Neutral/Gain	102009730-102076392		DCBLD2 ^§ , COL8A1 ^†
6p12.3-p12.2	KYSE150	Loss/Amp	51932658-52161439	1.9 Mb	PKHD1 ^§ , IL17A ^† , MCM3 ^†
	YES2	Gain/Gain	50261630-50627364		DEFB112 ^§ , TFAP2D ^†

^a Copy number status on the left and right side of the breakpoint regions. CN: copy number, Amp: amplification, Del: deletion.
^b The distance between two outermost breakpoints of all the different cell lines.
^c These genes are located at or close to breakpoints in each cell line. “^*”: Obvious breakpoints were detected inside of genes. “^§” and “^†”: Genes at the left and right side of the breakpoint regions, respectively. Genes that are not labeled are located in the breakpoint regions, but positions of the exact breakpoints are not determined. “^#”: Genes with an inside homozygous deletion (HD), and thus might also be disrupted.

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