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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 statusa BP Intervals (hg 18) in array-CGH Distance between cell linesb Genesc 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 †  
  1. a Copy number status on the left and right side of the breakpoint regions. CN: copy number, Amp: amplification, Del: deletion.
  2. b The distance between two outermost breakpoints of all the different cell lines.
  3. 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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BMC Cancer

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