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Table 1 High-level alterations detected by array CGH

From: Comprehensive copy number profiles of breast cancer cell model genomes

Cell line

Locus

Start clone

End clone

Size (kb)

 

Locus

Start clone

End clone

Size (kb)

MCF7

Amplifications

 

Deletions

 

1p13.3

N0451I14

N0228E23

1,290

 

3q13.31

N0747H24

N0362H11

700

 

1p13.2

N0099M15

N0795O09

288

 

4q34.3-35.2

N0442N05

N0746B09

7,100

 

1p13.2

N0626F04

N0517B05

1,330

 

6q25.2-27

M2007C03

M2258B24

14,400

 

3p14.2-14.1

N0669F02

N0589G04

3,180

 

8p arm

p

p

p

 

8q21.2-q24.21

N0133G02

N0315E09

43,300

 

11p15.5-11.2

N0412M16

M2326E01

45,300

 

15q21.1-21.3

N0416B20

N0664B09

4,930

 

11p11.2

N0070A09

M2326E01

1,940

 

17q23.2-24.3

N0716B04

N0203A19

113,200

 

11q11-q12.1

N0010E21

F0627I09

4,300

Peak:

17q23.2

N0760B22

N0433B24

4,900

 

11q14.2-23.3

N0282G16

N0004N09

30,000

 

17q25.1

N0076G04

N0552F03

766

 

11q23.3-25(tel)

N0196E01

N0715D10

15,400

 

20q12

N0385G02

N0476P15

1,790

 

13q14.2-34(tel)

N0155D15

M2323L19

66,900

 

20q13.12-20q13.33 (tel)

N0272C13

N0476I15

17,500

     

Peaks:

20q13.12-20q13.13 A

N0702E03

N0730O20

1,790

     
 

20q13.13 B

N0711M06

F0592G15

309

     
 

20q13.2 C

N0020J08

N0346B03

1,450

     
 

20q13.31 D

N0044A06

N0671P16

411

     
 

21q22.13-22.3(tel)

N0094J12

N0457P07

8,450

     

BT474

Amplifications

 

Amplifications

 

1q21.2-q25.1

    

15q11.2 -q12

N0607H20

N0208F21

5,030

Peaks:

1q21.2-q21.3 A

N0035F14

N0714N02

366

Peaks:

15q11.2 A

N0552D03

M2200G17

949

 

1q22-q23.1 B

N0647N20

N0740J19

510

 

15q11.2 B

N0484P15

N0710L06

624

 

1q24.2 C

N0137J06

N0616K15

540

 

17q12-21.2

N0196P12

N0278E15

4,090

 

1q31.3

N0662E13

N0141E20

1,661

 

17q21.32-23.2

N0771D19

M2014K24

13,800

 

1q32.1

N0783D13

N0617D19

936

Peaks:

17q21.32-q21.33 A

N0071G24

N0607H13

2,500

 

1q42.12-q42.13

M2185P06

M2016D17

500

 

17q22-23.2 B

N0515J20

N0473G17

2,180

 

1q43

N0236L13

N0614N14

449

 

17q23.2 C

N0399O18

N0767P09

1,170

 

1q44-q43

N0440F10

N0794A13

865

 

17q24.1-24.3

N0583F02

N0693H11

5,300

 

1q44

N0778E23

N0071K05

1,720

Peak:

17q24.1

N0583F02

N0394K10

482

 

4p16.1-15.33

N0270I03

N0652B07

1,210

 

19p13.2-13.12

N0295M02

N0441D06

6,310

 

4q21.1

N0598G02

N0772N01

2,700

 

20p12.1

N0134G22

N0022E15

800

 

9p13.3

N0069E18

N0795P12

2,060

 

20q11.22

N0601G07

N0552G16

1,300

 

9q33.1-34.13

M2248M11

N0738I14

12,600

 

20q13.11-13.32

N0809G24

N0261P09

14,800

 

11q13.1-13.5

N0813P09

N0360N22

19,800

 

20q13.33

N0648D07

N0694I10

305

Peaks:

11q13.1 A

N0029K11

N0804F01

704

 

20q13.33-tel

N0305P22

N0134L13

1,380

 

11q13.4 B

N0093M11

N0598G03

1,030

 

Deletions

 

11q22.1-22.2

N0795D03

N0347H03

3,560

 

5q14.1-14.3

N0129E04

N0291O24

5,390

 

14q11.2-q21.1

N0597A11

N0254B15

21,230

 

6q24.1

N0709J21

M22024J17

3,200

 

14q31.3-32.12

N0771O08

N0325L17

3,080

 

20q11.22

N0171G22

N0774C15

670

      

20p11.23-13.11

N0712N14

N0464F07

7,140

ZR 75 30

Amplifications

 

Amplifications

 

8q11.21

N0569I08

N0513O13

682

 

17q22-23.2

N0349F01

N0153J08

5,600

 

8q13.3

N0367C12

N0634L17

538

Peaks:

17q23.2 A

N0159D12

M2023J07

298

 

8q21.2

N0319A24

N0317J10

1,350

 

17q23.2 B

N0381A05

N0634F05

3,560

 

8q21.3

N0565H20

N0102D03

264

 

17q23.3-24.1

N0614F05

N0712A10

481

 

8q22.1

N0381I07

N0103P22

729

 

Deletions

 

8q22.2-24.3

N0281D17

N0620H01

45,600

 

1p36.33-35.3

N0206L10

N0758C04

26,700

Peaks:

8q23.1 A

N0078J05

N0357L07

907

 

1p35.2-35.1

N0629A12

N0068H10

775

 

8q24.12 B

N0760H22

N0088J18

1,440

 

1p34.3

N0452M14

N0020P17

1,510

 

8q24.22 C

N0100J23

N0422I20

440

 

1p21.2-13.3

N0293L15

N0813H10

10,800

 

8q24.3 D

N0662P06

F0530P15

2,740

 

4q21.1

N0184F15

N0184J11

151

 

17q11.1-11.2

N0260A09

N0147N18

3,050

 

11q13.5-25(tel)

N0149B15

M2270L17

57,600

 

17q12

N0600K04

N0560P04

980

 

17q11.2-12

N0082D14

N0104J23

6,020

 

17q12

N0722D15

N0062P03

1,360

 

17q21.1-21.32

N0278E15

N0046I22

7,700

 

17q12-21.1

N0689B15

N0032H06

490

 

17q23.33-22

N0368A16

N0379H09

994

 

17q21.32-21.33

N0771D19

M2190C10

3,910

 

17q22

N0466D20

N0515J20

881

      

21q11.2-q22.11

N0615H23

N0694N16

16,300

UACC 893

Amplifications

 

Deletions

 

7p21.1

N0116D07

N0746H13

733

 

11p15.1

N0118A14

N0614L12

995

 

11q13.3-q14.3

M2011L13

N0613M07

24,700

 

16p12.1

N0104F06

N0674B07

1,380

 

11q22.1

N0743I15

N0659E10

619

 

17p arm

p

p

p

 

17q12-21.2

N0600J16

N0686E05

1,490

     
 

17q21.33-24.2

N0095M07

N0068K09

17,700

     
 

17q25.1

N0076G04

N0449J21

999

     

SKBR3

Amplifications

 

Amplifications

 

3p22.2

N0091E04

N0325M12

432

 

17q12-21.2

N0062P03

N0606M07

3,390

 

3q25.1

N0739J07

N0118L18

678

 

17q25.3

N0305C04

N0781F24

1,550

 

3q22.3-q23

N0657M13

N0718H02

2,000

 

20p arm

p

p

p

 

3q26.2-q26.31

N0190I05

N0590E04

3,300

 

20q11.22-11.23

N0454F11

N0254N13

4,510

 

7q31.1-q32.3

M2023N18

N0019B03

17,800

 

20q12-13.32

N0434N22

N0290D09

16,200

 

8q13.3-21.13

N0746L20

N0125J17

10,600

 

Deletions

 

8q21.2-21.3

N0509F16

N0561A10

5,950

 

8q21.3-22.1

N0230C03

N0804A07

6,040

Peaks:

8q21.2 A

N0694L21

N0606L16

309

 

8q22.3-23.1

N0739L19

N0025P11

4,920

 

8q21.3 B

N0129P07

N0196C06

559

 

8q24.22

N0015L05

N1147M08

1,570

 

8q21.3 C

N0627A06

N0529J09

499

 

8q24.23-24.3

N0467B24

N0613F12

3,810

 

8q23.2-24.21

N0114O08

N0294P07

17,100

 

10q22.3-25.2

N0635P19

N0257E05

30,900

Peaks:

8q23.3 A

N0058O03

N0531C21

746

 

12q23.3-24.11

N0061L24

M2155D19

1,380

 

8q23.3 B

N0164M09

M2118B16

365

 

12q24.21-24.31

N0412G23

N0138I16

5,360

 

8q24.12 C

N0389M07

N0047A23

821

 

17q11.2-12

N0634A23

N0607B02

6,460

 

8q24.21 D

N0288B17

N0294P07

716

 

17q21.2-23.2

N0400F19

N0767P09

18,100

 

10q21.1-22.3

N0195P24

N0506E07

25,500

 

18q12.2-21.2

N0645I23

N0664P08

20,400

 

14q31.3-32.12

N0046B20

N0386D20

7,020

 

19p13.11

N0715L15

N0723M22

4,710

 

17q11.1-11.2

N0458L21

N0193M11

3,170

     

MDA MB 231

Amplifications

 

Deletions

 

6p21.31-21.2

N0479F12

N0450J18

3,510

 

8q24.13

N0346M14

N0391A17

1,020

 

6p21.2-21.1

N0259H15

N0769C16

3,290

 

9p24.2-22.2

N0654D08

N0460F23

14,500

 

7q35

N0703N05

N0340G20

670

Peak:

9p22.3-22.2

N0141K07

N0460F23

2,000

      

9p21.3-21.2

N0066P03

N0486D12

5,210

     

Peak:

9p21.3

N0315I14

N0730N17

280

T47D

Amplifications

 

Deletions

 

3q26.2-29(tel)

N0415B12

M2110L16

28,700

 

12p13.32-12.3

N0312A03

N0056F05

11,700

 

11q23.3-25(tel)

N0081I13

M2013A02

15,200

 

18p11.32-11.32

N0619C21

N0193E15

349

 

Deletions

 

18q21.1

N0699O23

N0093N16

311

 

8p23.1

N0485I05

M2185F10

1,000

 

Xq

q

q

q

 

8p23.1

N0367E11

N0801I21

704

     
  1. High-level peaks within complex alterations are denoted by italics. Alterations not previously characterized are in bold. Clones beginning with N0 or F0 belong to the Roswell Park Cancer Institute libraries 11 and 13 (RP11 and RP13), respectively; those beginning with M belong to the Caltech-D (CTD) library.