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Table 2 Bioinformatic analysis of the analyzed breakpoints

From: Non random distribution of genomic features in breakpoint regions involved in chronic myeloid leukemia cases with variant t(9;22) or additional chromosomal rearrangements

Cytogenetic Band

Case

Molecular Breakpoint

250 Kb interval

ALU

LINE

REF SEQ (IB)

REF SEQ (IC)

SD (IC)

SD (IB)

GC

1p34.2

2

RP11-318G20_RP11-632A13

chr1:40,158,249-40,408,249

2,27

0,77

0,71

2,16

0,67

0,21

1,06

1q32.1

1

RP11-219P13_RP11-1089F13

chr1:203,949,120-204,199,120

1,13

0,78

1,11

3,09

0,44

0,27

1,07

1q32.1

1

RP11-145I13_RP11-57I17

chr1:205,496,738-205,746,738

0,52

1,55

0,76

1,85

0,22

0,15

0,91

2q37.1

4

RP11-332L11_RP11-94I20

chr2:234,468,641-234,718,641

0,69

0,94

1,3

1,01

0

0

1,05

3p21.31

5

RP11-804H15_RP11-3B7

chr3:49,112,155-49,393,337

4,17

0,16

1,7

7,05

0

0

1,24

3p21.31

6

RP11-352L13_RP11-419G15

chr3: 48,395,535-48,645,535

2,37

0,38

1,84

9,88

0,77

0,44

1,32

3p21.31

7

RP11-316 M24

chr3:48,787,955-49,037,955

4,6

0,45

2,02

6,58

0

0

1,18

4p16.2

11

RP11-323F5_RP11-341O1

chr4:4,566,405-4,816,405

1,22

0,54

0,33

0,65

0

0

1,18

4p16.3

8

RP11-919N24

chr4:2,277,155-2,527,155

3,37

0,56

1,9

1,31

0,38

0,33

1,34

4q12

10

RP11-680 M13_RP11-167A8

hr4:58,262,438-58,512,438

0,39

1,34

0

0

0

0

0,94

4q12

10

RP11-622J1_RP11-793H8

chr4:58,796,340-59,046,340

0,5

1,28

0

0

0

0

0,95

6p12.3

12

RP3-347E1_RP11-446F17

chr6: 46,562,151-46,812,151

0,67

1,1

1,76

1,72

0

0

0,95

6p12.3

12

RP1-142O9_RP11-28H17

chr6:49,380,518-49,630,518

0,82

1,04

0,93

1,72

0

0

0,92

6p21.31

13

RP11-666K4_RP11-652G7

chr6: 36,095,599-36,345,599

1,52

0,82

1,63

4,32

0

0

1,09

6p22.1

41

RP11-635O11

chr6:27,927,951-28,177,951

1,2

0,78

0,21

4,75

1,05

0,49

0,98

6q14.1

14

RP11-1063N1_RP11-422O8

chr6:83,741,988-83,991,988

1,21

0,86

2,37

2,16

0

0

0,95

7p14.3

15

RP11-803J20_RP11-350H1

chr7:32,789,214-33,039,214

1,91

0,65

1,06

2,54

0,92

5,42

1,05

7q22.2

37

RP11-251G23

chr7:104,889,282-105,139,282

2,55

0,5

1,95

2,12

0,61

0,07

1,09

8p12

38

RP11-346L1_RP11-113G10

chr8:37,576,531-37,826,531

2,13

0,44

1,01

4,09

0

0

1,2

9p22.3

46

RP11-307K19_RP11-518K17

chr9:15,456,627-15,734,271

1,47

1,44

2,16

1,87

0

0

0,93

9p24.1

50

RP11-1084A8

chr9:6,611,140-6,861,140

3,44

0,34

1,78

2,34

0,16

0,05

1,07

9q22.31

17

RP11-412A12

chr9:93,506,167-93,756,167

1,18

0,78

2,32

0,46

0

0

1,12

10p11.22

39

RP11-241I20

chr10:32,250,540-32,500,540

2,18

0,68

0,49

0,82

0,47

0,15

1,02

11p15.4

46

RP11-120E20

chr11:3,312,588-3,573,461

1,56

0,64

0,43

1,1

40,59

18,97

1,1

11q12.1

50

RP11-624G17

chr11:56,933,830-57,183,830

2,55

0,44

1,1

3,85

0

0

1,17

11q13.1

19

RP11-665N17

chr11:64,231,470-64,481,470

2,03

0,24

1,73

6,88

0

0

1,32

11q13.1

19

RP11-821O7_RP11-755F10

chr11:65,514,670-65,764,670

1,28

1,4

2,01

2,2

0

0

1,11

11q14.2

48

RP11-185J12

chr11: 85,624,712-85,874,712

1,45

1,09

1,6

3,02

0

0

0,96

11q21

20

RP11-8N17

chr11:95,707,670-95,957,670

0,45

1,6

0,49

0,82

0

0

0,9

11q24.2

48

RP11-417F7

chr11:124,646,245-124,896,245

1,21

0,52

2

0,82

0

0

1,13

12p13.32

43

RP11-319E16

chr12:5,129,118-5,379,118

0,41

0,94

0

0

0

0

1,04

12q13.13

41

RP11-199A1_RP11-714I16

chr12:50,354,699-50,604,699

1,17

0,52

1,47

2

4,8

0,33

1,14

12q13.2

22

RP11-559I11_RP11-973D8

chr12:54,434,528-54,684,528

2,86

0,38

1,65

6,35

0,48

0,48

1,11

12q23.3

21

RP11-643D8_RP11-711H11

chr12:103,184,790-103,434,790

1,41

0,58

1,33

2,33

0

0

1,07

12q24.21

24

RP11-812F13_RP11-379F8

chr12:114,736,981-114,986,981

0,91

0,86

0,98

0,33

0

0

1,01

12q24.31

23

RP11-463O12_RP11-197N18

chr12:121,846,884-122,096,884

2,14

0,57

1,91

4,67

0

0

1,25

12q24.31

23

RP11-338K17_RP11-380L11

chr12:122,702,493-122,952,493

2,21

0,72

2,18

1,67

0

0

1,1

13q14.12

25

RP11-106H11

chr13:45,408,774-45,658,774

0,98

0,88

2,43

3,5

0

0

0,98

13q14.12

25

RP11-24B19

chr13:50,678,660-50,928,660

0,9

0,65

2,09

4,38

0

0

1,06

14q11.2

18

RP11-749G5_RP11-298I3

chr14:22,280,500-22,530,500

3,01

0,39

1,38

10,02

0

0

1,16

14q24.2

27

RP11-667E7

chr14:71,197,805-71,447,805

1,05

1,2

0,81

0,41

0

0

1,01

14q32.31

49

RP11-796G6_RP11-350L3

chr14:101,148,480-101,398,480

1

1,41

1,07

2,5

0,44

0,44

1,07

14q32.31

49

RP11-114H15_RP11-356L8

chr14:101,630,161-101,880,161

2,78

0,54

2,38

2,92

0

0

1,14

15q22.2

27

RP11-74K1

chr15:58,405,774-58,655,774

1,06

0,44

1,7

3,7

0,41

0,14

0,96

15q24.1

40

RP11-247C2

chr15:72,080,168-72,330,168

1,06

0,56

1

8,53

3,28

2,71

1,19

15q24.1

49

RP11-247C2

chr15:72,080,168-72,330,168

1,06

0,56

1

8,53

3,28

2,71

1,19

15q24.3

28

RP11-20 M10

chr15:75921863-76171863

0,88

0,47

0,82

1,48

6,78

5,58

1,2

16p11.2

29

RP11-779B17

chr16:31,765,790-32,015,790

2,15

0,56

0,39

0,28

6,11

5,91

0,93

16q24.3

30

RP11-79A1

chr16:88,199,243-88,449,243

1,92

0,21

1,86

5,1

0

0

1,21

17p13.1

30

RP11-89D11

chr17:7,395,110-7,645,110

1,66

0,64

1,56

6,66

0,29

0

1,1

17p13.3

33

RP5-1029F21

chr17:267,052-517,052

1,11

1,18

1,49

0,52

0,58

0,23

1,02

17q21.2

31

RP11-156A24

chr17:36,799,760-37,049,760

0,39

0,52

0,47

2,45

1,59

1,92

1,1

17q25.3

32

RP11-46E14

chr17:75,272,119-75,522,119

0,83

0,63

0,22

0,87

0,29

0,93

1,2

19q13.32

34

RP11-846 M4

chr19:51,871,627-52,121,627

1,41

0,64

0,93

1,77

0

0

1,03

20q13.33

42

RP4-591C20_RP11-266K16

chr20:62,058,835-62,308,835

0,95

0,29

1,47

4,29

1,87

0,91

1,27

21q22.13

35

RP11-315B15_RP11-777J19

chr21:37,536,287-37,809,765

2,2

0,89

1,77

2,67

0

0

0,98

21q22.13

35

RP11-105O24_RP11-1021I19

chr21:37,747,110-37,997,110

0,98

1,02

1,57

2,67

0

0

1,04

Xq13.1

36

RP11-69L22_RP11-237F13

chrX:68,788,268-69,038,268

0,66

1,58

3,32

1,95

0

0

0,97

  1. The 250 Kb size intervals covering the molecular breakpoints were analyzed for the presence of Alu, LINE, RefSeq Genes, SDs, and GC. The reported values were normalized to the mean value for each chromosome. In cases characterized by sequences deletions or the involvement of several chromosomes, more than one molecular breakpoints was identified.
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Molecular Cancer

ISSN: 1476-4598