Skip to main content

Table 4 Comparison of detected somatic breakpoints with those reported by Banet et al.

From: Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data

patient ID

predicted

detected

known

agree

rate

(a) Number of intra-chromosomal somatic breakpoints

22

51

17

13

6

46%

23

67

49

43

27

63%

39

113

92

91

72

79%

43

94

89

77

58

75%

45

48

42

30

21

70%

64

123

113

91

70

77%

71

11

10

9

2

22%

81

8

7

12

6

50%

90

44

39

29

19

66%

117

242

219

158

146

92%

126

55

17

11

7

64%

145

83

72

55

50

91%

172

179

139

135

91

67%

198

88

53

65

37

57%

207

72

65

58

49

84%

268

75

49

41

31

76%

Total

1353

1072

918

692

75%

(b) Number of inter-chromosomal somatic breakpoints

patient ID

predicted

detected

known

agree

rate

22

10

8

1

0

0%

23

14

12

5

2

40%

39

34

30

14

8

57%

43

19

18

9

5

56%

45

15

12

12

9

75%

64

14

11

9

3

33%

71

12

8

7

0

0%

81

5

4

4

0

0%

90

7

6

6

1

17%

117

17

15

6

3

50%

126

4

4

3

0

0%

145

41

37

20

14

70%

172

33

25

8

3

38%

198

8

7

1

0

0%

207

6

6

7

1

14%

208

9

9

7

3

43%

Total

248

212

119

52

44%

  1. [23].
  2. The second and third columns are the number of predicted somatic breakpoint regions and the number of detected somatic breakpoints, respectively, for each patient. The fourth column is the number somatic breakpoints reported by [23]. The fifth column is the number of breakpoints that are counted in the third column and in the forth column (i.e., the intersection of both columns). The last column is the ratio of the fifth column to the fourth column. The intra-chromosomal and inter-chromosomal somatic breakpoints are separately counted in Tables (a) and (b), respectively. Detailed lists of detected somatic breakpoints are given in Additional file 1. As for patient ID 71, evidential materials for detected somatic intra-chromosomal breakpoints are given in Additional file 3.