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Table 2 Active elements in individual tumours

From: Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis

Tumour

Element

Elements active

Inserts by discordant reads

Candidate Poly A inserts

TP53 Mutation

3

4

8

12_A

14

20

22

X_A

X_B

?

3109

3

 

1

 

26

1

1

   

5

32

150

MUT

3111†

   

1

      

1

1

96

MUT

3113

      

2

2

 

2

3

6

13

MUT

3115

      

3

  

1

2

4

33

MUT

3117

          

0

0

10

MUT

3119

          

0

0

8

—

3121

4

     

3

  

1

3

8

34

MUT

3125

          

0

0

7

—

3129

      

6

   

1

6

129

MUT

3131

    

1

  

1

  

2

2

12

MUT

3133

      

1

  

1

2

2

11

—

3135

      

6

  

1

2

7

16

MUT

3137

      

1

   

1

1

5

MUT

3149

    

5

 

3

7

  

3

15

19

MUT

3302

9

     

8

3

 

21

4

41

389

MUT

3305

      

5

  

2

2

7

16

MUT

3308

      

6

8

  

2

14

194

MUT

3311

      

1

5

 

1

3

7

95

MUT

3314

      

4

  

1

2

5

22

MUT

3317

    

14

 

4

  

1

3

19

70

MUT

3320

     

2

4

2

  

3

8

97

MUT

3323

      

3

  

1

2

4

27

MUT

7394

     

4

2

7

 

14

4

27

281

MUT

7396

2

     

10

8

 

35

4

55

830

MUT

7398

   

2

12

 

4

6

 

11

5

35

231

MUT

7401

1

   

2

 

2

2

1

3

6

11

138

MUT

7404†

   

2

      

1

2

13

MUT

7407

    

22

 

1

7

 

3

4

33

196

MUT

7409

    

85

3

10

1

15

35

6

149

416

MUT

7414

      

1

 

1

3

3

5

33

MUT

7416

    

0

 

4

  

11

2

15

196

MUT

7418

      

4

3

 

2

3

9

73

MUT

7420

 

1

2

   

6

2

1

1

6

13

100

MUT

7422

     

1

 

1

1

4

4

7

62

—

7424

8

2

    

5

  

32

4

47

352

MUT

7427

2

     

1

  

2

3

5

133

MUT

7430

    

1

 

5

  

2

3

8

30

MUT

7432

    

8

 

3

  

10

3

21

133

MUT

7434

  

3

   

2

  

2

3

7

125

MUT

7436

    

3

 

2

  

1

3

6

39

MUT

7438

      

2

2

 

1

3

5

64

MUT

7440

      

1

5

4

3

4

13

174

—

7442

      

2

8

 

3

3

13

198

MUT

Total tumours

7

2

3

3

11

5

36

19

6

31

    

Total inserts

29

3

6

5

179

11

129

80

23

210

 

675

5270

 

Average per tumour

16

123

 
  1. The elements that transduce unique sequence are listed individually, while all inserts mapped to L1s or polyA in the genome are combined in column marked ‘?’, because it is not certain that they were copied from any specific L1. Elements active, number of different elements active in a given tumour. Inserts by discordant reads, total inserts found from discordant paired reads. PolyA, candidate inserts found by searching for tumour-specific polyA. TP53 mutation, mutations in TP53 called from Illumina sequencing. MUT, mutated; −, no mutation detected. † Note that tumours 3111 and 7404 had verified tumour-specific inserts of the chr12_A element, so definitely had some mobile-element activity
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BMC Genomics

ISSN: 1471-2164

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