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Table 1 ‘Elements’ in the reference genome that mobile element inserts align to

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

ID

Chromo-some

Transduced sequence start

Transduced sequence end

L1, Alu etc.

Start

End

+/−

Gene

Total Inserts

Tumours

Method

Max Transduced (bp)

Hot L1 list

Tubio list

Reference L1s that transduce unique sequence

Chr 4

chr4

137213864

in L1

L1HS

137214650

137220701

-

none

3

2

L1

786

14

No

Chr 8

chr8

135082457

135082642

L1HS

135082987

135089016

-

none

6

3

L1

530

3

4

Chr 12_A

chr12

3606945

in L1

L1HS

3608362

3614394

-

PRMT8

5

3

L1

1417

35

6

Chr 20

chr20

23412922

23413624

L1HS

23406746

23412777

+

none

11

5

Cl

847

Not listed

8

Chr 22

chr22

29065365

29066424

L1HS

29059272

29065303

+

TTC28

129

36

Cl, L1

1121

7

137

Chr X_A

chrX

11731785

11732702

L1HS

11725369

11731399

+

none

80

19

Cl, L1

1303

19

7

Chr X_B

chrX

11952984

in L1

L1HS

11953208

11959433

-

none

23

6

L1

224

1

20

Non - reference L1s that transduce unique sequence

Chr 3

chr3

in L1

123595443

Polymorphic L1HS

123590726

123590724

+

MYLK

29

7

Cl

>4000

N/A

40

Chr 14

chr14

59220410

59221078

Polymorphic L1HS

59220404

59220404

+

none

179

11

Cl

 

N/A

40

Reference genome elements that inserts align to

Chr 6

chr6

  

L1HS

24811907

24817934

-

FAM65B

3

3

L1

Nil

2

N/A

Chr 7

chr7

  

L1HS plus 4bp and polyA

30478859

30484914

+

NOD1

84

9

L1

Nil

18

N/A

Chr8

 

see

footnote

L1HS

          

Chr 10

chr10

  

L1HS with polyA

111572121

111578215

-

none

6

6

L1

Nil

9

N/A

Chr 12_B

chr12

  

AluSx1 with polyA

66451373

66451739

-

none

98

21

Cl

Nil

N/A

N/A

Chr 15

chr15

  

AluYa5 with polyA

77910868

77911236

-

LINGO1

19

17

Cl

Nil

N/A

N/A

  1. Positions refer to reference genome GRCh37/hg19. The mobile ‘elements’ are identified by chromosome. At least two inserts were verified by PCR for each ‘element’ except the Chr 6 element (only one insert verified) and the Chr 3 element (not verified but described by Tubio et al. [13]). The Chr 3 and Chr 14 elements are polymorphic L1s that are not in the reference genome but were shown to transduce sequence by Tubio et al. [13]; their insertion point in the reference genome is given in italics. The polyA addition site for the Chr 14 element is at the end of a 36bp fragment of an L2a element. The Chr8 element showed both transduction and mapping to the native L1 insert—of the two inserts verified, one had 3’ unique sequence transduced and one was pure L1 3’ terminus
  2. Transduced sequence, maximum extent of unique sequence observed in inserts verified by PCR (Additional file 2), except for Chr 3 element where read map position is given. +/−, strand bearing polyA, which is same as orientation of L1 or Alu if present. Tumours, number of tumours with inserts. Method, method of identification: Cl, cluster of ‘translocation’ breakpoints from discordant reads; L1, cluster of breakpoints 3’ to a known active L1 (not exhaustive). Max transduced, maximum unique sequence transduced in cloned insert. Hot L1 list, rank in list of active L1s of Brouha et al. [24]. Tubio list, whether the elements that transduce 3’ sequence were listed by Tubio et al. [13] and how many inserts were reported; N/A, not applicable as were not transduction events
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BMC Genomics

ISSN: 1471-2164

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