Skip to main content

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