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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