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Fig. 1 | BMC Genomics

Fig. 1

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

Fig. 1

Inserts produced by L1 activity and how they are treated by paired-end sequencing. a, b Generation of inserts showing truncation and transduction (not to scale). mRNA (orange) is transcribed from an L1 in the germline (or from a newly inserted L1, if complete). Target site is nicked, and the end at the nick used to prime reverse transcription of the mRNA to cDNA (green and red), which is often incomplete (dotted line). cDNA is subsequently integrated, flanked by a short duplication of the target site. Some inserts have 5’ inversions, perhaps due to additional priming in the opposite direction [19]. a, simple L1 insert; b, Transduction of 3’ unique sequence. Transcription of an L1 sometimes reads through the L1 polyA addition site (asterisk) into 3’ unique sequence (red) until a polyA addition site (asterisk) is encountered. The resulting cDNA and insert includes a variable amount of the unique sequence and upstream L1 sequence. c Examples of inserts with transduced unique sequence, and resulting paired-end sequence reads. Reverse transcription of the mobile element RNA is often incomplete, resulting in 5’ -truncated inserts. These may or may not have any L1 sequence, and the most-truncated inserts may contain little more than polyA. Examples of possible read pairs are shown in black solid lines if the aligner can map (align) them uniquely to the reference genome; these will usually appear to be translocation junctions (Fig. 2). Many read pairs will not align (dashed lines) either because one read falls in a repeat, or the sequence is not present in the reference (fine dots). Yellow boxes are target site duplications. d Example of an insert of an L1 that does not transduce 3’ sequence but nevertheless may be mapped as a translocation junction. The parent L1 may have a unique sequence difference, e.g. a single base pair deviation (T > A) from the consensus, that identifies reads uniquely and maps them to its parent L1. Other reads (red) are aligned to an L1 (or Alu) in the reference sequence that has a polyA tail, e.g. the ‘element’ on chromosome 15 in Table 1. In some cases the alignment may be generated by the polyA alone. Such inserts are not in general from the element the read is mapped to. e Apparent junction that is not even a junction. Occasionally a read pair within an insert may be aligned to two different loci, appearing to report a rearrangement junction. For example, one read may map to a transduced sequence, while its pair contains polyA and is mapped to one of the polyA runs in the reference genome

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