Fig. 2. The somatic L1 retrotransposition activity in 290 cancers.

(A) Distribution of L1 retrotransposition activity in 290 cancers. Pie charts display the proportions of analyzed cancer samples with at least one transduction (blue), no transductions but at least one solo L1 (red), and no L1 retro-transposition (white). Bars represent the somatic L1 count of each cancer sample. Horizontal black lines indicate mean somatic retrotransposition counts for each cancer type. (B) The size distribution for L1 insertions (including solo L1s and transductions), in bins corresponding to 100-nucleotide increments in insertion lengths, shows an overrepresentation of truncated L1 insertions below 2 kb (average length of insertion is ~1.1 kb). Only insertions without 5′ inversion, or with inversion when it is lower than 500 bp, are shown. There are 81 L1 elements with estimated length >5.9 kb, of which 11 are partnered transductions.These full-length insertions represent ~5% (81/1752) of the total non–5′-inverted insertions (table S3). (C) The lengths of all L1 insertions (transductions included) are illustrated as a coverage plot over the schematic representation of a canonical solo-L1 sequence (~6 kb) and its downstream sequence (~12 kb). Most somatic L1 insertions (solo L1s and partnered transductions) are truncated at the 5′ end. For insertions with 5′ extreme inversion, the insertion length estimated corresponds to the minimal size that could be recognized (table S3), so it is underestimated. Full-length transductions and orphans mobilize nonrepetitive DNA sequences up to 12 kb away from the L1 source element end. Most of the transductions correspond to DNA material located within a distance of 1 kb to the end of the L1 source element.