Source elements that gave rise to somatic L1 insertions in the tumor. As in Figure 2, the bar diagrams in A–C depict mutations in the L1 sequences of source elements and somatic offspring relative to the reference element L1.3. Colored vertical lines represent single nucleotide mutations as outlined in Figure 2. The Circos plots show the somatic offspring L1 insertions that were generated by each FL-L1Hs source element. (A) The Chr 17 source element gave rise to five somatic insertions, including the insertion in APC. The mutation profile of the APC insertion uniquely and perfectly matches that of the Chr 17 FL-L1Hs source element to the extent that the APC insertion spans the 3′ region of the Chr 17 source element. Two of the Chr 17 somatic offspring (denoted by *) had extreme 5′ truncations and thus only had one mutation (C5788T) compared to L1.3. Although the mutation profiles of these offspring do not exclusively match that of the Chr 17 source element, the one remaining possible source element for these somatic offspring (ID 1:86392759) was ruled out due to lack of intact ORFs. (B) The Chr 14 source element gave rise to 12 somatic insertions. The mutation profiles for 11 of 12 (91.7%) of these offspring uniquely and perfectly match the mutation profile of the Chr 14 source element. The remaining somatic offspring (denoted by #) had one additional mutation (T4250G) that was not present in the Chr 14 source element. This mutation does not match any other source element and most likely was introduced during retrotransposition (which is error prone) (Gilbert et al. 2005). The blurry end of somatic offspring 16:56298643 represents ambiguity of the 5′ end because we did not sequence that end. (C) The Chr 12 source element gave rise to two somatic insertions. One was assigned to the Chr 12 source element using mutation profiles as outlined for the Chr 17 and Chr 14 source elements above, whereas the other was assigned using a 3′ transduction (purple box flanked by poly(A) tails in green) (Moran et al. 1999). (D) Circos plot depicting all 27 somatic insertions discovered in this tumor, including the somatic offspring with known source elements depicted above (A–C) and eight additional somatic offspring from an unknown source element: (green) unknown chromosome (Un).
