Assessing L1 retrotransposition events in human iPSCs through deep sequencing.

Long interspersed element-1 (LINE-1 or L1) retrotransposition induces insertional mutations that can result in diseases. The recent development of the induced pluripotent stem cells (iPSCs) technology has opened new possibilities for stem cell research. Given the potential of human iPSCs in therapeutic applications also, it is important to verify whether these cells harbor somatic insertions resulting from endogenous L1 retrotransposition. To detect potential somatic insertions in iPSCs caused by retotranspositions of L1Hs (the most active L1 subfamily in the human genome), we used a novel sequencing strategy. As opposed to conventional sequencing direction, we sequenced from the 3’ end of L1Hs to the genomic DNA, thus enabling the direct detection of the polyA tail signature of retrotransposition for verification of true insertions. Targeted L1Hs deep sequencing was thus performed on the parental cells as well as the corresponding iPSC clones.