Fig. 5

Full-length PCR validations and visual inspection. A Full-length PCR validation of the Alu insertion in CSDE1 and of the de novo L1 insertion in DAB1 in ASD cases. In lymphoblastoid cell line DNA, we validated the insertions in the ASD proband only. NTC: non-template control. B Integrative Genomics Viewer image at the insertion site in gene CSDE1 in an ASD case. For each individual, the sequencing coverage (top) and sequencing reads (bottom) are shown. The insertion shows the canonical signatures of target-primed reverse transcription (TPRT)-mediated retrotransposition: 15 bp target site duplication (TSD) between the two insertion breakpoints, a poly-A tail, supporting clipped reads, and discordant reads with mates mapping to the consensus Alu sequence. The mother has one small clipped read sequence at the breakpoint which has the same sequence as in the proband, suggesting that the insertion could be mosaic at a low allele frequency in the mother’s blood