Fig. 1: Overview of the novel intermediate-sized INDEL in PTENα.

a Differences in the structure between canonical PTEN (top) and PTENα (bottom). PTENα has an alternative start codon (CTG). b Detection of deletion junctions in PTENα. The alignment result of soft-clipped reads derived from the mutant allele (i.e., deletion–insertion) is shown. For comparison, the alignment result of reads that were not soft-clipped from the wild-type allele is also shown. The sequences color-coded by light red and blue indicate the sequences matched with that of the human reference genome. Highlighted bases indicate the sequences that are mismatched with the reference genome (i.e., inserted sequences). c A schematic representation with plausible junctions of the deletion–insertion in PTENα. The purple bar indicates an inserted sequence (68 bp), whereas the light green bars indicate PTENα sequences. Sanger sequencing confirmed the breakpoints of the deletion–insertion. Sanger sequencing using forward (left) and reverse (right) primers revealed aberrant electropherograms after the breakpoints of the deletion–insertion because the fluorescent signals from mutant and wild-type alleles were mixed. The breakpoints of the deletion–insertion are depicted as blue vertical lines. Sanger sequencing was performed using the BigDye Terminator v3.1 Cycle Sequencing Kit (Thermo Fisher Scientific, Waltham, MA, USA) on the ABI 3130x Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). The oligonucleotide sequences of the PCR primers are shown in Table S2. d A plausible mechanism of deletion and insertion at the same position. Light green and purple sequences indicate the reference and inserted sequences, respectively. Double-strand DNA breaks may result in a 47-bp deletion accompanied by a 68-bp insertion