CNV detection of multiple exon deletion in <i>PKD1</i> for patient 46 with breakpoint analysis.

<p><b>A</b> Coverage plots (IGV) of three control (ctrl) patients versus the index (idx) sample illustrate the statictical readout with a drop in coverage at <i>PKD1</i> exons 15–21 for the index (red double arrows) compared to controls indicating a deletion event at this position. Correspondingly, a within-sample decrease in coverage to surrounding exons can be observed in the index patient. The 5’ decrease in coverage is located at a clear-cut position at the beginning of exon 15 (red arrow). The <i>PKD1</i> gene is displayed from the right to the left. <b>B</b> Result from MLPA analysis displayed by MLPA module in JSI SeqPilot software showing the deletion of exons 15–21 in <i>PKD1</i>. The relative peak area (RPA) of the patient result file (green) and of the control result file (blue) with standard deviation (error bar) is shown. Ratio RPA was calculated as RPA of the patient versus controls. Deletions are indicated if the ratio RPA falls below 75%. <b>C</b> and <b>D</b> Evaluation of the exact breakpoint of the deletion using split reads. Initially, the ClipCrop tool identified an occurrence of excess split reads in exon 15, here visualized using IGV (D). The soft-clipped (unaligned) part of split reads was further inspected in part (C) by application of general motif search tools (GATA and BLASTN algorithm). The highest-scoring alignment within <i>PKD1</i> was found in the repeat-rich intronic region between exons 21 and 22, therefore representing the most likely 3’ deletion breakpoint. This repeat-rich region escapes sequence capture and probably represents a hotspot for chromosomal rearrangements.