Fig. 3

liWGS and lrWGS resolved a de novo gene-disrupting cxSV that was cryptic to standard siWGS. We performed lrWGS from 10X Genomics (Pleasanton, CA, USA) as a method of orthogonal validation for three large complex SVs detected by liWGS, two of which failed to fully validate by traditional methods. One notable example is shown here; the other two are provided in Additional file 2: Figures S4 and S5. a A de novo complex reciprocal translocation with three breakpoints between chromosomes 2 (pink) and 6 (green) was discovered by liWGS in a participant with ASD and predicted to result in LoF of PARK2 and CAMKMT. However, two of three breakpoints (breakpoints #1 and #3; orange) were not detectable by siWGS. b lrWGS heatmaps from Loupe software [113] analysis of lrWGS data showed clear evidence for each of the three SV breakpoints. c lrWGS resolved and phased all three breakpoints, including both breakpoints that failed molecular validation due to low-complexity repetitive sequence (blue), which were resolved by spanning the low-complexity sequence with 28 liWGS reads and 30 lrWGS molecules at breakpoint #1 and 12 liWGS reads and 41 lrWGS molecules at breakpoint #3