Identification of a novel de novo germline deletion in USP9X in a child with congenital anomalies and B-ALL. (A) Schematic of the SV analysis pipeline used to analyze WGS of 78 DNA samples. Five SV callers (orange boxes) were used based on their ability to detect distinct patterns in aligned reads. SV calls were merged, filtered, prioritized, and visualized as described (blue boxes). (B) IGV image showing break points of the de novo heterozygous deletion in USP9X in the GOBACK proband. (C) PCR validation of the deletion in DNA from the GOBACK proband, family members, and lymphoblastoid cell line (HG148) control.