Optimal management of acutely ill infants with monogenetic diseases requires rapid identification of causative haplotypes. Whole-genome sequencing (WGS) has been shown to identify pathogenic nucleotide variants in such infants. Deletion structural variants (DSVs, >50 nt) are implicated in many genetic diseases, and tools have been designed to identify DSVs using short-read WGS. Optimisation and integration of these tools into a WGS pipeline could improve diagnostic sensitivity and specificity of WGS. In addition, it may improve turnaround time when compared with current CNV assays, enhancing utility in acute settings. Here we describe DSV detection methods for use in WGS for rapid diagnosis in acutely ill infants: SKALD (Screening Konsensus and Annotation of Large Deletions) combines calls from two tools (Breakdancer and GenomeStrip) with calibrated filters and clinical interpretation rules. In four WGS runs, the average analytic precision (positive predictive value) of SKALD was 78%, and recall (sensitivity) was 27%, when compared with validated reference DSV calls. When retrospectively applied to a cohort of 36 families with acutely ill infants SKALD identified causative DSVs in two. The first was heterozygous deletion of exons 1-3 of
NPJ Genom Med
Noll, A. C., Miller, N. A., Smith, L. D., Yoo, B., Fiedler, S., Cooley, L. D., Willig, L. K., Petrikin, J. E., Cakici, J., Lesko, J., Newton, A., Detherage, K., Thiffault, I., Saunders, C. J., Farrow, E. G., Kingsmore, S. F. Clinical detection of deletion structural variants in whole-genome sequences. NPJ Genom Med 1, 16026-16026 (2016).