1 Abstract

Clinical-grade detection and interpretation of structural variation (SV) including copy number variation (CNV) from whole genome sequencing (WGS) has the potential to revolutionize genetic testing by replacing micro-arrays. Current WGS based approaches however showed high error rates, poor reproducibility, and difficulties in annotating, visualizing, and prioritizing rare variants.

We present ClinSV, a platform addressing these challenges, by integrating read depth, split and spanning read evidence, with extensive quality attributes and, by providing a comprehensive variant visualization procedure. By analyzing WGS from 500 healthy individuals, ClinSV annotates calls with population allele frequencies, enabling filtration of on average 5,800 SVs down to 16 rare gene-affecting variants per germline sample. We benchmarked ClinSV against clinical microarrays and gold standard deletion CNV calls from NA12878, as well as other popular SV callers. ClinSV identified 100% of the pathogenic CNV from microarrays, including seven that were not detected using only a structural variant caller. Finally, we found that 13% of CNV had surrounding pairs of repeats, causing reduced SR and DP evidence, and highlighting the utility of integrating complementary CNV detection approaches.