Criteria for Clinical Reporting of Variants from a Broad Target Capture NGS Assay without Sanger Verification

Abstract

Increasing clinical interest and decreasing sequencing costs are driving the wider implementation of clinical next generation sequencing assays for the diagnosis of inherited disease, including among a growing number of small to medium sized clinical laboratories. Therefore, an optimal combination of cost-effectiveness and clinical specificity is required to continue this broad adoption of genomic technology for clinical diagnosis. Sanger confirmation of all NGS variants is a common practice that increases both cost and turnaround time for clinical reporting. We reviewed 300 cases of Sanger verified NGS results as well as 60 suspected (and subsequently confirmed) artifacts, and developed a set of multiple criteria to report NGS variants without Sanger verification with 100% accuracy. Using these criteria, we project greater than 80% of clinically reported variants could be confidently released without Sanger confirmation.