Software-assisted manual review of clinical NGS data: an alternative to routine Sanger sequencing confirmation with equivalent results in >15,000 hereditary cancer screens

Clinical genomic tests increasingly utilize a next generation sequencing (NGS) platform due in part to the high fidelity of variant calls, yet rare errors are still possible. In hereditary cancer screening (HCS), failure to correct such errors could have serious consequences for patients, who may follow an unwarranted screening or surgical-management path. It has been suggested that routine orthogonal confirmation via Sanger sequencing is required to verify NGS results, especially for low-confidence positives with depressed allele balance ( 99% (1,711) as true positives (enriched for long indels and homopolymers) or true negatives (often conspicuous NGS artifacts), with the remaining