Clinical Validation of Somatic Mutation Detection by the Oncoscan CNV Plus Assay

The Oncoscan CNV Plus Assay (OS+) is a SNP microarray platform that can detect 74 hotspot somatic mutations (SM) in nine genes via molecular inversion probes. We report validation of the SM component of OS+ using a cohort of pediatric high-grade brain tumor (BT) specimens. SM calls were generated from 46 BT cases, most orthogonally tested via bi-directional Sanger sequencing. The initial calling algorithm result showed 31 tumors positive and 15 negative for SM, with a total of 71 OS+ SM calls: 28 'high-confidence' (HC) and 43 'low-confidence' (LC). Sanger sequencing was performed for 54 of the 71 calls (27 HC, 27 LC), as well as for 21 randomly selected hotspots across the 15 OS+ negative cases. HC calls (except EGFR) Sanger confirmed positive, negative calls confirmed negative, but none of the LC calls Sanger confirmed positive. An update of the OS+ algorithm resolved the LC calls, but of 11 HC SM EGFR calls, Sanger confirmed only one. Two PTEN SM calls by OS+ in two separate cases were also Sanger negative. The conclusion is that a majority of HC OS+ SM calls were accurate, except calls identified in EGFR and PTEN. Clinically, this laboratory reports SM identified by OS+ only after Sanger sequencing verification.