Brief Report: Calculating the Tumor Nuclei Content for Comprehensive Cancer Panel Testing

Abstract Comprehensive genetic panel (CGP) testing generally requires 20% or more percent tumor nuclei (%TN) of the analyzed tissues to achieve assay performance comparable to validated specifications. Pathologists play a crucial role in ensuring that the optimal results are achieved by accurately assigning %TN content of the available specimens and selecting the best material to submit for sequencing. This study addresses the issues in evaluating %TN, such as intra-observer variability, and examines whether focused training and feedback can improve the pathologist performance. Nine referring institution (RI) pathologists (all board-certificated, working at the Core Institute and the alignment hospitals under the National Cancer Genome scheme) evaluated 18 tumors, which had undergone CGP testing with the FoundationOne CDx assay. The %TN estimations by RI pathologists were compared with two standards: %TN assigned by the tumor sequencing institution’s (TSI) pathologist (a board-certified pathologist at Foundation Medicine Inc.), and the computational %TN estimated from the mutant allele frequencies after sequencing was completed. The pathologists generally overestimated %TN in the first pre-training round of the evaluation, and the differences in the averaged %TN from the TSI and computational standards were statistically significant. However, the pos-training second-round results became significantly concordant to the standards. This study suggests that %TN content is empirically overestimated but the evaluation skill can be improved by providing a training and feedback program from the testing facility on subsequent specimens.