Validating HER2 copy number variation assessment by NGS: A comparative analysis with immunohistochemistry and in situ hybridization

Introduction: Anti-HER2 drugs are becoming an important therapeutic option for various solid tumors, increasing the need for HER2 status testing. Comprehensive genomic profiling (CGP) panels, including FoundationOne®CDx, are commonly used to assess ERBB2 (encoding for HER2) copy number alterations. We aimed to evaluate the analytical validity of FoundationOne®CDx assay, by comparing ERBB2 copy number data with traditional HER2 status by immunohistochemistry (IHC)/in situ hybridization (ISH) assays in a heterogeneous cohort of solid tumor samples. Methods: We retrospectively reviewed the 531 cases evaluated by FoundationOne®CDx in our Institution, and HER2 status by IHC/ISH could be internally analyzed in 68 cases, including 31 (45.5%) gastroesophageal, 17 (25.0%) colorectal, four (5.8%) breast and two (2.9%) cholangiocarcinoma patients. Tumors with estimated ERBB2 copy number ⩾ 4 by FoundationOne®CDx, and tumors with strong and complete (3+) membranous staining by IHC and/or a HER2/CEP17 ratio ⩾2 by ISH were considered NGS positive and IHC/ISH positive, respectively. Results: We identified 21 NGS positive cases (30.9%); IHC/ISH analysis confirming overexpression/amplification in 16 cases (sensitivity: 76.2%), while among the 47 NGS negative cases, 45 were confirmed by IHC/ISH results (specificity: 90%), with a positive predictive value of 76.2% and a negative predictive value of 95.7%. Conclusions: FoundationOne®CDx provides an accurate evaluation of ERBB2 copy number status and may represent a cost-effective option in metastatic cancer patients for whom NGS testing is recommended.