HER2 Protein Overexpression, mRNA Expression, and DNA Amplification Across Solid Tumors: Comparison of Next-Generation Sequencing-Based Assays With Immunohistochemistry.

Abstract

The tumor-agnostic approach has been increasingly adopted in precision oncology. Immunohistochemistry (IHC) is the standard biomarker testing for human epidermal growth factor receptor 2 (HER2)-targeted therapies, whereas next-generation sequencing (NGS) has been widely incorporated in routine clinical practices. Here, we investigated the concordance between NGS-based assays and IHC in HER2 testing. Interfering factors leading to discordant results between the assays were also studied. Over 78,000 solid tumors across various types from two independent cohorts in the United States and Japan were investigated for <i>HER2</i> DNA copy number, mRNA expression, and protein overexpression by whole-exome sequencing (WES), whole-transcriptome sequencing (WTS), and IHC, respectively. In the US cohort (n = 77,267), <i>HER2</i> DNA amplification, mRNA overexpression, and IHC-positive (IHC-P) were detected in 4.9%, 10.1%, and 4.7% of the tumors, respectively. Positive results in at least one of the three assays were observed in 10.7% of tumors, while 3.9% were positive for all three assays. Using IHC as a comparator, WTS showed better sensitivity than WES but a lower positive predictive value. These results were consistent in the Japanese cohort (n = 1,225). Although the overall <i>HER2</i> RNA expression level correlated well with IHC score and DNA copy number, the degree of correlation varied among tumor types. Heterogeneous distribution of IHC-P tumor cells was associated with discordant results between NGS-based assays and IHC. HER2-positive status in protein, mRNA, and DNA showed concordance in general but varied among tumor types. NGS-based assays, especially WTS, could be a useful predictive tool for HER2 testing in tumor-agnostic settings. Intratumor heterogeneity in HER2 protein expression should be considered when bringing bulk sequencing tests into clinical settings.