Comparison of Biomarker Assays for <i>EGFR</i>: Implications for Precision Medicine in Patients with Glioblastoma.

Abstract

Patients with glioblastoma (GBM) have a poor prognosis and are in desperate need of better therapies. As therapeutic decisions are increasingly guided by biomarkers, and EGFR abnormalities are common in GBM, thus representing a potential therapeutic target, we systematically evaluated methods of assessing <i>EGFR</i> amplification by multiple assays. Specifically, we evaluated correlation among fluorescence <i>in situ</i> hybridization (FISH), a standard assay for detecting <i>EGFR</i> amplification, with other methods.<b>Experimental Design:</b> Formalin-fixed, paraffin-embedded tumor samples were used for all assays. <i>EGFR</i> amplification was detected using FISH (<i>N</i> = 206) and whole-exome sequencing (WES, <i>N</i> = 74). <i>EGFR</i> mRNA expression was measured using reverse transcription-polymerase chain reaction (RT-PCR, <i>N</i> = 206) and transcriptome profiling (RNAseq, <i>N</i> = 64). EGFR protein expression was determined by immunohistochemistry (IHC, <i>N</i> = 34). Significant correlations among various methods were determined using Cohen's kappa (κ = 0.61-0.80 defines substantial agreement) or <i>R</i> ² statistics. <i>EGFR</i> mRNA expression levels by RNA sequencing (RNAseq) and RT-PCR were highly correlated with <i>EGFR</i> amplification assessed by FISH (κ = 0.702). High concordance was also observed when comparing FISH to WES (κ = 0.739). RNA expression was superior to protein expression in delineating <i>EGFR</i> amplification. Methods for assessing <i>EGFR</i> mRNA expression (RT-PCR, RNAseq) and copy number (WES), but not protein expression (IHC), can be used as surrogates for <i>EGFR</i> amplification (FISH) in GBM. Collectively, our results provide enhanced understanding of available screening options for patients, which may help guide EGFR-targeted therapeutic approaches.