Comparison of Biomarker Assays for EGFR : Implications for Precision Medicine in Patients with Glioblastoma

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 amplification by multiple assays. Specifically, we evaluated correlation among fluorescence hybridization (FISH), a standard assay for detecting amplification, with other methods. Formalin-fixed, paraffin-embedded tumor samples were used for all assays. amplification was detected using FISH ( = 206) and whole-exome sequencing (WES, = 74). mRNA expression was measured using reverse transcription-polymerase chain reaction (RT-PCR, = 206) and transcriptome profiling (RNAseq, = 64). EGFR protein expression was determined by immunohistochemistry (IHC, = 34). Significant correlations among various methods were determined using Cohen's kappa (κ = 0.61-0.80 defines substantial agreement) or statistics. mRNA expression levels by RNA sequencing (RNAseq) and RT-PCR were highly correlated with 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 amplification. Methods for assessing mRNA expression (RT-PCR, RNAseq) and copy number (WES), but not protein expression (IHC), can be used as surrogates for amplification (FISH) in GBM. Collectively, our results provide enhanced understanding of available screening options for patients, which may help guide EGFR-targeted therapeutic approaches.