| Literature DB >> 31125418 |
Pim J French1, Marica Eoli2, Juan Manuel Sepulveda3, Iris de Heer1, Johan M Kros4, Annemiek Walenkamp5, Jean-Sebastien Frenel6, Enrico Franceschi7, Paul M Clement8, Michael Weller9, Peter Ansell10, Jim Looman10, Earle Bain10, Marie Morfouace11, Thierry Gorlia11, Martin van den Bent1.
Abstract
BACKGROUND: Precision medicine trials targeting the epidermal growth factor receptor (EGFR) in glioblastoma patients require selection for EGFR-amplified tumors. However, there is currently no gold standard in determining the amplification status of EGFR or variant III (EGFRvIII) expression. Here, we aimed to determine which technique and which cutoffs are suitable to determine EGFR amplification status.Entities:
Keywords: EGFR; EGFRvIII; FISH; amplification; biomarker; glioblastoma; screening
Year: 2019 PMID: 31125418 PMCID: PMC6784284 DOI: 10.1093/neuonc/noz096
Source DB: PubMed Journal: Neuro Oncol ISSN: 1522-8517 Impact factor: 12.300
Fig. 1CONSORT diagram of the study population assessed for biomarkers.
Fig. 2Frequency histogram of the percentage of EGFR-amplified nuclei per tumor sample by FISH (A). Note that most samples either contain almost no EGFR-amplified nuclei or almost entirely consist of EGFR-amplified nuclei. The histogram of EGFR RT-qPCR data (B) also shows a bimodal distribution suggesting that RT-qPCR data can also be used to determine EGFR amplification status. Models of the 2 distributions (dashed lines) are plotted on top of the frequency histogram. The intersect of these 2 curves at −3.56 gives highest concordance between FISH and RT-qPCR data. The cutoff value for type I errors in calling EGFR amplification was calculated at −2.48.
Fig. 3RT-qPCR can function as a surrogate to determine EGFR amplification status. (A) Ranked ΔCt values from RT-qPCR data show a wide range of EGFR expression between samples. Samples with high EGFR expression often had EGFR amplification. (B) RT-qPCR plotted against the percentage of EGFR-amplified cells per sample highlights the observation that higher percentages of EGFR-amplified cells also express EGFR at higher levels. (C) ROC curves show that EGFR expression can predict EGFR gene amplification by FISH. ROC curves were plotted for 4 different cutoffs (% of EGFR-amplified cells) to determine EGFR amplification by FISH.
Concordance between FISH and RT-qPCR
| FISH Status (77%) | |||
|---|---|---|---|
| Negative | Positive | ||
| RT-qPCR status ΔCt −3.56 | Negative | 506 | 49 |
| Positive | 69 | 411 | |
| FISH Status (77%) | |||
| Negative | Positive | ||
| RT-qPCR status ΔCt −2.48 | Negative | 539 | 107 |
| Positive | 36 | 353 |
Fig. 4EGFRvIII expression is found in samples with high levels of EGFR expression. As can be seen, samples that express EGFRvIII (y-axis) are found in samples that have high levels of EGFR expression (x-axis). Dark-gray dots indicate those that have been classified as EGFRvIII positive tumors (ie, Ct values of EGFRvIII <30).
Fig. 5Comparison between EGFR amplification as determined by NGS with FISH and RT-qPCR. (A) Ranked copy number estimates by NGS show that samples with low copy numbers also had relatively few EGFR-amplified nuclei (darker points). Note the steep increase from <5 copy numbers to >10 copy numbers. (B) Copy number estimates by NGS correlate with gene expression derived from RT-qPCR. Samples with low copy numbers often had low levels of EGFR expression.
Fig. 6RT-qPCR and NGS show high correlation in determining levels of EGFR and presence of EGFRvIII. (A) EGFR expression by RT-qPCR is highly correlated with expression derived from NGS data. (B) Samples in which EGFRvIII expression is identified by RT-qPCR (ie, ΔCt < 30) often also show detectable levels of EGFRvIII by panel-based RNA-seq.