Unique detection and visualization of EGFRVIII splice variant in FFPE sample

The epidermal growth factor receptor (EGFR) is overexpressed in a variety of human epithelial tumors, often as a consequence of gene amplification, including primary glioblastoma (GBM). Tumors with EGFR gene amplification frequently contain EGFR gene rearrangements, with the most common extracellular domain mutation being EGFRvIII, which results from an in-frame deletion of exons 2–7. About 50% of GBM patients with EGFR amplification harbor EGFRvIII but EGFRvIII can also be present independently of EGFR amplification.

In this case study, made-to-order BaseScope™ probes were used to detect expression of EGFR and EGFRvIII in glioblastoma tissue demonstrating that BaseScope™ Assay has been used successfully to :

    • Analyze exon junction in FFPE sample
    • Visualize low to overexpression of a specific target
    • Differentiate expression of wild type and splice variant
    • Localize co-expression of wild and mutant target in tissue
    • Demonstrate the heterogeneous expression inside a tissue sample

BaseScope Assay Design for EGFRVIII detection

The BaseScope™ Assay is a more recently developed product from ACD, based on the same platform of proven and established RNAscope™ technology. It enables detection of exon junctions in FFPE tissue with morphological context by using only one ZZ  probe uniquely designed on the specific exon junction of interest.

4 BaseScope™ probes have been designed to detect specific exon junctions, as shown in figure1. Probe E1-E2 and E7-E8 are specific to EGFR, while probe E8-E9 detects both EGFR and EGFRVIII and probe E1-E8 will detect specifically EGFRVIII. 7 samples were analyzed to determine their EGFRvIII status.

Figure 1: Schematic of BaseScope™ probe design for detection of EGFR and EGFRVIII


Example of EGFRVIII positive sample


Figure 2: Sample ACD2274 (WHO grade 4) presents a positive expression of EGFR and overexpression of EGFRvIII. it also shows heterogeneous expression of the target inside the tissue.


Example of EGFRVIII negative sample

Figure 3: Sample ACD2724 (WHO grade 4) presents overexpression of EGFR and absence of EGFRvIII expression. 


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