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Rapid and ultrasensitive profiling of EGFRvIII mutations in cancer and normal tissue

A method to rapidly detect the presence of EGFRvIII mutations in cancers and normal tissue using digital PCR.

Problem:

Glioblastoma multiforme (GBM) is a devastating brain cancer with poor prognosis.

EGFRvIII is a mutation in the Extracellular Growth Factor Receptor that frequently occurs in GBM tumors. Targeting EGFRvIII mutations is an emerging therapeutic strategy for GBM therapy, however knowing which patients’ tumors have these mutations and who will benefit from EGFRvIII targeted therapies is hard. Routine molecular profiling of solid tumors takes several weeks and requires relatively large amounts of starting tissue.

More rapid identification of EGFRvIII mutations will help doctors find appropriate patients for new EGFRvIII-targeting therapies and guide patient enrollment in clinical trials.

Solution:

Digital polymerase chain reaction (dPCR) is used to identify EGFRvIII mutations from small amounts of patient tissue samples.

Technology Overview:

The inventors have identified sets of primers that can detect the EGFRvIII mutation with high sensitivity and specificity. These primers are used to amplify the relevant DNA sequences to determine whether or not EGFRvIII mutations are present within a tissue sample using digital PCR.

Because of the high sensitivity of digital PCR, the presence of EGFRvIII mutations can be detected from small amounts of starting tissue and heterogenous groups of cells. The performance of this assay was validated against next-generation sequencing in a pilot study using GBM tumor samples collected from 40 patients.

Advantages:

Rapid detection of EGFRvIII mutations within 24 hours
Sensitive, can detect 1 picogram of EGFRvIII on the background of 6,000 picograms of EGFR wild-type
Requires only small amounts of tissue to capture EGFRvIII mutation heterogeneity in samples

Overview of dPCR workflow to identify EGFRvIII mutations from various tissue sources. The dPCR assay facilitates detection of EGFRvIII variants within 24 hours of receiving tissue samples. RNA is extracted from patient samples and used to synthesize cDNA. The cDNA is then purified and amplified across many partitioned reactions using dPCR. The high sensitivity and specificity of dPCR facilitates mutations to be identified in heterogenous patient samples beginning with small amounts of tissue.