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Abstract
Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTMBRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction-based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The IdyllaTMBRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation-detecting tests.
Highlights
With the identification of druggable molecular aberrations in cancer, we have increased our understanding of cancer biology and identified novel molecular targets for cancer therapy. [1,2,3,4,5,6] In particular, the identification of the BRAF V600 mutation hotspot in melanoma and other malignancies has led to the development of smallmolecule kinase inhibitors targeting the BRAF oncogene
To determine the specificity of the IdyllaTM BRAF Mutation Test in detecting BRAF V600 mutations, we used the test to analyze a high number of wild-type BRAF genomic DNA copies (8 × 104 per polymerase chain reaction (PCR) reaction) from the BRAF wild-type CHL-1 cell line to identify the extent of cross-reactivity between the BRAF wild-type allele and the BRAF V600E and V600K reactions
Unlike the DNA recovered from formalin-fixed paraffin-embedded (FFPE) samples, which is degraded by the formalin fixation and only partially amplifiable by PCR, the unfixed, high-quality genomic DNA recovered from the CHL-1 cell line enabled us to maximally challenge the specificity of the assay
Summary
With the identification of druggable molecular aberrations in cancer, we have increased our understanding of cancer biology and identified novel molecular targets for cancer therapy. [1,2,3,4,5,6] In particular, the identification of the BRAF V600 mutation hotspot in melanoma and other malignancies has led to the development of smallmolecule kinase inhibitors targeting the BRAF oncogene. [1,2,3,4,5,6] In particular, the identification of the BRAF V600 mutation hotspot in melanoma and other malignancies has led to the development of smallmolecule kinase inhibitors targeting the BRAF oncogene. These BRAF inhibitors have revolutionized therapy for patients with BRAF V600–mutant advanced melanoma and demonstrated promising results in patients with other BRAF mutation–harboring diseases, including histiocytosis, hairy cell leukemia, non–small cell lung cancer, and biliary cancer. Unlike current routinely used technologies for BRAF mutation detection, the IdyllaTM BRAF Mutation Test does not require manual sample preprocessing steps such as deparaffinization, FFPE tissue digestion, or DNA extraction because all these steps are integrated within a single-use cartridge. We compared the performance of the IdyllaTM BRAF Mutation Test with that of other routinely used diagnostic methods for detecting BRAF V600 mutations
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