Research Papers:

BRAF mutation testing with a rapid, fully integrated molecular diagnostics system

Filip Janku _, Bart Claes, Helen J. Huang, Gerald S. Falchook, Benoit Devogelaere, Mark Kockx, Isabelle Vanden Bempt, Martin Reijans, Aung Naing, Siqing Fu, Sarina A. Piha-Paul, David S. Hong, Veronica R. Holley, Apostolia M. Tsimberidou, Vanda M. Stepanek, Sapna P. Patel, E. Scott Kopetz, Vivek Subbiah, Jennifer J. Wheler, Ralph G. Zinner, Daniel D. Karp, Rajyalakshmi Luthra, Sinchita Roy-Chowdhuri, Erwin Sablon, Funda Meric-Bernstam, Geert Maertens and Razelle Kurzrock

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Oncotarget. 2015; 6:26886-26894. https://doi.org/10.18632/oncotarget.4723

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Filip Janku1,*, Bart Claes2,*, Helen J. Huang1, Gerald S. Falchook1,3, Benoit Devogelaere2,9, Mark Kockx10, Isabelle Vanden Bempt10, Martin Reijans2, Aung Naing1, Siqing Fu1, Sarina A. Piha-Paul1, David S. Hong1, Veronica R. Holley1, Apostolia M. Tsimberidou1, Vanda M. Stepanek1, Sapna P. Patel4, E. Scott Kopetz5, Vivek Subbiah1, Jennifer J. Wheler1, Ralph G. Zinner1, Daniel D. Karp1, Rajyalakshmi Luthra6, Sinchita Roy-Chowdhuri7, Erwin Sablon2, Funda Meric-Bernstam1, Geert Maertens2, Razelle Kurzrock1,8

1Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

2Biocartis NV, 2800 Mechelen, Belgium

3Sarah Cannon Research Institute at HealthONE, Denver, CO 80218, USA

4Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

5Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

6Molecular Diagnostics Laboratory, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

7Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

8Center for Personalized Cancer Therapy, Moores Cancer Center, The University of California San Diego, La Jolla, CA 92093, USA

9Cartagenia, 3001 Leuven, Belgium

10HistoGeneX NV, 2600 Berchem, Belgium

*These authors have contributed equally to this work

Correspondence to:

Filip Janku, e-mail: [email protected]

Keywords: BRAF, rapid, integrated, qPCR

Received: June 03, 2015     Accepted: July 17, 2015     Published: July 27, 2015


Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTM BRAF 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 IdyllaTM BRAF 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.

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