Actionable mutations in plasma cell-free DNA in patients with advanced cancers referred for experimental targeted therapies

// Filip Janku 1 , Philipp Angenendt 2 , Apostolia M. Tsimberidou 1 , Siqing Fu 1 Aung Naing 1 , Gerald S. Falchook 1 , David S. Hong 1 , Veronica R. Holley 1 , Goran Cabrilo 1 , Jennifer J. Wheler 1 , Sarina A. Piha-Paul 1 , Ralph G. Zinner 1 , Agop Y. Bedikian 3 , Michael J. Overman 4 , Bryan K. Kee 4 , Kevin B. Kim 3 , E. Scott Kopetz 4 , Rajyalakshmi Luthra 5 , Frank Diehl 2 , Funda Meric-Bernstam 1 , Razelle Kurzrock 1, 6 1 Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX, USA 2 Sysmex Inostics GmbH, Hamburg, Germany 3 Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 4 Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 5 Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 6 Moores Cancer Center, The University of California San Diego, La Jolla, CA, USA Correspondence to: Filip Janku, e-mail: fjanku@mdanderson.org Keywords: EGFR, BRAF, KRAS, PIK3CA, cell-free DNA Received: December 16, 2014      Accepted: February 11, 2015      Published: March 25, 2015 ABSTRACT Cell-free (cf) DNA in the plasma of cancer patients offers an easily obtainable source of biologic material for mutation analysis. Plasma samples from 157 patients with advanced cancers who progressed on systemic therapy were tested for 21 mutations in BRAF, EGFR, KRAS , and PIK3CA using the BEAMing method and results were compared to mutation analysis of archival tumor tissue from a CLIA-certified laboratory obtained as standard of care from diagnostic or therapeutic procedures. Results were concordant for archival tissue and plasma cfDNA in 91% cases for BRAF mutations (kappa = 0.75, 95% confidence interval CI 0.63 – 0.88), in 99% cases for EGFR mutations (kappa = 0.90, 95% CI 0.71– 1.00), in 83% cases for KRAS mutations (kappa = 0.67, 95% CI 0.54 – 0.80) and in 91% cases for PIK3CA mutations (kappa = 0.65, 95% CI 0.46 – 0.85). Patients ( n = 41) with > 1% of KRAS mutant cfDNA had a shorter median survival compared to 20 patients with 1% of mutant cfDNA ( BRAF, EGFR, KRAS , or PIK3CA ) had a shorter median survival compared to 33 patients with </= 1% of mutant cfDNA (5.5 vs. 9.8 months, p = 0.001), which was confirmed in multivariable analysis.