Abstract B26: Actionable mutations in cell-free DNA in plasma of patients with advanced cancers referred for experimental targeted therapies.
Authors: Janku Filip , Angenendt Philipp , Naing Aung , Falchook Gerald S. , Tsimberidou Apostolia M. , Holley Veronica R. , Fu Siqing , Hong David S. , Wheler Jennifer J. , Piha-Paul Sarina A. , Zinner Ralph G. , Karp Daniel D. , Subbiah Vivek , Kim Kevin B. , Meric-Bernstam Funda , Diehl Frank , Kurzrock Razelle 
Published: August 2014

Abstract
Background: Actionable mutations confer a survival advantage to cancer cells and can provide therapeutic targets. Cell-free (cf) DNA in the plasma of cancer patients offers an easily obtainable, low-risk, and inexpensive source of biologic material for mutation analysis.
Methods: cfDNA in plasma samples from patients with advanced cancers who progressed on systemic therapy was tested for 21 mutations in BRAF (codon 600), EGFR (exons 19-21), KRAS (codons 12, 13), and PIK3CA (exons 9, 20) using the BEAMing method. Results were compared to mutation analysis results from archival primary or metastatic tumor tissue from a CLIA-certified laboratory.
Results: cfDNA was extracted from 155 patients with advanced cancers. BRAF mutations were detected in 27% (33/122) plasma samples and in 30% (37/122) of archival tumor samples resulting in agreement in 88.5% cases (kappa=0.72, 95% confidence interval [CI] 0.58- 0.86). EGFR mutations were detected in 8% (6/77) plasma samples and in 6% (5/77) tumor samples resulting in agreement in 98.7% cases (kappa=0.90, 95% CI 0.71- 1.09). KRAS mutations were detected in 50% (55/110) of plasma samples and in 53% (58/110) of tumor samples, resulting in agreement in 82.7% cases (kappa=0.66, 95% CI 0.51- 0.80). PIK3CA mutations were detected in 20% (19/94) of plasma samples and in 14% (13/94) of tumor samples, resulting in concordance in 91.5% cases (kappa=0.70, 95% CI 0.51- 0.89). Of interest, 2 of 9 patients with BRAF mutations (both melanoma) in the tumor, but not in cfDNA had plasma collection at the time of progression on prior BRAF targeting therapy. Also, a patient with V600E BRAF-mutated melanoma, who previously progressed on a MEK inhibitor, displayed a G12R KRAS mutation in cfDNA and a patient with V600K BRAF-mutated melanoma with additional E542K and H1047R PIK3CA mutations in cfDNA was ultimately refractory to BRAF inhibitor treatment. Also, a V600K BRAF mutation was found in the cfDNA of a patient with colorectal cancer and a G12V KRAS mutation. In addition, 2 patients with EGFR-mutated lung adenocarcinoma (exon 19 and L858R), who progressed on erlotinib, had T790M EGFR (n=2) and E545K PIK3CA (n=1) mutations in cfDNA, plausibly explaining secondary resistance to erlotinib. A patient with Erdheim-Chester disease and a V600E BRAF mutation also had a T790M EGFR mutation in cfDNA. Finally, a patient with H1047R PIK3CA mutant ovarian cancer showed an additional G12C KRAS mutation in cfDNA and experienced a partial response followed by early progression on a PI3K inhibitor. Patient characteristics, mutation types and detailed discrepancy analysis will be presented.
Conclusions: Detecting actionable mutations in cfDNA is a noninvasive alternative to mutation testing in tumor tissue with an acceptable level of concordance, and should be investigated further for selecting appropriate targeted therapies and monitoring mutation profiles.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B26.
Citation Format: Filip Janku, Philipp Angenendt, Aung Naing, Gerald S. Falchook, Apostolia M. Tsimberidou, Veronica R. Holley, Siqing Fu, David S. Hong, Jennifer J. Wheler, Sarina A. Piha-Paul, Ralph G. Zinner, Daniel D. Karp, Vivek Subbiah, Kevin B. Kim, Funda Meric-Bernstam, Frank Diehl, Razelle Kurzrock. Actionable mutations in cell-free DNA in plasma of patients with advanced cancers referred for experimental targeted therapies. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B26.