Abstract 2407: Multiplex KRAS G12/G13 mutation testing of 16ng of unamplified cell-free DNA from plasma of patients with advanced cancers using Droplet Digital PCR
Authors: Huang Helen J. , Shelton Dawne N. , Fu Siqing , Piha-Paul Sarina A. , Tsimberidou Apostolia M. , Zinner Ralph G. , Wheler Jennifer J. , Naing Aung , Hong David S. , Falckook Gerald S. , Kopetz Scott , Luthra Rajyalakshmi , Kee Bryan K. , Karlin-Neumann George A. , Meric-Bernstam Funda , Janku Filip 
Published: August 2015

Abstract
Background: Cell-free (cf) DNA from the plasma of cancer patients offers an easily obtainable, low-risk, inexpensive and repeatedly applicable source of biologic material for mutation analysis of druggable targets and monitoring molecular changes in tumor(s) during and after therapeutic interventions. Novel, multiplex, and accurate diagnostic systems using low amounts of DNA are needed for further development of plasma cfDNA testing in personalized therapy.
Methods: cfDNA from plasma samples of patients with advanced cancers who progressed on systemic therapy was purified and 16 ng of DNA was tested with a KRAS multiplex assay to distinguish wild-type allele from 7 of the most common mutations in in the G12/G13 hotspot of exon 2 using the QX200 Droplet Digital PCR™ platform (Bio-Rad, Pleasanton, CA). Results were compared to mutation analysis of archival primary or metastatic tumor tissue obtained at different points of clinical care from a CLIA-certified laboratory.
Results: cfDNA was extracted from plasma samples of 94 patients with advanced cancers (colorectal, n = 60; melanoma, n = 9; non-small cell lung, n = 9; appendiceal, n = 3; ovarian, n = 3; endometrial, n = 3; other cancers, n = 7). KRAS G12/G13 mutations were detected in 62% (58/94) of plasma samples and in 68% (64/94) of archival tumor samples, resulting in concordance in 84 (89%) of patients (kappa = 0.77, 95% confidence interval [CI] 0.63- 0.90) with sensitivity 88% (95% CI 0.77-0.94), specificity 93% (95% CI 0.78-0.99), positive and negative predictive values 97% (95% CI 0.88-0.99) and 78% (95% CI 0.61-0.90), respectively. Overall, 8 patients had KRAS G12/G13 mutation in the tumor, but not in cfDNA and 2 patients had KRAS G12/G13 mutation in cfDNA, but not in the tumor. Of interest, 1 of 2 patients with KRAS G12/G13 mutation (colorectal cancer) in cfDNA, but not in the tumor, experienced rapid disease progression after 1 cycle of cetuximab with chemotherapy. Discrepancies will be addressed with testing of tissue samples using the Bio-Rad QX200 system and repeating cfDNA testing with an increased amount of DNA. Results will be presented at the meeting.
Conclusions: Multiplex detecting of KRAS G12/G13 mutations in a low amount of unamplified cfDNA from plasma using the Bio-Rad QX200 platform is a noninvasive alternative to mutation testing of tumor tissue with an acceptable level of concordance and sensitivity, and should be investigated further for testing of KRAS mutation status in patients with cancer.
Citation Format: Helen J. Huang, Dawne N. Shelton, Siqing Fu, Sarina A. Piha-Paul, Apostolia M. Tsimberidou, Ralph G. Zinner, Jennifer J. Wheler, Aung Naing, David S. Hong, Gerald S. Falckook, Scott Kopetz, Rajyalakshmi Luthra, Bryan K. Kee, George A. Karlin-Neumann, Funda Meric-Bernstam, Filip Janku. Multiplex KRAS G12/G13 mutation testing of 16ng of unamplified cell-free DNA from plasma of patients with advanced cancers using Droplet Digital PCR. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2407. doi:10.1158/1538-7445.AM2015-2407