Frequency of concurrent gene mutations and copy number alterations in circulating cell-free DNA (cfDNA) from refractory metastatic CRC patients.

Tumor Biology
Session Type and Session Title: 
General Poster Session, Tumor Biology
Abstract Number: 
J Clin Oncol 32:5s, 2014 (suppl; abstr 11117)
M. Pia Morelli, Michael J. Overman, Eduardo Vilar Sanchez, Van Karlyle Morris, Imad Shureiqi, Chris R. Garrett, David R. Fogelman, Kanwal Pratap Singh Raghav, Bryan K. Kee, Laurel Deaton, Cathy Eng, Robert A. Wolff, Dragan Sebisanovic, LaiMun Siew, Aubrey Zapanta, Gangwu Mei, Ben Schiller, Helmy Eltoukhy, AmirAli Talasaz, Scott Kopetz; The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX; Guardant Health, Inc., Redwood City, CA

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Abstract Disclosures


Background: cfDNA allows non-invasive assessment of gene mutations, but has not been reported with copy number alterations. Methodologies to integrate mutation and copy number would allow improved insights into mechanisms of resistance and therapeutic opportunities. Methods: cfDNA extracted from metastatic CRC patient (pt) plasma samples were analyzed by GUARDANT sequencing technology for mutation and amplification of 54 genes. The lower limit of detection was 0.1% mutant alleles in a wild-type background. All patients were enrolled in the ATTACC program for mCRC patients who progressed on standard treatment, and had sequencing of the primary tumor performed for a 46-gene panel. Results: 71 pt plasma samples were analyzed. All pts were refractory to 5-FU-based therapy, with 49 pts previously treated with anti-EGFR monoclonal antibodies (mAbs). In patients treated with EGFR mAbs, 30% of pts (n=15) had detection of KRAS mutations not detectable in the primary tumor, compared to 5% (n=1) of pts without EGFR mAb treatment (odds ratio 8.6, P=0.027). In 6 of the 15 cases, newly detectable KRAS mutations were associated with KRAS gene amplification, compared to 0 of 16 cases with KRAS mutations detected in the primary tumor (P=0.007). 7 ectodomain mutations in EGFR that may alter binding affinity of EGFR mAbs were detected in EGFR mAb treated patients, including S492R (n=4) and three previously unreported mutations G465V, I491R, K467I; concurrent EGFR amplifications were present in 6 of the 7 cases. 14% of EGFR mAbs treated patients developed detectable MET amplifications, which co-existed with KRAS or EGFR mutations in 4 of the 7 cases. Amplifications in EGFR, BRAF, MYC, and SMO were detected in the plasma in 23%, 11%, 11%, and 4% of cases, respectively, representing rates higher than reported in untreated primary tumors. Conclusions: Advances in sequencing and bioinformatics allow detection of copy number alternations from cfDNA in plasma. Copy number alterations in treatment refractory mCRC are more common than previously described, and frequently co-exist with mutations after EGFR mAb treatment.