You are here
Identification of novel EGFR ectodomain mutations based on a large database of clinical circulating cell-free DNA sequencing tests.
Identification of novel EGFR ectodomain (ECD) mutations based on a database of clinical circulating cell-free DNA sequencing testsBackground: The Cancer Genome Atlas primarily sequenced early stage, treatment-naïve cancers, whereas our laboratory primarily sequences treatment refractory metastatic solid tumors. Circulating cell-free DNA (cfDNA) next generation sequencing (NGS) has enhanced sensitivity, which may aid in the detection of emerging resistant clones. In patients with RAS wild-type metastatic colorectal cancer (mCRC) EGFRECD mutations are associated with acquired resistance to anti-EGFR therapies. Here we report the frequencies of ECD mutations in patients with mCRC. Methods: Guardant360 is a cfDNA NGS test targeting 70 genes with complete exon sequencing for single nucleotide variants (SNVs), including all 28 exons in EGFR. Analytical sensitivity ranges to 0.05% mutant allele fraction (MAF) with analytic specificity for SNVs > 99.9999%. The 25th, 50th and 75thpercentile MAF for all 13,987 patients tested from June 2014 through January 2016 were 0.2%, 0.4% and 2.5%. Results: From 2014-2016 1,347 tests were performed on 1,257 patients with mCRC. Exon 12 EGFR SNVs [median MAF(range)] with > 3 recurrences were: 8 S464X [0.9%(0.1-3.1)]; 18 G465X [0.5%(.1-3.1); 3 K467X [0.3%(.2-1.0)]; 4 I491X [0.9%(0.3-1.6)]; 11 S492X [2.1%(0.3-5.1)]. Two novel EGFR SNVs were: 20 V441X [1.3%(0.1-2.8)]; and 5 S442X [0.2%(.1-2.7)]. Range of EGFR SNVs per case was 1-6, with a single hypermutated case demonstrating many resistance sub-clones: 6 EGFR exon 12 SNVs, and 4 KRAS and 3 NRAS SNVs in codons 12 and 61, and an STRN-ALKfusion at 0.1% MAF. Conclusions: A database of cfDNA NGS results in patients with mCRC revealed EGFR ECD SNVs known to drive anti-EGFR therapy resistance. Two spatially co-located SNVs of unknown significance were discovered, and these occurred in some cases at the highest MAF of EGFR SNVs. This analysis suggests that these two novel SNVs may function as major drivers of clonal resistance.
Abstracts by Christine Elaine Lee:
Case series of EGFR C797S mutations in non-small cell lung cancer identified with cell-free circulating tumor DNA next generation sequencing.Meeting: 2016 ASCO Annual Meeting | Abstract No: e23021Category: Tumor Biology - Circulating Biomarkers
Investigating the Utility of comprehensive genomic Profiling for patients with newly diagnosed breast cancer.Meeting: 2016 ASCO Annual Meeting | Abstract No: TPS11617