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Identification of multiple informative genomic mutations by deep sequencing of circulating cell-free tumor DNA in plasma of metastatic melanoma patients.
Abstracts that were granted an exception in accordance with ASCO's Conflict of Interest Policy are designated with a caret symbol (^).
Background: We have been assesseing the prognostic utility of genomic changes in circulating cell-free DNA(cfDNA) in melanoma patients. The limitation has been assessing a few selected genomic targets and sensitivity. The approach of cfDNA analysis in melanoma patients offers detection of potential targeted tumor-related genes mutation(mt) without tumor biopsy. Methods: AJCC stage IV melanoma patients (n=18; different metastasis sites) plasma and paired metastatic tumor tissues resected after blood draw were assessed. The assay was performed on 2 ml filtered plasma. We employed Guardant360, a single-molecule digital sequencing assay that enables detection of rare genomic abnormalities with ultra high-specificity and sensitivity. Using bioinformatics and single molecule sensitivity, rare variants could be detected in cfDNA. Results: In an initial 8 patients, BRAF and TP53 in tumor genomic DNA were sequenced. We found ctDNA with somatic mt in 6/8 matched tumor and plasma specimens(mt allele frequency of 0.2-23.1%) with an overall concordance of 86% for the status of BRAF and TP53 mt in a single bleed. To note known BRAFmt at multiple exons were detectable. Subsequently, matched tumor and plasma from 10 patients were analyzed. We found ctDNA mt in 8/10 cases (mt allele frequency of 0.1-19.1%). Well known frequent melanoma-related mt were detected in patients cfDNA(BRAF, TP53). Other known tumor mt were also detected(CDKN2A, NRAS, PTEN, NOTCH1, EGFR, JAK2) that have not been reported. We established the overall concordance of cfDNA mt with metastatic melanomas across all 54 genes and 80kbps to be 49% whereby, individual single gene concordance were significantly much higher. Conclusions: This ongoing study demonstrates that using Guardant360, cfDNA mt can be detected that match with paired melanomas. The approach offers a more comprehensive approach of monitoring metastatic melanoma patients’ blood for multiple mt during tumor progression. This unique approach will allow for much more comprehensive blood tumor genetic profiling to provide better treatment decision and monitoring for multiple drugable targeted genes without tissue biopsies.
Abstracts by Dave S. B. Hoon:
Identification of functional DNA methylation aberrations associated with outcome in melanoma patients with brain metastasis.Meeting: 2013 ASCO Annual Meeting | Abstract No: 9095
Assessment of a novel immunological biomarker SNP panel from a phase III trial of Bacillus Calmette-Guérin (BCG) adjuvant treatment in stage III melanoma patients.Meeting: 2012 ASCO Annual Meeting | Abstract No: 2519