3348 Cell-free DNA V600E measurements during vemurafenib therapy of metastatic melanoma patients

Abstract BACKGROUND A substantial number of melanoma patients develop local or metastatic recurrence, and early detection of these is vital to maximise benefit from new therapies such as inhibitors of BRAF and MEK, or immune checkpoints. This study explored the use of novel DNA copy-number profiles in circulating cell-free DNA (cfDNA) as a potential biomarker of active disease and survival. PATIENTS AND METHODS Melanoma patients were recruited from oncology and dermatology clinics in Sheffield, UK, and cfDNA was isolated from stored blood plasma. Using low-coverage whole-genome sequencing, we created copy-number profiles from cfDNA from 83 melanoma patients, 44 of whom had active disease. We used scoring algorithms to summarize copy-number aberrations and investigated their utility in multivariable logistic and Cox regression analyses. RESULTS The copy-number aberration score (CNAS) was a good discriminator of active disease (odds ratio, 3.1; 95% CI, 1.5–6.2; P = 0.002), and CNAS above or below the 75th percentile remained a significant discriminator in multivariable analysis for active disease (P = 0.019, with area under ROC curve of 0.90). Additionally, mortality was higher in those with CNASs above the 75th percentile than in those with lower scores (HR, 3.4; 95% CI, 1.5–7.9; P = 0.005), adjusting for stage of disease, disease status (active or resected), BRAF status, and cfDNA concentration. CONCLUSIONS This study demonstrates the potential of a de novo approach utilizing copy-number profiling of cfDNA as a biomarker of active disease and survival in melanoma. Longitudinal analysis of copy-number profiles as an early marker of relapsed disease is warranted.

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Multiparametric Analysis of Cell-Free DNA in Melanoma Patients

PLoS ONE ◽

10.1371/journal.pone.0049843 ◽

2012 ◽

Vol 7 (11) ◽

pp. e49843 ◽

Cited By ~ 46

Author(s):

Francesca Salvianti ◽

Pamela Pinzani ◽

Paolo Verderio ◽

Chiara Maura Ciniselli ◽

Daniela Massi ◽

...

Keyword(s):

Cell Free Dna ◽

Free Dna ◽

Multiparametric Analysis ◽

Melanoma Patients

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O64: GENOMIC PROFILING USING CIRCULATING NUCLEIC ACIDS IN STAGE IV MELANOMA PATIENTS RECEIVING IMMUNOTHERAPY REVEALS A NOVEL GENE AMPLIFICATION LANDSCAPE AND ALLOWS FOR DETECTION OF ACTIONABLE GENE MUTATIONS

British Journal of Surgery ◽

10.1093/bjs/znab117.064 ◽

2021 ◽

Vol 108 (Supplement_1) ◽

Author(s):

M Ita ◽

JH Wang ◽

P O'Leary ◽

Y Nolan ◽

A Toulouse ◽

...

Keyword(s):

Disease Progression ◽

Gene Amplification ◽

Somatic Mutation ◽

Therapeutic Response ◽

Stage Iv ◽

Cell Free Dna ◽

Circulating Nucleic Acids ◽

Free Dna ◽

Melanoma Patients ◽

Stage Iv Melanoma

Abstract Introduction Serial monitoring for disease progression and therapeutic efficacy at the molecular level in metastatic melanoma is hampered by a lack of reliable blood borne biomarkers. Molecular profiling of melanoma tumours is almost impractical in metastatic disease due to risks of procedure related morbidity and sampling inefficiency in representing tumour heterogeneity. Cell free DNA allows monitoring of molecular changes in melanoma over the course of immunotherapy. We investigated the utility of somatic mutation and gene amplification analyses in melanoma patients receiving immunotherapy. Method Cell free DNA was extracted from plasma using a QIAamp Circulating Nucleic Acid Kit (Qiagen). Pathway focused profiling of somatic mutation status was performed by ARMs PCR using QBiomarker Somatic Mutation PCR Arrays (Qiagen). Gene amplification analysis was performed by Real Time Quantitative PCR (Roche) using RT2 Profiler PCR Arrays (Qiagen). Result A total of twenty patients with stage IV melanoma receiving immunotherapy were enrolled in this study. The BRAF p.V600E mutation was detected in the cfDNA of 80% of BRAF positive patients. Cell free DNA was also profiled for a total of 84 genes of the cancer inflammation and immunity pathway. There was a significant difference in the copy numbers of several genes (CTLA-4, CXCL12, CXCL5, IDO1, TGFB, IFNG, IL4, PTGS2, AICDA, HLA-A, CCL4, ACKR3, TP53, MYC) between patients with progressive disease and therapeutic response (n=20, p < 0.05). Conclusion We postulate that cell free DNA pathway focused somatic mutation and gene amplification analyses may be useful in evaluating disease progression and therapeutic response. Take-home message Genomic analysis of circulating nucleic acids may be useful in evaluating disease progression and therapeutic response in metastatic melanoma.

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Sensitive droplet digital PCR method for detection of TERT promoter mutations in cell free DNA from patients with metastatic melanoma

Oncotarget ◽

10.18632/oncotarget.20354 ◽

2017 ◽

Vol 8 (45) ◽

pp. 78890-78900 ◽

Cited By ~ 27

Author(s):

Ashleigh C. McEvoy ◽

Leslie Calapre ◽

Michelle R. Pereira ◽

Tindaro Giardina ◽

Cleo Robinson ◽

...

Keyword(s):

Metastatic Melanoma ◽

Digital Pcr ◽

Droplet Digital Pcr ◽

Cell Free Dna ◽

Free Dna ◽

Tert Promoter ◽

Tert Promoter Mutations ◽

Pcr Method ◽

Promoter Mutations

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Characterization and Clinical Utility of BRAFV600 Mutation Detection Using Cell-Free DNA in Patients with Advanced Melanoma

Cancers ◽

10.3390/cancers13143591 ◽

2021 ◽

Vol 13 (14) ◽

pp. 3591

Author(s):

Piotr Rutkowski ◽

Patrick Pauwels ◽

Joseph Kerger ◽

Bart Jacobs ◽

Geert Maertens ◽

...

Keyword(s):

Objective Response ◽

Treatment Phase ◽

Progression Free Survival ◽

Cell Free Dna ◽

Mutation Status ◽

Free Survival ◽

Free Dna ◽

Phase 2 Study ◽

Melanoma Patients ◽

Test Result

Tissue-based tests for BRAFV600 mutation-positive melanoma involve invasive biopsy procedures, and can lead to an erroneous diagnosis when the tumor samples degrade. Herein, we explored a minimally invasive, cell-free deoxyribonucleic acid (cfDNA)-based platform, to retest patients for BRAFV600 mutations. This phase 2 study enrolled adult patients with unresectable/metastatic melanoma. A prescreening testing phase evaluated the concordance between a prior tissue-based BRAFV600 mutation test result and a subsequent plasma cfDNA-based test result. A treatment phase evaluated the patients who were confirmed as BRAFV600 mutation-positive, and were treated with cobimetinib plus vemurafenib. It was found that 35/54 patients (64.8%) with a mutant BRAF status by prior tissue test had a positive BRAFV600 mutation with the cfDNA test. Further, 7/118 patients (5.9%) with a wild-type BRAF status had a positive BRAFV600 mutation cfDNA test; tissue retests on archival samples confirmed BRAFV600 mutation positivity in 5/7 patients (71.4%). One of these patients received BRAF pathway-targeted therapy (cobimetinib plus vemurafenib), and had progression-free survival commensurate with previous experience. In the overall cobimetinib plus vemurafenib-treated population, 29/36 patients (80.6%) had an objective response. The median progression-free survival was 13.6 months (95% confidence interval, 9.5–16.5). Cell-free DNA–based tests may be a fast and convenient option to identify BRAF mutation status in melanoma patients, and help inform treatment decisions.

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