Clinical significance of BRAF mutation status in circulating tumor DNA of metastatic melanoma patients at baseline

2016 ◽  
Vol 25 (10) ◽  
pp. 783-788 ◽  
Author(s):  
Anne C. Knol ◽  
Audrey Vallée ◽  
Guillaume Herbreteau ◽  
Jean-Michel Nguyen ◽  
Emilie Varey ◽  
...  
Keyword(s):  
Metastatic Melanoma ◽  
Clinical Significance ◽  
Braf Mutation ◽  
Circulating Tumor Dna ◽  
Mutation Status ◽  
Melanoma Patients ◽  
Tumor Dna

scholarly journals Monitoring BRAF and NRAS mutations with cell-free circulating tumor DNA from metastatic melanoma patients

Oncotarget ◽  
2018 ◽  
Vol 9 (90) ◽  
pp. 36238-36249 ◽  
Author(s):  
Elodie Long-Mira ◽  
Marius Ilie ◽  
Emmanuel Chamorey ◽  
Florence Leduff-Blanc ◽  
Henri Montaudié ◽  
...  
Keyword(s):  
Metastatic Melanoma ◽  
Circulating Tumor Dna ◽  
Melanoma Patients ◽  
Tumor Dna

The impact of BRAF mutation status on clinical outcomes with single-agent PD-1 inhibitor versus combination ipilimumab/nivolumab.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 10024-10024
Author(s):  
Vincent The-Luc Ma ◽  
Stephanie Daignault ◽  
Jessica Waninger ◽  
Leslie Anne Fecher ◽  
Michael Green ◽  
...  
Keyword(s):  
Metastatic Melanoma ◽  
Retrospective Analysis ◽  
Braf Mutation ◽  
Univariate Analysis ◽  
Single Agent ◽  
Mutation Status ◽  
Melanoma Patients ◽  
The Impact ◽  
Braf Mutant ◽  
Braf V600 Mutation

10024 Background: Nearly half of all metastatic melanoma patients possess the BRAF V600 mutation. Several therapies are approved for BRAF mutant metastatic melanoma, but it is unclear if there is a differential outcome to various immunotherapy regimens. Our aim was to better assess if BRAF mutation status has any impact on survival to combination ipilimumab/nivolumab (I/N) versus single-agent PD-1 inhibitor (PD-1i). Methods: We performed a single center, retrospective analysis on a cohort of patients diagnosed with metastatic or unresectable melanoma from 2012 to 2019 at the University of Michigan who were treated with standard I/N or PD-1i (nivolumab or pembrolizumab). A univariate analysis of progression free survival (PFS) and overall survival (OS) was stratified by treatment type and BRAF mutation status. A multivariate Cox regression of survival was used to compare the effects of the treatment groups adjusted by BRAF status, age, gender, pre-treatment LDH level, prior treatment status, and brain metastases status. Results: 323 patients were identified. 132 had BRAF V600 mutation and 191 had BRAF wildtype (WT) status. 138 patients received I/N and 185 patients received PD-1i. In our univariate analysis, there was no difference in PFS [HR: 0.72, 95% CI, 0.46 – 1.13] or OS [HR: 0.78, 0.44 – 1.38] with I/N versus PD-1i in the BRAF mutant cohort, but there was improved PFS [HR: 0.55, 0.35 – 0.88) and OS [HR: 0.52, 0.28 – 0.95] with I/N compared to PD-1i in the BRAF WT group. In the multivariate analysis, the BRAF WT group continued to show PFS benefit with I/N compared to PD-1i [HR: 0.57, 95% CI, 0.35 – 0.95], but the OS benefit no longer achieved statistical significance [HR: 0.54, 0.28 – 1.03]. Conclusions: Our study results were discordant with the observation in the landmark CheckMate 067 trial, which noted improved PFS and OS with I/N compared to nivolumab alone in the BRAF mutant group and no difference in the BRAF WT group. In our real-world retrospective analysis, I/N over PD-1i should be considered as initial immunotherapy for metastatic melanoma patients regardless of BRAF mutation status, but even more favorably in BRAF WT.

scholarly journals Circulating Tumor DNA as a Marker for Treatment Response in Metastatic Melanoma Patients Using Next-Generation Sequencing—A Prospective Feasibility Study

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 3101
Author(s):  
Marina Berger ◽  
Andrea Thueringer ◽  
Doritt Franz ◽  
Nadia Dandachi ◽  
Emina Talakić ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Metastatic Melanoma ◽  
Single Molecule ◽  
Progression Free Survival ◽  
Circulating Tumor Dna ◽  
Next Generation ◽  
Dna Amount ◽  
Melanoma Patients ◽  
Tumor Dna ◽  
Generation Sequencing

We prospectively performed a longitudinal analysis of circulating tumor DNA (ctDNA) from 149 plasma samples and CT scans in Stage III and IV metastatic melanoma patients (n = 20) treated with targeted agents or immunotherapy using two custom next-generation sequencing (NGS) Ion AmpliSeq™ HD panels including 60 and 81 amplicons in 18 genes, respectively. Concordance of matching cancer-associated mutations in tissue and plasma was 73.3%. Mutant allele frequency (MAF) levels showed a range from 0.04% to 28.7%, well detectable with NGS technologies utilizing single molecule tagging like the AmpliSeq™ HD workflow. Median followup time of the tissue and/or plasma positive cohort (n = 15) was 24.6 months and median progression-free survival (PFS) was 7.8 months. Higher MAF ≥ 1% at baseline was not significantly associated with a risk of progression (Odds Ratio = 0.15; p = 0.155). Although a trend could be seen, MAF levels did not differ significantly over time between patients with and without a PFS event (p = 0.745). Depending on the cell-free DNA amount, NGS achieved a sensitivity down to 0.1% MAF and allowed for parallel analysis of multiple mutations and previously unknown mutations. Our study indicates that NGS gene panels could be useful for monitoring disease burden during therapy with ctDNA in melanoma patients.

scholarly journals BRAF Mutation Status in Circulating Tumor DNA from Patients with Metastatic Colorectal Cancer: Extended Mutation Analysis from the AGEO RASANC Study

Cancers ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 998 ◽  
Author(s):  
Leo Mas ◽  
Jean-Baptiste Bachet ◽  
Valerie Taly ◽  
Olivier Bouché ◽  
Julien Taieb ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Liver Metastasis ◽  
Metastatic Colorectal Cancer ◽  
Mutation Analysis ◽  
Braf Mutation ◽  
Circulating Tumor Dna ◽  
Kappa Coefficient ◽  
Plasma Samples ◽  
Mutation Status ◽  
Tumor Dna

In patients with metastatic colorectal cancer (mCRC), RAS and BRAF mutations are currently determined by tumor sample analysis. Here, we report BRAF mutation status analysis in paired tumor tissue and plasma samples of mCRC patients included in the AGEO RASANC prospective cohort study. Four hundred and twenty-five patients were enrolled. Plasma samples were analyzed by next-generation sequencing (NGS). When no mutation was identified, we used two methylated specific biomarkers (digital droplet PCR) to determine the presence or absence of circulating tumor DNA (ctDNA). Patients with conclusive ctDNA results were defined as those with at least one mutation or one methylated biomarker. The kappa coefficient and accuracy were 0.79 (95% CI: 0.67–0.91) and 97.3% (95% CI: 95.2–98.6%) between the BRAF status in plasma and tissue for patients with available paired samples (n = 405), and 0.89 (95% CI: 0.80–0.99) and 98.5% (95% CI: 96.4–99.5%) for those with conclusive ctDNA (n = 323). The absence of liver metastasis was the main factor associated to inconclusive ctDNA results. In patients with liver metastasis, the kappa coefficient was 0.91 (95% CI, 0.81–1.00) and accuracy was 98.6% (95% CI, 96.5–99.6%). We demonstrate satisfying concordance between tissue and plasma BRAF mutation detection, especially in patients with liver metastasis, arguing for plasma ctDNA testing for routine BRAF mutation analysis in these patients.

scholarly journals Hypermethylation of Circulating Free DNA in Cutaneous Melanoma

2019 ◽  
Vol 9 (23) ◽  
pp. 5074
Author(s):  
Russell Diefenbach ◽  
Jenny Lee ◽  
David Chandler ◽  
Yinan Wang ◽  
Christian Pflueger ◽  
...  
Keyword(s):  
Metastatic Melanoma ◽  
Circulating Tumor Dna ◽  
Advanced Melanoma ◽  
Dna Hypermethylation ◽  
Diagnosis And Prognosis ◽  
Circulating Free Dna ◽  
Healthy Control ◽  
Melanoma Patients ◽  
Tumor Dna ◽  
Generation Sequencing

Changes in DNA methylation are well documented in cancer development and progression and are typically identified through analyses of genomic DNA. The capability of monitoring tumor-specific methylation changes in circulating tumor DNA (ctDNA) has the potential to improve the sensitivity of ctDNA for the diagnosis and prognosis of solid tumors. In this study we profiled the methylation of seven gene targets (all known to be hypermethylated in metastatic melanoma) within the plasma of patients with advanced melanoma using amplicon-based next generation sequencing of bisulfite-treated DNA. Hypermethylation of 6/7 gene targets, including paraoxonase 3 (PON3) was significantly elevated in patients with metastatic melanoma (n = 4) compared to healthy control samples (n = 5). In addition, the degree of hypermethylation of PON3 and MEOX2 were significantly correlated with ctDNA copy number in melanoma patients, confirming the utility of methylated ctDNA in the absence of tumor mutation data for genes such as BRAF, RAS or EGFR.

scholarly journals Small EVs-Associated DNA as Complementary Biomarker to Circulating Tumor DNA in Plasma of Metastatic Colorectal Cancer Patients

2021 ◽  
Vol 14 (2) ◽  
pp. 128
Author(s):  
Silvia Galbiati ◽  
Francesco Damin ◽  
Dario Brambilla ◽  
Lucia Ferraro ◽  
Nadia Soriani ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Metastatic Colorectal Cancer ◽  
Cancer Patients ◽  
Digital Pcr ◽  
Extracellular Vesicle ◽  
Circulating Tumor Dna ◽  
Mutation Status ◽  
Promising Practice ◽  
Colorectal Cancer Patients ◽  
Tumor Dna

It is widely accepted that assessing circular tumor DNA (ctDNA) in the plasma of cancer patients is a promising practice to evaluate somatic mutations from solid tumors noninvasively. Recently, it was reported that isolation of extracellular vesicles improves the detection of mutant DNA from plasma in metastatic patients; however, no consensus on the presence of dsDNA in exosomes has been reached yet. We analyzed small extracellular vesicle (sEV)-associated DNA of eleven metastatic colorectal cancer (mCRC) patients and compared the results obtained by microarray and droplet digital PCR (ddPCR) to those reported on the ctDNA fraction. We detected the same mutations found in tissue biopsies and ctDNA in all samples but, unexpectedly, in one sample, we found a KRAS mutation that was not identified either in ctDNA or tissue biopsy. Furthermore, to assess the exact location of sEV-associated DNA (outside or inside the vesicle), we treated with DNase I sEVs isolated with three different methodologies. We found that the DNA inside the vesicles is only a small fraction of that surrounding the vesicles. Its amount seems to correlate with the total amount of circulating tumor DNA. The results obtained in our experimental setting suggest that integrating ctDNA and sEV-associated DNA in mCRC patient management could provide a complete real-time assessment of the cancer mutation status.

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