Isolation and Quantification of Plasma Circulating Tumor DNA from Melanoma Patients

2021 ◽  
pp. 247-263
Author(s):  
Gabriela Marsavela ◽  
Anna Reid ◽  
Elin S. Gray ◽  
Leslie Calapre
Keyword(s):  
Circulating Tumor Dna ◽  
Melanoma Patients ◽  
Tumor Dna

scholarly journals Liquid Profiling of Circulating Tumor DNA in Plasma of Melanoma Patients for Companion Diagnostics and Monitoring of BRAF Inhibitor Therapy

2018 ◽  
Vol 64 (5) ◽  
pp. 830-842 ◽  
Author(s):  
Verena Haselmann ◽  
Christoffer Gebhardt ◽  
Ingrid Brechtel ◽  
Angelika Duda ◽  
Claudia Czerwinski ◽  
...  
Keyword(s):  
Clinical Course ◽  
Braf Inhibitor ◽  
Circulating Tumor Dna ◽  
Inhibitor Therapy ◽  
Response To Treatment ◽  
Companion Diagnostics ◽  
Mutational Status ◽  
Melanoma Patients ◽  
Braf Mutant ◽  
Tumor Dna

Abstract BACKGROUND The current standard for determining eligibility of patients with metastatic melanoma for BRAF-targeted therapy is tissue-based testing of BRAF mutations. As patients are rarely rebiopsied, detection in blood might be advantageous by enabling a comprehensive assessment of tumor mutational status in real time and thereby representing a noninvasive biomarker for monitoring BRAF therapy. METHODS In all, 634 stage I to IV melanoma patients were enrolled at 2 centers, and 1406 plasma samples were prospectively collected. Patients were assigned to 3 separate study cohorts: study 1 for assessment of circulating tumor DNA (ctDNA) as part of companion diagnostics, study 2 for assessment of ctDNA for patients with low tumor burden and for follow-up, and study 3 for monitoring of resistance to BRAF inhibitor (BRAFi) or mitogen-activated protein kinase inhibitor therapy. RESULTS Overall, a high degree of concordance between plasma and tissue testing results was observed at 90.9% (study 1) and 90.1% (study 2), respectively. Interestingly, discrepant results were in some cases associated with nonresponse to BRAFi (n = 3) or a secondary BRAF-mutant malignancy (n = 5). Importantly, ctDNA results correlated with the clinical course of disease in 95.7% and with response to treatment. Significantly, the detection of BRAF mutant ctDNA preceded relapse assessed by Response Evaluation Criteria in Solid Tumors, and was more specific than serum S100 and lactate dehydrogenase. CONCLUSIONS Blood-based testing compares favorably with standard-of-care tissue-based BRAF mutation testing. Importantly, blood-based BRAF testing correlates with the clinical course, even for early-stage patients, and may be used to predict response to treatment, recurrence, and resistance before radioimaging under BRAFi therapy, thereby enabling considerable improvements in patient treatment.

scholarly journals Circulating Tumor DNA Predicts Outcome from First-, but not Second-line Treatment and Identifies Melanoma Patients Who May Benefit from Combination Immunotherapy

2020 ◽  
Vol 26 (22) ◽  
pp. 5926-5933 ◽  
Author(s):  
Gabriela Marsavela ◽  
Jenny Lee ◽  
Leslie Calapre ◽  
Stephen Q. Wong ◽  
Michelle R. Pereira ◽  
...  
Keyword(s):  
Circulating Tumor Dna ◽  
Line Treatment ◽  
Second Line ◽  
Combination Immunotherapy ◽  
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

scholarly journals Circulating tumor DNA (ctDNA) detection is associated with shorter progression-free survival in advanced melanoma patients

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Gabriella Taques Marczynski ◽  
Ana Carolina Laus ◽  
Mariana Bisarro dos Reis ◽  
Rui Manuel Reis ◽  
Vinicius de Lima Vazquez
Keyword(s):  
Somatic Mutations ◽  
Limit Of Detection ◽  
Progression Free Survival ◽  
Circulating Tumor Dna ◽  
Advanced Melanoma ◽  
Plasma Samples ◽  
Free Survival ◽  
Melanoma Patients ◽  
Digital Polymerase Chain Reaction ◽  
Tumor Dna

Abstract BRAF, NRAS and TERT mutations occur in more than 2/3 of melanomas. Its detection in patient’s blood, as circulating tumor DNA (ctDNA), represents a possibility for identification and monitoring of metastatic disease. We proposed to standardize a liquid biopsy platform to identify hotspot mutations in BRAF, NRAS and TERT in plasma samples from advanced melanoma patients and investigate whether it was associated to clinical outcome. Firstly, we performed digital polymerase chain reaction using tumor cell lines for validation and determination of limit of detection (LOD) of each assay and screened plasma samples from healthy individuals to determine the limit of blank (LOB). Then, we selected 19 stage III and IV patients and determined the somatic mutations status in tumor tissue and track them in patients’ plasma. We established a specific and sensitive methodology with a LOD ranging from 0.13 to 0.37%, and LOB ranging from of 0 to 5.201 copies/reaction. Somatic mutations occurred in 17/19 (89%) patients, of whom seven (41%) had ctDNA detectable their paired plasma. ctDNA detection was associated with shorter progression free survival (p = 0.01). In conclusion, our data support the use of ctDNA as prognosis biomarker, suggesting that patients with detectable levels have an unfavorable outcome.

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 Plasma Circulating Tumor DNA Levels for the Monitoring of Melanoma Patients: Landscape of Available Technologies and Clinical Applications

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Benoit Busser ◽  
Julien Lupo ◽  
Lucie Sancey ◽  
Stéphane Mouret ◽  
Patrice Faure ◽  
...  
Keyword(s):  
Acquired Resistance ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Clinical Applications ◽  
Molecular Heterogeneity ◽  
Liquid Biopsies ◽  
Melanoma Patients ◽  
Ctdna Analysis ◽  
Next Generation Sequencing Ngs ◽  
Tumor Dna

Melanoma is a cutaneous cancer with an increasing worldwide prevalence and high mortality due to unresectable or metastatic stages. Mutations inBRAF,NRAS, orKITare present in more than 60% of melanoma cases, but a useful blood-based biomarker for the clinical monitoring of melanoma patients is still lacking. Thus, the analysis of circulating tumor cells (CTCs) and/or cell-free circulating tumor DNA (ctDNA) analysis from blood (liquid biopsies) appears to be a promising noninvasive, repeatable, and systemic sampling tool for detecting and monitoring melanoma. Here, we review the molecular biology-based strategies used for ctDNA quantification in melanoma patients, as well as their main clinical applications. Droplet digital PCR (ddPCR) and next generation sequencing (NGS) technologies appear to be two versatile and complementary strategies to study rare variant mutations for the detection and monitoring of melanoma progression. Among the different clinical uses of ctDNA, we highlight the assessment of molecular heterogeneity and the identification of genetic determinants for targeted therapy as well as the analysis of acquired resistance. Importantly, ctDNA quantification might also be a novel biomarker with a prognostic value for melanoma patients.

scholarly journals Undetectable circulating tumor DNA (ctDNA) levels correlate with favorable outcome in metastatic melanoma patients treated with anti-PD1 therapy

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Teofila Seremet ◽  
Yanina Jansen ◽  
Simon Planken ◽  
Hassan Njimi ◽  
Mélanie Delaunoy ◽  
...  
Keyword(s):  
Metastatic Melanoma ◽  
Circulating Tumor Dna ◽  
Favorable Outcome ◽  
Melanoma Patients ◽  
Tumor Dna
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