Efficient Detection of BRAF Mutation in Plasma of Patients after Long-term Storage of Blood in Cell-Free DNA Blood Collection Tubes

Denis, Marc G.; Knol, Anne-Chantal; Théoleyre, Sandrine; Vallée, Audrey; Dréno, Brigitte

doi:10.1373/clinchem.2015.238352

Cited by 25 publications

(15 citation statements)

References 5 publications

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“…We and others have previously demonstrated discordances in the BRAF mutational status between different tumor sites in some patients, possibly related to intertumor heterogeneity. We therefore performed a detailed analysis of the 38 patients included in our study.…”

Section: Resultsmentioning

confidence: 71%

“…The absence of BRAF V600 mutation in one tumor biopsy sample may not be a definitive result and the analysis of other biopsies at the same time from different tumor lesions is not practical. We and others already reported that BRAF discordant status between distinct tumor samples from the same patient can be found in a significant proportion of melanoma patients (about 10%–15%) and that this can be related to intertumor heterogeneity, and also probably to false‐negative results of tissue testing. In the present work, our data also clearly demonstrated that ctDNA reflects the BRAF status in any lesion of the body, and therefore that ctDNA analysis could be more useful than tissue analysis to select melanoma patients for therapy based on BRAF inhibitors.…”

Section: Discussionmentioning

confidence: 80%

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

Knol

Vallée

Herbreteau

et al. 2016

Experimental Dermatology

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Circulating tumor DNA is a promising non-invasive tool for cancer monitoring. The main objective of our work was to investigate the relationship between mutant BRAF DNA in plasma and clinical response. Thirty-eight stage IV patients with a V600 mutated BRAF melanoma were included prior to any treatment. DNA was extracted from plasma and mutant DNA was detected using the amplification-refractory mutation system method. Before the beginning of any treatment, the corresponding BRAF mutation was detected in 29 of the 38 tested plasma samples (76.3% positive per cent agreement). We observed a strong correlation between the presence of circulating mutated DNA and overall survival (OS; P=.02), and with the number of metastatic sites (P=.01). The presence of circulating mutated DNA was also strongly correlated with serum LDH activity (P<.01) and S100 protein concentration (P<.01). Finally, seven patients presented discordant BRAF status in different tumor sites. In all these patients, the test performed on ctDNA was positive, suggesting that ctDNA analysis might be less sensitive to tumor heterogeneity. Altogether, these results suggest that plasmatic mutant BRAF DNA is a prognostic factor of OS, correlated with tumor burden. In addition, it represents an interesting alternative source of DNA to detect BRAF mutations before treatment.

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Section: Resultsmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 80%

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

Knol

Vallée

Herbreteau

et al. 2016

Experimental Dermatology

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“…Streck cell-free DNA BCT ® tubes have also been shown to prevent lysis and cellular release of genomic DNA from ctDNA samples of patients with metastatic breast cancer, compared with PAXgene tubes (PreAnalytiX, Feldbachstrasse, Hombrechtikon, Switzerland) [33]. Furthermore, blood samples from patients with melanoma stored in Streck cell-free DNA BCT ® tubes at room temperature were found to remain serviceable for ctDNA testing, even after long-term storage (up to 10 days at room temperature) [34]. …”

Section: Pre-analytical Factorsmentioning

confidence: 99%

Guide to detecting epidermal growth factor receptor (EGFR) mutations in ctDNA of patients with advanced non-small-cell lung cancer

et al. 2016

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Cancer treatment is evolving towards therapies targeted at specific molecular abnormalities that drive tumor growth. Consequently, to determine which patients are eligible, accurate assessment of molecular aberrations within tumors is required. Obtaining sufficient tumor tissue for molecular testing can present challenges; therefore, circulating free tumor-derived DNA (ctDNA) found in blood plasma has been proposed as an alternative source of tumor DNA. The diagnostic utility of ctDNA for the detection of epidermal growth factor receptor (EGFR) mutations harbored in tumors of patients with advanced non-small-cell lung cancer (NSCLC) is supported by the results of several large studies/meta-analyses. However, recent real-world studies suggest that the performance of ctDNA testing varies between geographic regions/laboratories, demonstrating the need for standardized guidance. In this review, we outline recommendations for obtaining an accurate result using ctDNA, relating to pre-analytical plasma processing, ctDNA extraction, and appropriate EGFR mutation detection methods, based on clinical trial results. We conclude that there are several advantages associated with ctDNA, including the potential for repeated sampling particularly following progression after first-line tyrosine kinase inhibitor (TKI) therapy, as TKIs targeting resistance mutations (eg T790M) are now approved for use in the USA/EU/Japan (at time of writing). However, evidence suggests that ctDNA does not allow detection of EGFR mutations in all patients with known mutation-positive NSCLC. Therefore, although tumor tissue should be the first sample choice for EGFR testing at diagnosis, ctDNA is a promising alternative diagnostic approach.

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“…Cell-free specific blood collection tubes contain stabilizing reagents which have been shown to minimize both ctDNA degradation and sample contamination with blood-cell derived genomic DNA. 36,37 This is particularly important for potential biomarkers in rare diseases where cooperative group studies require long-distance sample deliveries, necessitating strategies to eliminate the issue of substrate degradation. Finally, the technical platforms are particularly appropriate in terms of reproducibility and cost-effectiveness.…”

Section: Discussionmentioning

confidence: 99%

Plasma DNA-Based Molecular Diagnosis, Prognostication, and Monitoring of Patients With EWSR1 Fusion-Positive Sarcomas

Shukla

Patel

Magnan

et al. 2017

JCO Precision Oncology

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Purpose Ewing Sarcoma (ES) and Desmoplastic Small Round Cell Tumors (DSRCT) are aggressive sarcomas molecularly characterized by EWSR1 gene fusions. As pathognomonic genomic events in these respective tumor types, EWSR1 fusions represent robust potential biomarkers for disease monitoring. Patients and Methods To investigate the feasibility of identifying EWSR1 fusions in plasma derived cell-free DNA (cfDNA) from ES and DSRCT patients, we evaluated two complementary approaches in samples from 17 patients with radiographic evidence of disease. The first approach involved identification of patient-specific genomic EWSR1 fusion breakpoints in formalin-fixed, paraffin-embedded tumor DNA using a broad, hybridization capture-based next generation sequencing (NGS) panel, followed by design of patient-specific droplet digital PCR (ddPCR) assays for plasma cfDNA interrogation . The second approach employed a disease-tailored targeted hybridization capture-based NGS panel applied directly to cfDNA which included EWSR1 as well as several other genes with potential prognostic utility. Results EWSR1 fusions were identified in 11/11 (100%) ES and 5/6 (83%) DSRCT samples by ddPCR, while 10/11 (91%) and 4/6 (67%) were identified by NGS. The ddPCR approach had higher sensitivity, ranging between 0.009–0.018% sensitivity. However, the hybrid capture-based NGS assay identified the precise fusion breakpoints in the majority of cfDNA samples, as well as mutations in TP53 and STAG2, two other recurrent, clinically significant alterations in ES, all without prior knowledge of the tumor sequencing results. Conclusion These results provide a compelling rationale for an integrated approach utilizing both NGS and ddPCR for plasma cfDNA-based biomarker evaluations in prospective cooperative group studies.

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Efficient Detection of BRAF Mutation in Plasma of Patients after Long-term Storage of Blood in Cell-Free DNA Blood Collection Tubes

Cited by 25 publications

References 5 publications

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

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

Guide to detecting epidermal growth factor receptor (EGFR) mutations in ctDNA of patients with advanced non-small-cell lung cancer

Plasma DNA-Based Molecular Diagnosis, Prognostication, and Monitoring of Patients With EWSR1 Fusion-Positive Sarcomas

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