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Direct comparison study between droplet digital PCR and a combination of allele-specific PCR, asymmetric rapid PCR and melting curve analysis for the detection of BRAF V600E mutation in plasma from melanoma patients

  • Eleni Tzanikou , Verena Haselmann , Athina Markou , Angelika Duda , Jochen Utikal , Michael Neumaier and Evi S. Lianidou EMAIL logo
Published/Copyright: January 18, 2020
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Clinical Chemistry and Laboratory Medicine (CCLM)
From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 58 Issue 11

Abstract

Background

In metastatic melanoma, 40%–50% of patients harbor a BRAF V600E mutation and are thereby eligible to receive a combined BRAF/MEK inhibitor therapy. Compared to standard-of-care tissue-based genetic testing, analysis of circulating tumor DNA (ctDNA) from blood enables a comprehensive assessment of tumor mutational status in real-time and can be used for monitoring response to therapy. The aim of our study was to directly compare the performance of two highly sensitive methodologies, droplet digital PCR (ddPCR) and a combination of ARMS/asymmetric-rapid PCR/melting curve analysis, for the detection of BRAF V600E in plasma from melanoma patients.

Methods

Cell-free DNA (cfDNA) was isolated from 120 plasma samples of stage I to IV melanoma patients. Identical plasma-cfDNA samples were subjected to BRAF V600E mutational analysis using in parallel, ddPCR and the combination of ARMS/asymmetric-rapid PCR/melting curve analysis.

Results

BRAF V600E mutation was detected in 9/117 (7.7%) ctDNA samples by ddPCR and in 22/117 (18.8%) ctDNA samples by the combination of ARMS/asymmetric- rapid PCR/melting curve analysis. The concordance between these two methodologies was 85.5% (100/117). The comparison of plasma-ctDNA analysis using ddPCR and tissue testing revealed an overall agreement of 79.4% (27/34), while the corresponding agreement using the combination of ARMS/asymmetric-rapid PCR/melting curve analysis was 73.5% (25/34). Moreover, comparing the detection of BRAF-mutant ctDNA with the clinics, overall agreement of 87.2% (48/55) for ddPCR and 79.2% (42/53) was demonstrated. Remarkably, the duration of sample storage was negatively correlated with correctness of genotyping results highlighting the importance of pre-analytical factors.

Conclusions

Our direct comparison study has shown a high level of concordance between ddPCR and the combination of ARMS/asymmetric-rapid PCR/melting curve analysis for the detection of BRAF V600E mutations in plasma.

Keywords: BRAF mutation; ctDNA analysis; liquid biopsy; melanoma; plasma
Corresponding author: Dr. Evi S. Lianidou, Analysis of Circulating Tumor Cells Lab, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, 15771 Athens, Greece, Phone: +30 210 7274319, Fax: +30 210 7274750
aEleni Tzanikou and Verena Haselmann contributed equally to this work.

Acknowledgments

The authors thank RomyEichner for helping to collect samples and Victor Costina for critically reading the manuscript.

  1. Author contributions: Eleni Tzanikou: experiments, manuscript writing and editing, Verena Haselmann: study design, supervising experimental procedures, statistical analysis, manuscript writing and editing, Athina Markou: experiments, Angelika Duda: experiments, Michael Neumaier: study design, Jochen Utikal: patient enrollment, Evi Lianidou: study design, supervising experimental procedures, manuscript writing and editing. All authors contributed to revision of the manuscript and approved it for submission. All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission. The ethical approval was requires for this study.

  2. Research funding: This research has been co-financed by the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH–CREATE–INNOVATE (project code: T1RCI-02935).

  3. Employment or leadership: None declared.

  4. Honorarium: None declared.

  5. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

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Received: 2019-08-12
Accepted: 2019-12-09
Published Online: 2020-01-18
Published in Print: 2020-10-25

©2020 Walter de Gruyter GmbH, Berlin/Boston

Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Biotin interference in cardiac troponin immunoassay – where the wild things are?
  4. Review
  5. Laboratory-related issues in the measurement of cardiac troponins with highly sensitive assays
  6. Mini Review
  7. Chromatographic methods development for clinical practice: requirements and limitations
  8. Opinion Paper
  9. Harmonising EQA schemes the next frontier: challenging the status quo
  10. Genetics and Molecular Diagnostics
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  45. Successful implementations of automated minimum re-test intervals to overcome ferritin over-requesting in a Spanish hospital laboratory
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https://doi.org/10.1515/cclm-2019-0783
Keywords for this article
BRAF mutation; ctDNA analysis; liquid biopsy; melanoma; plasma

Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Biotin interference in cardiac troponin immunoassay – where the wild things are?
  4. Review
  5. Laboratory-related issues in the measurement of cardiac troponins with highly sensitive assays
  6. Mini Review
  7. Chromatographic methods development for clinical practice: requirements and limitations
  8. Opinion Paper
  9. Harmonising EQA schemes the next frontier: challenging the status quo
  10. Genetics and Molecular Diagnostics
  11. Direct comparison study between droplet digital PCR and a combination of allele-specific PCR, asymmetric rapid PCR and melting curve analysis for the detection of BRAF V600E mutation in plasma from melanoma patients
  12. A novel mitochondrial m.14430A>G (MT-ND6, p.W82R) variant causes complex I deficiency and mitochondrial Leigh syndrome
  13. Obesity status modifies the association between rs7556897T>C in the intergenic region SLC19A3-CCL20 and blood pressure in French children
  14. General Clinical Chemistry and Laboratory Medicine
  15. Influence of reagent lots and multiple measuring systems on estimating the coefficient of variation from quality control data; implications for uncertainty estimation and interpretation of QC results
  16. Electrophoretic α1-globulin for screening of α1-antitrypsin deficient variants
  17. A continued method performance monitoring approach for the determination of pediatric renin samples – application within a European clinical trial
  18. Pilot study for cystic fibrosis neonatal screening: the Cuban experience
  19. Validation of the analytical performance of the NOVEOS™ System, a system which improves upon the third-generation in vitro allergy testing technology
  20. IgE cross-reactivity measurement of cashew nut, hazelnut and peanut using a novel IMMULITE inhibition method
  21. Sexual dimorphism in the cerebrospinal fluid total protein content
  22. Current state of the morphological assessment of urinary erythrocytes in The Netherlands: a nation-wide questionnaire
  23. Reference Values and Biological Variations
  24. Within-subject and between-subject biological variation of first morning void urine amino acids in 12 healthy subjects
  25. Proenkephalin as a new biomarker for pediatric acute kidney injury – reference values and performance in children under one year of age
  26. Hematology and Coagulation
  27. Quality performance for indirect Xa inhibitor monitoring in patients using international external quality data
  28. Cardiovascular Diseases
  29. Clinical risk assessment of biotin interference with a high-sensitivity cardiac troponin T assay
  30. Short- and long-term biological variation of cardiac troponin I in healthy individuals, and patients with end-stage renal failure requiring haemodialysis or cardiomyopathy
  31. Infectious Diseases
  32. Monocyte distribution width (MDW) as a screening tool for sepsis in the Emergency Department
  33. Performance of a Toxo IgM prototype assay for the diagnosis of maternal and congenital Toxoplasma infections
  34. Letters to the Editors
  35. Evaluation of an ELISA for SARS-CoV-2 antibody testing: clinical performances and correlation with plaque reduction neutralization titer
  36. Preliminary evaluation of Roche Cobas Elecsys Anti-SARS-CoV-2 chemiluminescence immunoassay
  37. Hypoalbuminemia and elevated D-dimer in COVID-19 patients: a call for result harmonization
  38. Total pathway to method validation
  39. Derivation of performance specifications for uncertainty of serum C-reactive protein measurement according to the Milan model 3 (state of the art)
  40. FGF23 measurement in burosumab-treated patients: an emerging treatment may induce a new analytical interference
  41. Use of a modified IDS-ISYS intact PTH assay for intraoperative PTH measurements
  42. Agreement of dried blood spot lyso-Gb3 concentrations obtained from different laboratories in patients with Fabry disease
  43. Influence of delayed separation of plasma from whole blood and centrifugation protocol on Zn plasma concentration
  44. A survey of order of draw on inpatient wards and adherence to EFLM-COLABIOCLI recommendations
  45. Successful implementations of automated minimum re-test intervals to overcome ferritin over-requesting in a Spanish hospital laboratory
  46. Remarkable pseudoleucocytosis induced by mild cryoglobulinemia
  47. Massive hemolysis due to Clostridium perfringens: a laboratory’s perspective
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