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Results of the first external quality assessment scheme (EQA) for isolation and analysis of circulating tumour DNA (ctDNA)

  • Verena Haselmann EMAIL logo , Parviz Ahmad-Nejad , Wolf J. Geilenkeuser , Angelika Duda , Merle Gabor , Romy Eichner , Simon Patton and Michael Neumaier EMAIL logo
Published/Copyright: August 25, 2017
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Clinical Chemistry and Laboratory Medicine (CCLM)
From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 56 Issue 2

Abstract

Background:

Circulating tumour DNA (ctDNA) is considered to have a high potential for future management of malignancies. This pilot external quality assessment (EQA) scheme aimed to address issues of analytical quality in this new area of laboratory diagnostics.

Methods:

The EQA scheme consisted of three 2-mL EDTA-plasma samples spiked with fragmented genomic DNA with a mutant allele frequency ranging from 0% to 10% dedicated to the analysis of nine known sequence variations in KRAS codon 12/13 and of BRAF V600E. Laboratories reported: (1) time elapsed for processing, (2) storage temperatures, (3) methods for extraction and quantification, (4) genotyping methodologies and (5) results.

Results:

Specimens were sent to 42 laboratories from 10 European countries; 72.3% reported to isolate cell-free DNA (cfDNA) manually, 62.5% used the entire plasma volume for cfDNA isolation and 38.5% used >10% of cfDNA extracted for downstream genotyping. Of the methods used for quantification, PicoGreen demonstrated the lowest coefficient of variation (33.7%). For genotyping, 11 different methods were reported with the highest error rate observed for Sanger sequencing and the lowest for highly sensitive approaches like digital PCR. In total, 197 genotypes were determined with an overall error rate of 6.09%.

Conclusions:

This pilot EQA scheme illustrates the current variability in multiple phases of cfDNA processing and analysis of ctDNA resulting in an overall error rate of 6.09%. The areas with the greatest variance and clinical impact included specimen volume, cfDNA quantification method, and preference of genotyping platform. Regarding quality assurance, there is an urgent need for harmonisation of procedures and workflows.

Keywords: circulating DNA; external quality assessment scheme; liquid biopsy; liquid profiling; plasma
Corresponding authors: Dr. med. Verena Haselmann and Professor Dr. med. Michael Neumaier, Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany, Phone: 0049-621-383-3561 (V. Haselmann); 0049-621-383-2222 (M. Neumaier), Fax: 0049-621-383-3819

Acknowledgments

The authors thank Nadine Kraft, Ingrid Brechtel and Simona Helfert for their excellent technical assistance and Jan-Hendrik Haselmann and Victor Costina for reviewing the manuscript.

  1. Author contributions: Scheme organisers: V.H., P.A.N., S.P., M.N.; scheme administrator: W.J.G.; technical performance: M.G., A.D., R.E., V.H.; data analyses: V.H., W.J.G.; writing of paper: V.H., P.A.N., S.P., M.N. All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: None declared.

  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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Supplemental Material:

The online version of this article offers supplementary material (https://doi.org/10.1515/cclm-2017-0283).

Received: 2017-04-01
Accepted: 2017-07-25
Published Online: 2017-08-25
Published in Print: 2018-01-26

©2018 Walter de Gruyter GmbH, Berlin/Boston

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https://doi.org/10.1515/cclm-2017-0283
Keywords for this article
circulating DNA; external quality assessment scheme; liquid biopsy; liquid profiling; plasma

Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Need for better PTH assays for clinical research and patient treatment
  4. Reviews
  5. Liquid biopsy in ovarian cancer: recent advances on circulating tumor cells and circulating tumor DNA
  6. Hair testing of GHB: an everlasting issue in forensic toxicology
  7. Opinion Paper
  8. The use of error and uncertainty methods in the medical laboratory
  9. Genetics and Molecular Diagnostics
  10. Results of the first external quality assessment scheme (EQA) for isolation and analysis of circulating tumour DNA (ctDNA)
  11. The importance of biochemical and genetic findings in the diagnosis of atypical Norrie disease
  12. General Clinical Chemistry and Laboratory Medicine
  13. Various glycolysis inhibitor-containing tubes for glucose measurement cannot be used interchangeably due to clinically unacceptable biases between them
  14. Measurement uncertainty of γ-glutamyltransferase (GGT) in human serum by four approaches using different quality assessment data
  15. Oxidation of PTH: in vivo feature or effect of preanalytical conditions?
  16. A comparison between high resolution serum protein electrophoresis and screening immunofixation for the detection of monoclonal gammopathies in serum
  17. The key incident monitoring and management system – history and role in quality improvement
  18. Is it necessary for all samples to quantify 25OHD2 and 25OHD3 using LC-MS/MS in clinical practice?
  19. Contamination of dried blood spots – an underestimated risk in newborn screening
  20. Comparative study of the diagnostic and prognostic value of antibodies against chimeric citrullinated synthetic peptides and CCP3/CCP3.1 assays
  21. Development and validation of a multivariable prediction rule for detecting a severe acquired ADAMTS13 activity deficiency in patients with thrombotic microangiopathies
  22. Use of the sFlt-1/PlGF ratio to rule out preeclampsia requiring delivery in women with suspected disease. Is the evidence reproducible?
  23. Evaluation of a new free light chain ELISA assay: bringing coherence with electrophoretic methods
  24. Hematology and Coagulation
  25. The frequency of occurrence of fish-shaped red blood cells in different haematologic disorders
  26. Reference Values and Biological Variations
  27. Pediatric reference intervals for 29 Ortho VITROS 5600 immunoassays using the CALIPER cohort of healthy children and adolescents
  28. Cancer Diagnostics
  29. Prevalence and causes of abnormal PSA recovery
  30. Cardiovascular Diseases
  31. Serum omentin-1 is a novel biomarker for predicting the functional outcome of acute ischemic stroke patients
  32. Letters to the Editor
  33. BD Vacutainer® Barricor tube in the emergency department: reduced hemolysis rates using partial draw tubes with reduced vacuum
  34. The risk of unjustified BRCA testing after the “Angelina Jolie effect”: how can we save (laboratory) medicine from the Internet?
  35. Sweat travels: the issue of sweat chloride transportation
  36. Individual values of antineutrophil cytoplasmic antibodies do not correspond between antigen-specific assays
  37. False negative results caused by erroneous automated result interpretation algorithm on the FilmArray 2.0 instrument
  38. Quantification of 1,25-dihydroxyvitamin D – value of manufacturers’ product information
  39. Interference between ethosuximide and barbiturates in an immunochromatographic method
  40. In vivo interference of Ioversol in serum and urine capillary electrophoresis: an optimized protocol for sample collection
  41. Evaluation of the new Elecsys SCC assay: comparison with the Kryptor SCC assay
  42. Congress Abstracts
  43. 9th National Congress of the Portuguese Society of Clinical Chemistry, Genetics and Laboratory Medicine
  44. ACBI 2017 40TH Annual Conference
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