Startseite Performance comparison of two next-generation sequencing panels to detect actionable mutations in cell-free DNA in cancer patients
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Performance comparison of two next-generation sequencing panels to detect actionable mutations in cell-free DNA in cancer patients

  • Mónica Macías , Eva Cañada-Higueras , Estibaliz Alegre , Arancha Bielsa , Javier Gracia , Ana Patiño-García , Roser Ferrer-Costa , Teresa Sendino , María P. Andueza , Beatriz Mateos , Javier Rodríguez , Jesús Corral , Alfonso Gúrpide , José M. Lopez-Picazo , Jose L. Perez-Gracia , Ignacio Gil-Bazo , Gorka Alkorta-Aranburu und Álvaro González EMAIL logo
Veröffentlicht/Copyright: 12. März 2020
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Clinical Chemistry and Laboratory Medicine (CCLM)
Aus der Zeitschrift Clinical Chemistry and Laboratory Medicine (CCLM) Band 58 Heft 8

Abstract

Background

Genomic alterations studies in cell-free DNA (cfDNA) have increasing clinical use in oncology. Next-generation sequencing (NGS) technology provides the most complete mutational analysis, but nowadays limited data are available related to the comparison of results reported by different platforms. Here we compare two NGS panels for cfDNA: Oncomine™ Pan-Cancer Cell-Free Assay (Thermo Fisher Scientific), suitable for clinical laboratories, and Guardant360® (GuardantHealth), with more genes targeted but only available in an outsourcing laboratory.

Methods

Peripheral blood was obtained from 16 advanced cancer patients in which Guardant360® (G360) was requested as part of their clinical assistance. Blood samples were sent to be analyzed with G360 panel, and an additional blood sample was drawn to obtain and analyze cfDNA with Oncomine™ Pan-Cancer (OM) panel in an Ion GeneStudio S5™ System.

Results

cfDNA analysis globally rendered 101 mutations. Regarding the 55/101 mutations claimed to be included by manufacturers in both panels, 17 mutations were reported only by G360, 10 only by OM and 28 by both. In those coincident cases, there was a high correlation between the variant allele fractions (VAFs) calculated with each panel (r = 0.979, p < 0.01). Regarding the six actionable mutations with an FDA-approved therapy reported by G360, one was missed with OM. Also, 12 mutations with clinical trials available were reported by G360 but not by OM.

Conclusions

In summary, G360 and OM can produce different mutational profile in the same sample, even in genes included in both panels, which is especially important if these mutations are potentially druggable.

Keywords: actionable mutations; cancer; cell-free DNA (cfDNA); liquid biopsy; next-generation sequencing (NGS); variant allele fractions (VAFs)
Corresponding author: Álvaro González, PhD, Service of Biochemistry, Clínica Universidad de Navarra, Avenida Pío XII 36, 31008 Pamplona, Spain; and IdiSNA, Navarra Institute for Health Research, Pamplona, Spain, Phone: +34 948 255400, Fax: +34 948 296 500
aMónica Macías, Eva Cañada-Higueras, Gorka Alkorta-Aranburu and Álvaro González contributed equally to this work.

Acknowledgments

The authors thank the information provided by GuardantHealth and Thermo Fisher Scientific to make this work possible, Dr. María Romero for her support and the Biobank of the University of Navarra for its collaboration.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This study was supported by a Gobierno de Navarra grant (DIANA: Diagnóstico biomédico e Innovación Abierta en Navarra); grant number: [0011-1411-2017-000033].

  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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Supplementary Material

The online version of this article offers supplementary material (https://doi.org/10.1515/cclm-2019-1267).

Received: 2019-12-09
Accepted: 2020-02-10
Published Online: 2020-03-12
Published in Print: 2020-07-28

©2020 Walter de Gruyter GmbH, Berlin/Boston

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https://doi.org/10.1515/cclm-2019-1267
Schlagwörter für diesen Artikel
actionable mutations; cancer; cell-free DNA (cfDNA); liquid biopsy; next-generation sequencing (NGS); variant allele fractions (VAFs)

Artikel in diesem Heft

  1. Frontmatter
  2. Editorial
  3. Quality controls for serology: an unfinished agenda
  4. A modern and pragmatic definition of Laboratory Medicine
  5. Reviews
  6. Blood biochemical characteristics of patients with coronavirus disease 2019 (COVID-19): a systemic review and meta-analysis
  7. ISO/TS 20914:2019 – a critical commentary
  8. Mini Review
  9. Reporting of D-dimer data in COVID-19: some confusion and potential for misinformation
  10. Opinion Paper
  11. Implementation of metrological traceability in laboratory medicine: where we are and what is missing
  12. IFCC Recommendation
  13. Recommendation for performance verification of patient-based real-time quality control
  14. Genetics and Molecular Diagnostics
  15. Comparison of BCR-ABL1 quantification in peripheral blood and bone marrow using an International Scale-standardized assay for assessment of deep molecular response in chronic myeloid leukemia
  16. General Clinical Chemistry and Laboratory Medicine
  17. Risk assessment of the total testing process based on quality indicators with the Sigma metrics
  18. Determination of hemolysis cut-offs for biochemical and immunochemical analytes according to their value
  19. A computer model for professional competence assessment according to ISO 15189
  20. Traceability validation of six enzyme measurements on the Abbott Alinity c analytical system
  21. Evaluating the need for free glycerol blanking for serum triglyceride measurements at Charlotte Maxeke Johannesburg Academic Hospital
  22. Challenges of LC-MS/MS ethyl glucuronide analysis in abstinence monitoring of liver transplant candidates
  23. Changes in the result of antinuclear antibody immunofluorescence assay on HEp-2 cells reflect disease activity status in systemic lupus erythematosus
  24. Reference Values and Biological Variations
  25. Long-term biological variation estimates of 13 hematological parameters in healthy Chinese subjects
  26. Age-specific reference values improve the diagnostic performance of AMH in polycystic ovary syndrome
  27. Establishment of reference intervals for immunoassay analytes of adult population in Saudi Arabia
  28. Hematology and Coagulation
  29. Total haemoglobin – a reference measuring system for improvement of standardisation
  30. Laboratory testing for activated protein C resistance: rivaroxaban induced interference and a comparative evaluation of andexanet alfa and DOAC Stop to neutralise interference
  31. Cancer Diagnostics
  32. Identification of a four-gene methylation biomarker panel in high-grade serous ovarian carcinoma
  33. Performance comparison of two next-generation sequencing panels to detect actionable mutations in cell-free DNA in cancer patients
  34. Diabetes
  35. Availability and analytical quality of hemoglobin A1c point-of-care testing in general practitioners’ offices are associated with better glycemic control in type 2 diabetes
  36. Infectious Diseases
  37. Validation of a chemiluminescent assay for specific SARS-CoV-2 antibody
  38. Dynamic profile and clinical implications of hematological parameters in hospitalized patients with coronavirus disease 2019
  39. Does a change in quality control results influence the sensitivity of an anti-HCV test?
  40. Letters to the Editor
  41. Variability between testing methods for SARS-CoV-2 nucleic acid detection 16 days post-discharge: a case report
  42. L-index, more than a screening tool for hypertriglyceridemia
  43. Neutralization of biotin interference: preliminary evaluation of the VeraTest Biotin™, VeraPrep Biotin™ and BioT-Filter®
  44. Counting and reporting band count is unreliable practice due to the high inter-observer variability
  45. Cigarette smoking prior to blood sampling acutely affects serum levels of the chronic obstructive pulmonary disease biomarker surfactant protein D
  46. How reliable is the detection of anti-mitochondrial antibodies on murine triple-tissue?
  47. Further advices on measuring lipoprotein(a) for reducing the residual cardiovascular risk on statin therapy
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