1
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Ntzifa A, Lianidou E. Pre-analytical conditions and implementation of quality control steps in liquid biopsy analysis. Crit Rev Clin Lab Sci 2023; 60:573-594. [PMID: 37518938 DOI: 10.1080/10408363.2023.2230290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
Over the last decade, great advancements have been made in the field of liquid biopsy through extensive research and the development of new technologies that facilitate the use of liquid biopsy for cancer patients. This is shown by the numerous liquid biopsy tests that gained clearance by the US Food and Drug Administration (FDA) in recent years. Liquid biopsy has significantly altered cancer treatment by providing clinicians with powerful and immediate information about therapeutic decisions. However, the clinical integration of liquid biopsy is still challenging and there are many critical factors to consider prior to its implementation into routine clinical practice. Lack of standardization due to technical challenges and the definition of the clinical utility of specific assays further complicates the establishment of Standard Operating Procedures (SOPs) in liquid biopsy. Harmonization of laboratories to established guidelines is of major importance to overcome inter-lab variabilities observed. Quality control assessment in diagnostic laboratories that offer liquid biopsy testing will ensure that clinicians can base their therapeutic decisions on robust results. The regular participation of laboratories in external quality assessment schemes for liquid biopsy testing aims to promptly pinpoint deficiencies and efficiently educate laboratories to improve their quality of services. Accreditation of liquid biopsy diagnostic laboratories based on the ISO15189 standard in Europe or by CLIA/CAP accreditation procedures in the US is the best way to achieve the adaptation of liquid biopsy into the clinical setting by assuring reliable results for the clinicians and their cancer patients. Nowadays, various organizations from academia, industry, and regulatory agencies collaborate to set a framework that will include all procedures from the pre-analytical phase and the analytical process to the final interpretation of results. In this review, we underline several challenges in the analysis of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) concerning standardization of protocols, quality control assessment, harmonization of laboratories, and compliance to specific guidelines that need to be thoroughly considered before liquid biopsy enters the clinic.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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2
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Hallermayr A, Keßler T, Fujera M, Liesfeld B, Bernstein S, von Ameln S, Schanze D, Steinke-Lange V, Pickl JMA, Neuhann TM, Holinski-Feder E. Impact of cfDNA Reference Materials on Clinical Performance of Liquid Biopsy NGS Assays. Cancers (Basel) 2023; 15:5024. [PMID: 37894392 PMCID: PMC10605119 DOI: 10.3390/cancers15205024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Liquid biopsy enables the non-invasive analysis of genetic tumor variants in circulating free DNA (cfDNA) in plasma. Accurate analytical validation of liquid biopsy NGS assays is required to detect variants with low variant allele frequencies (VAFs). METHODS Six types of commercial cfDNA reference materials and 42 patient samples were analyzed using a duplex-sequencing-based liquid biopsy NGS assay. RESULTS We comprehensively evaluated the similarity of commercial cfDNA reference materials to native cfDNA. We observed significant differences between the reference materials in terms of wet-lab and sequencing quality as well as background noise. No reference material resembled native cfDNA in all performance metrics investigated. Based on our results, we established guidelines for the selection of appropriate reference materials for the different steps in performance evaluation. The use of inappropriate materials and cutoffs could eventually lead to a lower sensitivity for variant detection. CONCLUSION Careful consideration of commercial reference materials is required for performance evaluation of liquid biopsy NGS assays. While the similarity to native cfDNA aids in the development of experimental protocols, reference materials with well-defined variants are preferable for determining sensitivity and precision, which are essential for accurate clinical interpretation.
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Affiliation(s)
- Ariane Hallermayr
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Thomas Keßler
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Moritz Fujera
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
| | - Ben Liesfeld
- Limbus Medical Technologies GmbH, 18055 Rostock, Germany; (B.L.); (S.B.)
| | - Samuel Bernstein
- Limbus Medical Technologies GmbH, 18055 Rostock, Germany; (B.L.); (S.B.)
| | - Simon von Ameln
- Immune-Oncological Centre Cologne (IOZK), 50674 Cologne, Germany;
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, 39120 Magdeburg, Germany;
| | - Verena Steinke-Lange
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Julia M. A. Pickl
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
| | - Teresa M. Neuhann
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
| | - Elke Holinski-Feder
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
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3
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Vollbrecht C, Hoffmann I, Lehmann A, Merkelbach-Bruse S, Fassunke J, Wagener-Ryczek S, Ball M, Dimitrova L, Hartmann A, Stöhr R, Erber R, Weichert W, Pfarr N, Bohlmann L, Jung A, Dietmaier W, Dietel M, Horst D, Hummel M. Proficiency testing of PIK3CA mutations in HR+/HER2-breast cancer on liquid biopsy and tissue. Virchows Arch 2022; 482:697-706. [PMID: 36367572 PMCID: PMC10067656 DOI: 10.1007/s00428-022-03445-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/09/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
AbstractPrecision oncology based on specific molecular alterations requires precise and reliable detection of therapeutic targets in order to initiate the optimal treatment. In many European countries—including Germany—assays employed for this purpose are highly diverse and not prescribed by authorities, making inter-laboratory comparison difficult. To ensure reproducible molecular diagnostic results across many laboratories and different assays, ring trials are essential and a well-established tool. Here, we describe the design and results of the ring trial for the detection of therapeutically relevant PIK3CA hotspot mutations in HR+/HER2-breast cancer tissue and liquid biopsy (LB). For PIK3CA mutation detection in tissue samples, 43 of the 54 participants (80%) provided results compliant with the reference values. Participants using NGS-based assays showed higher success rate (82%) than those employing Sanger sequencing (57%). LB testing was performed with two reference materials differing in the length of the mutated DNA fragments. Most participants used NGS-based or commercial real-time PCR assays (70%). The 167 bp fragments led to a successful PIK3CA mutation detection by only 31% of participants whereas longer fragments of 490 bp were detectable even by non-optimal assays (83%). In conclusion, the first ring trial for PIK3CA mutation detection in Germany showed that PIK3CA mutation analysis is broadly established for tissue samples and that NGS-based tests seem to be more suitable than Sanger sequencing. PIK3CA mutation detection in LB should be carried out with assays specifically designed for this purpose in order to avoid false-negative results.
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Affiliation(s)
- Claudia Vollbrecht
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.
| | - Inga Hoffmann
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Annika Lehmann
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Sabine Merkelbach-Bruse
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Jana Fassunke
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Svenja Wagener-Ryczek
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Markus Ball
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | | | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Comprehensive Cancer Center Erlangen-EMN, 91054, Erlangen, Germany
| | - Robert Stöhr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Comprehensive Cancer Center Erlangen-EMN, 91054, Erlangen, Germany
| | - Ramona Erber
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Comprehensive Cancer Center Erlangen-EMN, 91054, Erlangen, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Lisa Bohlmann
- Pathologisches Institut of the Ludwig-Maximilian-Universität München, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Andreas Jung
- Pathologisches Institut of the Ludwig-Maximilian-Universität München, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | | | - Manfred Dietel
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - David Horst
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Michael Hummel
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
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4
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The Overview of Perspectives of Clinical Application of Liquid Biopsy in Non-Small-Cell Lung Cancer. Life (Basel) 2022; 12:life12101640. [PMID: 36295075 PMCID: PMC9604747 DOI: 10.3390/life12101640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 01/19/2023] Open
Abstract
The standard diagnostics procedure for non-small-cell lung cancer (NSCLC) requires a pathological evaluation of tissue samples obtained by surgery or biopsy, which are considered invasive sampling procedures. Due to this fact, re-sampling of the primary tumor at the moment of progression is limited and depends on the patient’s condition, even if it could reveal a mechanism of resistance to applied therapy. Recently, many studies have indicated that liquid biopsy could be provided for the noninvasive management of NSCLC patients who receive molecularly targeted therapies or immunotherapy. The liquid biopsy of neoplastic patients harbors small fragments of circulating-free DNA (cfDNA) and cell-free RNA (cfRNA) secreted to the circulation from normal cells, as well as a subset of tumor-derived circulating tumor cells (CTCs) or circulating tumor DNA (ctDNA). In NSCLC patients, a longitudinal assessment of genetic alterations in “druggable” genes in liquid biopsy might improve the follow-up of treatment efficacy and allow for the detection of an early progression before it is detectable in computed tomography or a clinical image. However, a liquid biopsy may be used to determine a variety of relevant molecular or genetic information for understanding tumor biology and its evolutionary trajectories. Thus, liquid biopsy is currently associated with greater hope for common diagnostic and clinical applications. In this review, we would like to highlight diagnostic challenges in the application of liquid biopsy into the clinical routine and indicate its implications on the metastatic spread of NSCLC or monitoring of personalized treatment regimens.
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5
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Jöhrens K, Grassow M, Baretton G, Sperling F. [Interlaboratory comparisons-a central means of external quality assurance]. PATHOLOGIE (HEIDELBERG, GERMANY) 2022; 43:346-350. [PMID: 35948656 DOI: 10.1007/s00292-022-01102-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The precise performance of immunohistochemical and molecular examinations of diagnostic and predictive markers is essential for the further therapy of patients. Due to the increasing number of biomarkers and their detection at the immunohistochemical and molecular level in patient tissue, the pathology has a direct influence on the therapy of patients, which increases the value of external quality assurance (EQA). In pathology, various forms are available for this purpose, such as proficiency tests. The standards of both the certification and accreditation procedures of pathology require regular participation in EQA and a statement on the EQA policy of the institutes. The quality of an EQA depends on the scientific concept, the adequate selection of material, the evaluation concept, and the communication of results.
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Affiliation(s)
- Korinna Jöhrens
- Institut für Pathologie, Universitätsklinikum Carl Gustav Carus Dresden, Fetscherstr. 74, 01307, Dresden, Deutschland.
- Qualitätssicherungs-Initiative Pathologie QuIP GmbH, Berlin, Deutschland.
| | - Maja Grassow
- Qualitätssicherungs-Initiative Pathologie QuIP GmbH, Berlin, Deutschland
| | - Gustavo Baretton
- Institut für Pathologie, Universitätsklinikum Carl Gustav Carus Dresden, Fetscherstr. 74, 01307, Dresden, Deutschland
| | - Florian Sperling
- Qualitätssicherungs-Initiative Pathologie QuIP GmbH, Berlin, Deutschland
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6
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Fairley JA, Cheetham MH, Patton SJ, Rouleau E, Denis M, Dequeker EMC, Schuuring E, van Casteren K, Fenizia F, Normanno N, Deans ZC. Results of a worldwide external quality assessment of cfDNA testing in lung Cancer. BMC Cancer 2022; 22:759. [PMID: 35820813 PMCID: PMC9275131 DOI: 10.1186/s12885-022-09849-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Circulating cell free DNA (cfDNA) testing of plasma for EGFR somatic variants in lung cancer patients is being widely implemented and with any new service, external quality assessment (EQA) is required to ensure patient safety. An international consortium, International Quality Network for Pathology (IQNPath), has delivered a second round of assessment to measure the accuracy of cfDNA testing for lung cancer and the interpretation of the results. METHODS A collaboration of five EQA provider organisations, all members of IQNPath, have delivered the assessment during 2018-19 to a total of 264 laboratories from 45 countries. Bespoke plasma reference material containing a range of EGFR mutations at varying allelic frequencies were supplied to laboratories for testing and reporting according to routine procedures. The genotyping accuracy and clinical reporting was reviewed against standardised criteria and feedback was provided to participants. RESULTS The overall genotyping error rate in the EQA was found to be 11.1%. Low allelic frequency samples were the most challenging and were not detected by some testing methods, resulting in critical genotyping errors. This was reflected in higher false negative rates for samples with variant allele frequencies (VAF) rates less than 1.5% compared to higher frequencies. A sample with two different EGFR mutations gave inconsistent detection of both mutations. However, for one sample, where two variants were present at a VAF of less than 1% then both mutations were correctly detected in 145/263 laboratories. Reports often did not address the risk that tumour DNA may have not been tested and limitations of the methodologies provided by participants were insufficient. This was reflected in the average interpretation score for the EQA being 1.49 out of a maximum of 2. CONCLUSIONS The variability in the standard of genotyping and reporting highlighted the need for EQA and educational guidance in this field to ensure the delivery of high-quality clinical services where testing of cfDNA is the only option for clinical management.
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Affiliation(s)
- Jennifer A Fairley
- GenQA, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4SA, UK.
| | - Melanie H Cheetham
- EMQN CIC, Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Simon J Patton
- EMQN CIC, Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Etienne Rouleau
- Medical Biology and Pathology Department, Gustave Roussy, Villejuif, France
| | - Marc Denis
- Department of Biochemistry and INSERM U1232, Centre Hospitalier Universitaire de Nantes, 9 quai Moncousu, F-44093, Nantes Cedex, France
| | - Elisabeth M C Dequeker
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, KU Leuven, Kapucijnenvoer 35d, 3000, Leuven, Belgium
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kaat van Casteren
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, KU Leuven, Kapucijnenvoer 35d, 3000, Leuven, Belgium
| | | | - Nicola Normanno
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Napoli, Italy
| | - Zandra C Deans
- GenQA, Nine, Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4SA, UK
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7
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Werner TV, Kock S, Weber I, Kayser G, Werner M, Lassmann S. Validation of a DNA-Based Next-Generation Sequencing Test for Molecular Diagnostic Variant and Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tissue Specimens and Liquid Biopsy Plasma/Cell-Free DNA Samples. J Mol Diagn 2022; 24:784-802. [PMID: 35787794 DOI: 10.1016/j.jmoldx.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/26/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
This study evaluated two DNA-based next-generation sequencing approaches for detection of single-nucleotide variants (SNVs) and fusions in formalin-fixed, paraffin-embedded (FFPE) tissue specimens and liquid biopsies (AVENIO Targeted and Surveillance Panels). Reference standards (n = 7 with SNVs and structural variants) and real-world FFPE tissue specimens (n = 26 lung, colorectal, pancreas, ovary, breast, prostate, melanoma, and soft tissue cancer cases with n = 27 samples), liquid biopsies [n = 29 cases with n = 40 plasma/cell-free DNA (cfDNA) samples], and one pleural effusion (lung cancer) were analyzed by the AVENIO workflow for known SNVs (BRAF, BRCA1/2, CTNNB1, EGFR, KRAS, MET exon 14 skipping, NRAS, PIK3CA, and TP53), insertions and deletions (ERBB2 and KIT), and fusions (ALK and ROS1). Detection of SNVs, insertions and deletions, and fusions was reliable in 24 of 26 FFPE tissue specimen cases and at 1% allele frequency in 5 of 5 cfDNA reference standards and 37 of 40 plasma/cfDNA samples. Pitfalls were identified for the AVENIO workflow in calling and listing of clinically relevant variants, requiring additional manual inspection. Moreover, laboratory workflows are distinct for FFPE tissue specimens and liquid biopsies as well as time-consuming for sample quality control assays. In summary, the DNA-based next-generation sequencing approaches may be suitable for routine molecular pathology diagnostics on careful data interpretation and further optimization of the technical and laboratory workflows.
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Affiliation(s)
- Tamara V Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Sylvia Kock
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Isabel Weber
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Gian Kayser
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany.
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8
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Magios N, Bozorgmehr F, Volckmar AL, Kazdal D, Kirchner M, Herth FJ, Heussel CP, Eichhorn F, Meister M, Muley T, Elshafie RA, Fischer JR, Faehling M, Kriegsmann M, Schirmacher P, Bischoff H, Stenzinger A, Thomas M, Christopoulos P. Real-world implementation of sequential targeted therapies for EGFR-mutated lung cancer. Ther Adv Med Oncol 2021; 13:1758835921996509. [PMID: 34408792 PMCID: PMC8366107 DOI: 10.1177/1758835921996509] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/27/2021] [Indexed: 11/15/2022] Open
Abstract
Background: Epidermal growth factor receptor-mutated (EGFR+) non-small-cell lung cancer (NSCLC) patients failing tyrosine kinase inhibitors (TKI) can benefit from next-line targeted therapies, but implementation is challenging. Methods: EGFR+ NSCLC patients treated with first/second-generation (1G/2G) TKI at our institution with a last follow-up after osimertinib approval (February 2016), were analyzed retrospectively, and the results compared with published data under osimertinib. Results: A total of 207 patients received erlotinib (37%), gefitinib (16%) or afatinib (47%). The median age was 66 years, with a predominance of female (70%), never/light-smokers (69%). T790M testing was performed in 174/202 progressive cases (86%), positive in 93/174 (53%), and followed by osimertinib in 87/93 (94%). Among the 135 deceased patients, 94 (70%) received subsequent systemic treatment (43% chemotherapy, 39% osimertinib), while 30% died without, either before (4%) or after progression, due to rapid clinical deterioration (22%), patient refusal of further therapy (2%), or severe competing illness (2%). Lack of subsequent treatment was significantly (4.5x, p < 0.001) associated with lack of T790M testing, whose most frequent cause (in approximately 50% of cases) was also rapid clinical decline. Among the 127 consecutive patients with failure of 1G/2G TKI started after November 2015, 47 (37%) received osimertinib, with a median overall survival of 36 months versus 24 and 21 months for patients with alternative and no subsequent therapies (p = 0.003). Conclusion: Osimertinib after 1G/2G TKI failure prolongs survival, but approximately 15% and 30% of patients forego molecular retesting and subsequent treatment, respectively, mainly due to rapid clinical deterioration. This is an important remediable obstacle to sequential TKI treatment for EGFR+ NSCLC. It pertains also to other actionable resistance mechanisms emerging under 1G/2G inhibitors or osimertinib, whose rate for lack of next-line therapy is similar (approximately 35% in the FLAURA/AURA3 trials), and highlights the need for closer monitoring alongside broader profiling of TKI-treated EGFR+ NSCLC in the future.
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Affiliation(s)
- Nikolaus Magios
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Farastuk Bozorgmehr
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix J Herth
- Department of Pneumology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Claus-Peter Heussel
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Florian Eichhorn
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Rami A Elshafie
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen R Fischer
- Department of Thoracic Oncology, Lungenklinik Löwenstein, Löwenstein, Germany
| | - Martin Faehling
- Department of Cardiology, Angiology and Pneumology, Klinikum Esslingen, Esslingen, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Helge Bischoff
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | | | - Michael Thomas
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Röntgenstraße 1, Heidelberg, Baden-Württemberg 69126, Germany
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9
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Siemanowski J, Heydt C, Merkelbach-Bruse S. Predictive molecular pathology of lung cancer in Germany with focus on gene fusion testing: Methods and quality assurance. Cancer Cytopathol 2021; 128:611-621. [PMID: 32885916 DOI: 10.1002/cncy.22293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022]
Abstract
Predictive molecular testing has become an important part of the diagnosis of any patient with lung cancer. Using reliable methods to ensure timely and accurate results is inevitable for guiding treatment decisions. In the past few years, parallel sequencing has been established for mutation testing, and its use is currently broadened for the detection of other genetic alterations, such as gene fusion and copy number variations. In addition, conventional methods such as immunohistochemistry and in situ hybridization are still being used, either for formalin-fixed, paraffin-embedded tissue or for cytological specimens. For the development and broad implementation of such complex technologies, interdisciplinary and regional networks are needed. The Network Genomic Medicine (NGM) has served as a model of centralized testing and decentralized treatment of patients and incorporates all German comprehensive cancer centers. Internal quality control, laboratory accreditation, and participation in external quality assessment is mandatory for the delivery of reliable results. Here, we provide a summary of current technologies used to identify patients who have lung cancer with gene fusions, briefly describe the structures of NGM and the national NGM (nNGM), and provide recommendations for quality assurance.
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Affiliation(s)
- Janna Siemanowski
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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10
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The evolving landscape of biomarker testing for non-small cell lung cancer in Europe. Lung Cancer 2021; 154:161-175. [PMID: 33690091 DOI: 10.1016/j.lungcan.2021.02.026] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 12/31/2022]
Abstract
The discovery of oncogenic driver mutations rendering non-small cell lung cancer (NSCLC) targetable by small-molecule inhibitors, and the development of immunotherapies, have revolutionised NSCLC treatment. Today, instead of non-selective chemotherapies, all patients with advanced NSCLC eligible for treatment (and increasing numbers with earlier, less extensive disease) require fast and comprehensive screening of biomarkers for first-line patient selection for targeted therapy, chemotherapy, or immunotherapy (with or without chemotherapy). To avoid unnecessary re-biopsies, biomarker screening before first-line treatment should also include markers that are actionable from second-line onwards; PD-L1 expression testing is also mandatory before initiating treatment. Population differences exist in the frequency of oncogenic driver mutations: EGFR mutations are more frequent in Asia than Europe, whereas the converse is true for KRAS mutations. In addition to approved first-line therapies, a number of emerging therapies are being investigated in clinical trials. Guidelines for biomarker testing vary by country, with the number of actionable targets and the requirement for extensive molecular screening strategies expected to increase. To meet diagnostic demands, rapid screening technologies for single-driver mutations have been implemented. Improvements in DNA- and RNA-based next-generation sequencing technologies enable analysis of a group of genes in one assay; however, turnaround times remain relatively long. Consequently, rapid screening technologies are being implemented alongside next-generation sequencing. Further challenges in the evolving landscape of biomarker testing in NSCLC are actionable primary and secondary resistance mechanisms to targeted therapies. Therefore, comprehensive testing on re-biopsies, collected at the time of disease progression, in combination with testing of circulating tumour DNA may provide important information to guide second- or third-line therapies. Furthermore, longitudinal biomarker testing can provide insights into tumour evolution and heterogeneity during the course of the disease. We summarise best practice strategies for Europe in the changing landscape of biomarker testing at diagnosis and during treatment.
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11
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Dufraing K, Fenizia F, Torlakovic E, Wolstenholme N, Deans ZC, Rouleau E, Vyberg M, Parry S, Schuuring E, Dequeker EMC. Biomarker testing in oncology - Requirements for organizing external quality assessment programs to improve the performance of laboratory testing: revision of an expert opinion paper on behalf of IQNPath ABSL. Virchows Arch 2020; 478:553-565. [PMID: 33047156 PMCID: PMC7550230 DOI: 10.1007/s00428-020-02928-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/16/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022]
Abstract
In personalized medicine, predictive biomarker testing is the basis for an appropriate choice of therapy for patients with cancer. An important tool for laboratories to ensure accurate results is participation in external quality assurance (EQA) programs. Several providers offer predictive EQA programs for different cancer types, test methods, and sample types. In 2013, a guideline was published on the requirements for organizing high-quality EQA programs in molecular pathology. Now, after six years, steps were taken to further harmonize these EQA programs as an initiative by IQNPath ABSL, an umbrella organization founded by various EQA providers. This revision is based on current knowledge, adds recommendations for programs developed for predictive biomarkers by in situ methodologies (immunohistochemistry and in situ hybridization), and emphasized transparency and an evidence-based approach. In addition, this updated version also has the aim to give an overview of current practices from various EQA providers.
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Affiliation(s)
- K Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 35 blok d, 3000, Leuven, Belgium
| | - F Fenizia
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - E Torlakovic
- Department of Pathology and Laboratory Medicine, Royal University Hospital, College of Medicine, University of Saskatchewan and Saskatchewan Health Authority, Saskatoon, Saskatchewan, Canada
| | - N Wolstenholme
- European Molecular Quality Network (EMQN), Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, M13 9WL, UK
| | - Z C Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, EH16 4SA, UK
| | - E Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, Villejuif, France
| | - M Vyberg
- NordiQC, Institute of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - S Parry
- UK NEQAS ICC & ISH, University College London Cancer Institute, London, UK
| | - E Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30001, 9700, RB, Groningen, The Netherlands
| | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 35 blok d, 3000, Leuven, Belgium.
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12
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Abstract
Abstract
It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.
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Affiliation(s)
- Michael Fleischhacker
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Drontheimer Str. 39 – 40 , 13359 Berlin , Germany
| | - Bernd Schmidt
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Berlin , Germany
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13
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External Quality Assessment Schemes for Biomarker Testing in Oncology: Comparison of Performance between Formalin-Fixed, Paraffin-Embedded-Tissue and Cell-Free Tumor DNA in Plasma. J Mol Diagn 2020; 22:736-747. [PMID: 32205291 DOI: 10.1016/j.jmoldx.2020.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 02/08/2020] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Liquid biopsies have emerged as a useful addition to tissue biopsies in molecular pathology. Literature has shown lower laboratory performances when a new method of variant analysis is introduced. This study evaluated the differences in variant analysis between tissue and plasma samples after the introduction of liquid biopsy in molecular analysis. Data from a pilot external quality assessment scheme for the detection of molecular variants in plasma samples and from external quality assessment schemes for the detection of molecular variants in tissue samples were collected. Laboratory performance and error rates by sample were compared between matrices for variants present in both scheme types. Results showed lower overall performance [65.6% (n = 276) versus 89.2% (n = 1607)] and higher error rates [21.0% to 43.5% (n = 138) versus 8.7% to 16.7% (n = 234 to 689)] for the detection of variants in plasma compared to tissue, respectively. In the plasma samples, performance was decreased for variants with an allele frequency of 1% compared to 5% [56.5% (n = 138) versus 74.6% (n = 138)]. The implementation of liquid biopsy in the detection of circulating tumor DNA in plasma was associated with poor laboratory performance. It is important both to apply optimal detection methods and to extensively validate new methods for testing circulating tumor DNA before treatment decisions are made.
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14
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Dufraing K, Keppens C, Tack V, Siebers AG, Kafatos G, Dube S, Demonty G, Lowe K, Kroeze LI, Ligtenberg M, Normanno N, Tembuyser L, Sara VB, van Krieken JH, C Dequeker EM. Evolution of RAS testing over time: factors influencing mutation rates in metastatic colorectal cancer patients. COLORECTAL CANCER 2020. [DOI: 10.2217/crc-2019-0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Aim: Correct identification of RAS gene variants is key for targeted treatment decisions in patients with metastatic colorectal cancer. Published RAS mutation rates differ and could be influenced by several factors including testing methods. This study aimed to describe the performance of laboratories to correctly identify RAS variants over time and to understand how RAS testing has evolved in Europe. Materials & methods: Misclassification and test failure rates were calculated and related to the used test methodology for 239 unique laboratories participating in external quality assessment for metastatic colorectal cancer between 2013 and 2018. In addition, 33 laboratories completed a survey aiming to obtain more details on their routine testing strategies, number of samples analyzed and RAS mutation rates between 2013 and 2017. Results: The mutation status was correctly analyzed in 96.1% (N = 5471) RAS and BRAF tests. A total of 4.6% (N = 2860) RAS tests included false-negative results. In 1.6% (N = 5562) RAS and BRAF tests, an analysis failure occurred. Misclassifications and technical failures both decreased between 2013 and 2018. The number of next-generation sequencing users increased from 6.9% (N = 130) in 2013 to 44.6% (N = 112) in 2018. Over time, more codons were included in the methodologies, yet 23.2% (N = 112) did not offer full RAS testing (exon 2, 3, 4) in 2018. Based on the survey the overall RAS mutation rate was estimated as 45.2% (N = 27,325). Conclusion: This is the largest observational study reporting RAS mutation rates to-date. There was no trend of RAS mutation rates over time despite having a clear shift to more sensitive tests and increased quality of testing.
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Affiliation(s)
- Kelly Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health & Primary Care, University of Leuven, Leuven, Belgium
| | - Cleo Keppens
- Biomedical Quality Assurance Research Unit, Department of Public Health & Primary Care, University of Leuven, Leuven, Belgium
| | - Véronique Tack
- Biomedical Quality Assurance Research Unit, Department of Public Health & Primary Care, University of Leuven, Leuven, Belgium
| | - Albert Gerrit Siebers
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | | | - Leonie Ilse Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicola Normanno
- Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori – Fondazione Pascale, Naples, Italy
| | - Lien Tembuyser
- Biomedical Quality Assurance Research Unit, Department of Public Health & Primary Care, University of Leuven, Leuven, Belgium
| | - Vander Borght Sara
- Pathologische Ontleedkunde, Department of Pathology, University Hospitals Leuven, Belgium
| | | | - Elisabeth Marie C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health & Primary Care, University of Leuven, Leuven, Belgium
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15
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Ntzifa A, Kroupis C, Haliassos A, Lianidou E. A pilot plasma-ctDNA ring trial for the Cobas® EGFR Mutation Test in clinical diagnostic laboratories. Clin Chem Lab Med 2019; 57:e97-e101. [PMID: 30267626 DOI: 10.1515/cclm-2018-0676] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/20/2018] [Indexed: 11/15/2022]
Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Kroupis
- Department of Clinical Biochemistry and Molecular Diagnostics, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece
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16
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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17
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Lehmann U, Bartels S. [Liquid biopsy in tumor diagnostics : Applications, perspectives, and limitations of the "cancer liquidome"]. DER PATHOLOGE 2019; 40:250-255. [PMID: 31049676 DOI: 10.1007/s00292-019-0604-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The detection of tumor-specific genetic alterations in body fluids as an addition to or even replacement for established tissue-based tumor diagnostics is currently a hot topic in academic research and industry. Progress in methods for nucleic acid analyses together with promising results from clinical studies have raised great expectations for cancer screening, diagnosis, prognosis, and therapy monitoring by means of a minimally invasive blood draw. Individual focused assays have already been introduced into routine diagnostics and represent a valuable option in cases where no tissue samples are available. However, before the use of liquid biopsy outside of clinical studies is enforced and more complex markers (like tumor mutational burden) are analyzed, several practical challenges and principal problems have to be addressed. This review focusses on the detection of free-circulating nucleic acids in blood plasma and critically discusses established and future applications as well as challenges and limitations of this new method.
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Affiliation(s)
- U Lehmann
- Institut für Pathologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland.
| | - S Bartels
- Institut für Pathologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland
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18
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Oellerich M, Christenson RH, Beck J, Walson PD. Plasma EGFR mutation testing in non-small cell lung cancer: A value proposition. Clin Chim Acta 2019; 495:481-486. [DOI: 10.1016/j.cca.2019.05.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 12/16/2022]
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19
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Nørøxe DS, Østrup O, Yde CW, Ahlborn LB, Nielsen FC, Michaelsen SR, Larsen VA, Skjøth-Rasmussen J, Brennum J, Hamerlik P, Poulsen HS, Lassen U. Cell-free DNA in newly diagnosed patients with glioblastoma - a clinical prospective feasibility study. Oncotarget 2019; 10:4397-4406. [PMID: 31320993 PMCID: PMC6633897 DOI: 10.18632/oncotarget.27030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Glioblastoma (GB) is an incurable brain cancer with limited treatment options. The aim was to test the feasibility of using cell-free DNA (cfDNA) to support evaluation of treatment response, pseudo-progression and whether progression could be found before clinical and/or radiologic progression.
Results: CfDNA fluctuated during treatment with the highest levels before diagnostic surgery and at progression. An increase was seen in 3 out of 4 patients at the time of progression while no increase was seen in 3 out of 4 patients without progression. CfDNA levels could aid in 3 out of 3 questionable cases of pseudo-progression.
Methods: Eight newly diagnosed GB patients were included. Blood samples were collected prior to diagnosis, before start and during oncologic treatment until progression. Seven patients received concurrent radiotherapy/Temozolomide with adjuvant Temozolomide with one of the patients included in a clinical trial with either immunotherapy or placebo as add-on. One patient received radiation alone. CfDNA concentration was determined for each blood sample.
Conclusions: It was feasible to measure cfDNA concentration. Despite the limited cohort size, there was a good tendency between cfDNA and treatment course and -response, respectively with the highest levels at progression.
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Affiliation(s)
- Dorte Schou Nørøxe
- Department of Radiation Biology, Rigshospitalet, 2100 Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark
| | | | | | | | | | | | | | - Jannick Brennum
- Department of Neurosurgery, Rigshospitalet, 2100 Copenhagen, Denmark
| | | | - Hans Skovgaard Poulsen
- Department of Radiation Biology, Rigshospitalet, 2100 Copenhagen, Denmark.,Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Ulrik Lassen
- Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
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20
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Saarenheimo J, Eigeliene N, Andersen H, Tiirola M, Jekunen A. The Value of Liquid Biopsies for Guiding Therapy Decisions in Non-small Cell Lung Cancer. Front Oncol 2019; 9:129. [PMID: 30891428 PMCID: PMC6411700 DOI: 10.3389/fonc.2019.00129] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/13/2019] [Indexed: 12/15/2022] Open
Abstract
Targeted therapies have allowed for an individualized treatment approach in non-small-cell lung cancer (NSCLC). The initial therapeutic decisions and success of targeted therapy depend on genetic identification of personal tumor profiles. Tissue biopsy is the gold standard for molecular analysis, but non-invasive or minimally invasive liquid biopsy methods are also now used in clinical practice, allowing for later monitoring and optimization of the cancer treatment. The inclusion of liquid biopsy in the management of NSCLC provides strong evidence on early treatment response, which becomes a basis for determining disease progression and the need for changes in treatment. Liquid biopsies can drive the decision making for treatment strategies to achieve better patient outcomes. Cell-free DNA and circulating tumor cells obtained from the blood are promising markers for determining patient status. They may improve cancer treatments, allow for better treatment control, enable early interventions, and change decision making from reactive actions toward more predictive early interventions. This review aimed to present current knowledge on and the usefulness of liquid biopsy studies in NSCLC from the perspective of how it has allowed individualized treatments according to gene profiling and how the method may alter the treatment decisions in the future.
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Affiliation(s)
- Jatta Saarenheimo
- Department of Pathology, Vasa Central Hospital, Vaasa, Finland.,Department of Biological and Environmental Science, Nano Science Center, University of Jyväskylä, Jyväskylä, Finland
| | - Natalja Eigeliene
- Department of Oncology, Vasa Central Hospital, Vaasa, Finland.,Department of Oncology and Radiotherapy, University of Turku, Turku, Finland
| | - Heidi Andersen
- Department of Pulmonology, Vasa Central Hospital, Vaasa, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, Nano Science Center, University of Jyväskylä, Jyväskylä, Finland
| | - Antti Jekunen
- Department of Oncology, Vasa Central Hospital, Vaasa, Finland.,Department of Oncology and Radiotherapy, University of Turku, Turku, Finland
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21
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Shin DH, Shim HS, Kim TJ, Park HS, Choi YL, Kim WS, Kim L, Chang SH, Song JS, Kim HJ, Han JH, Lee CH, Lee GK, Jang SJ. Provisional Guideline Recommendation for EGFR Gene Mutation Testing in Liquid Samples of Lung Cancer Patients: A Proposal by the Korean Cardiopulmonary Pathology Study Group. J Pathol Transl Med 2019; 53:153-158. [PMID: 30813707 PMCID: PMC6527939 DOI: 10.4132/jptm.2019.02.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/20/2019] [Indexed: 12/29/2022] Open
Abstract
Liquid biopsy for detection of mutation from circulating tumor DNA is a new technology which is attractive in that it is non-invasive. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) is an effective first line drug for advanced non-small cell lung cancer patients who harbor activating EGFR mutation. During the course of treatment, resistance against TKI arises which can be contributed to EGFR T790M mutation in about 50-60% of patients. Third generation TKI may overcome the resistance. In patients who cannot undergo tissue biopsy due to variable reasons, liquid biopsy is an excellent alternative for the detection of EGFR T790M mutation. However, this relatively novel method requires standardization and vigorous quality insurance. Thus, a standard set of guideline recommendations for liquid biopsy for EGFR mutation testing suitable for the Korean medical community is necessary. In this article, we propose a set of provisional guideline recommendations that was discussed and approved by the Cardiopulmonary Pathology Study Group of the Korean Society of Pathologists.
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Affiliation(s)
- Dong Hoon Shin
- Department of Pathology, Pusan National University School of Medicine, Yangsan, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Jung Kim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Heae Surng Park
- Department of Pathology, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Yun La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Lucia Kim
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
| | - Sun Hee Chang
- Department of Pathology, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang, Korea
| | - Joon Seon Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyo Jin Kim
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jung Ho Han
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang Hun Lee
- Department of Pathology, Pusan National University School of Medicine, Yangsan, Korea
| | - Geon Kook Lee
- Department of Pathology, National Cancer Center, Goyang, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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22
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A Comparative Study for Detection of EGFR Mutations in Plasma Cell-Free DNA in Korean Clinical Diagnostic Laboratories. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7392419. [PMID: 29854785 PMCID: PMC5964486 DOI: 10.1155/2018/7392419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/12/2018] [Accepted: 04/02/2018] [Indexed: 01/08/2023]
Abstract
Liquid biopsies to genotype the epidermal growth factor receptor (EGFR) for targeted therapy have been implemented in clinical decision-making in the field of lung cancer, but harmonization of detection methods is still scarce among clinical laboratories. We performed a pilot external quality assurance (EQA) scheme to harmonize circulating tumor DNA testing among laboratories. For EQA, we created materials containing different levels of spiked cell-free DNA (cfDNA) in normal plasma. The limit of detection (LOD) of the cobas® EGFR Mutation Test v2 (Roche Molecular Systems) was also evaluated. From November 2016 to June 2017, seven clinical diagnostic laboratories participated in the EQA program. The majority (98.94%) of results obtained using the cobas assay and next-generation sequencing (NGS) were acceptable. Quantitative results from the cobas assay were positively correlated with allele frequencies derived from digital droplet PCR measurements and showed good reproducibility among laboratories. The LOD of the cobas assay was 5~27 copies/mL for p.E746_A750del (exon 19 deletion), 35~70 copies/mL for p.L858R, 18~36 copies/mL for p.T790M, and 15~31 copies/mL for p.A767_V769dup (exon 20 insertion). Deep sequencing of materials (>100,000X depth of coverage) resulted in detection of low-level targets present at frequencies of 0.06~0.13%. Our results indicate that the cobas assay is a reliable and rapid method for detecting EGFR mutations in plasma cfDNA. Careful interpretation is particularly important for p.T790M detection in the setting of relapse. Individual laboratories should optimize NGS performance to maximize clinical utility.
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23
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Volckmar AL, Sültmann H, Riediger A, Fioretos T, Schirmacher P, Endris V, Stenzinger A, Dietz S. A field guide for cancer diagnostics using cell-free DNA: From principles to practice and clinical applications. Genes Chromosomes Cancer 2017; 57:123-139. [DOI: 10.1002/gcc.22517] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Holger Sültmann
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
| | - Anja Riediger
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
| | - Thoas Fioretos
- Department of Clinical Genetics; Lund University; Lund Sweden
- Department of Clinical Genetics; University and Regional Laboratories; Region Skåne Lund Sweden
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Steffen Dietz
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
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