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Calvete O, Mestre J, Durmaz A, Gurnari C, Maciejewski JP, Solé F. Are the current guidelines for identification of myelodysplastic syndrome with germline predisposition strong enough? Br J Haematol 2023; 201:e5-e11. [PMID: 36717968 DOI: 10.1111/bjh.18676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 02/01/2023]
Affiliation(s)
- Oriol Calvete
- Myelodysplastic Syndrome Group, Josep Carreras Leukaemia Research Institute, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Julia Mestre
- Myelodysplastic Syndrome Group, Josep Carreras Leukaemia Research Institute, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Ohio, Cleveland, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Ohio, Cleveland, USA.,Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Ohio, Cleveland, USA
| | - Francesc Solé
- Myelodysplastic Syndrome Group, Josep Carreras Leukaemia Research Institute, ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Barcelona, Spain
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Kalmer M, Pannen K, Lemanzyk R, Wirths C, Baumeister J, Maurer A, Kricheldorf K, Schifflers J, Gezer D, Isfort S, Brümmendorf TH, Koschmieder S, Chatain N. Clonogenic assays improve determination of variant allele frequency of driver mutations in myeloproliferative neoplasms. Ann Hematol 2022. [PMID: 36269400 DOI: 10.1007/s00277-022-05000-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/01/2022] [Indexed: 11/27/2022]
Abstract
Molecular diagnostics moves more into focus as technology advances. In patients with myeloproliferative neoplasms (MPN), identification and monitoring of the driver mutations have become an integral part of diagnosis and monitoring of the disease. In some patients, none of the known driver mutations (JAK2V617F, CALR, MPL) is found, and they are termed "triple negative" (TN). Also, whole-blood variant allele frequency (VAF) of driver mutations may not adequately reflect the VAF in the stem cells driving the disease. We reasoned that colony forming unit (CFU) assay-derived clonogenic cells may be better suited than next-generation sequencing (NGS) of whole blood to detect driver mutations in TN patients and to provide a VAF of disease-driving cells. We have included 59 patients carrying the most common driver mutations in the establishment or our model. Interestingly, cloning efficiency correlated with whole blood VAF (p = 0.0048), suggesting that the number of disease-driving cells correlated with VAF. Furthermore, the clonogenic VAF correlated significantly with the NGS VAF (p < 0.0001). This correlation was lost in patients with an NGS VAF <15%. Further analysis showed that in patients with a VAF <15% by NGS, clonogenic VAF was higher than NGS VAF (p = 0.003), suggesting an enrichment of low numbers of disease-driving cells in CFU assays. However, our approach did not enhance the identification of driver mutations in 5 TN patients. A significant correlation of lactate dehydrogenase (LDH) serum levels with both CFU- and NGS-derived VAF was found. Our results demonstrate that enrichment for clonogenic cells can improve the detection of MPN driver mutations in patients with low VAF and that LDH levels correlate with VAF.
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Smith JT, Balar A, Lakhani DA, Kluwe C, Zhao Z, Kopparapu P, Almodovar K, Muterspaugh A, Yan Y, York S, Horn L, Antic S, Bertucci C, Shaffer T, Hodsdon L, Garg K, Hosseini SA, Lim L, Osmundson E, Massion PP, Lovly CM, Iams W. Circulating Tumor DNA as a Biomarker of Radiographic Tumor Burden in SCLC. JTO Clin Res Rep 2021; 2:100110. [PMID: 34589992 PMCID: PMC8474385 DOI: 10.1016/j.jtocrr.2020.100110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/02/2022] Open
Abstract
Introduction Blood-based next-generation sequencing assays of circulating tumor DNA (ctDNA) have the ability to detect tumor-associated mutations in patients with SCLC. We sought to characterize the relationship between ctDNA mean variant allele frequency (VAF) and radiographic total-body tumor volume (TV) in patients with SCLC. Methods We identified matched blood draws and computed tomography (CT) or positron emission tomography (PET) scans within a prospective SCLC blood banking cohort. We sequenced plasma using our previously developed 14-gene SCLC-specific ctDNA assay. Three-dimensional TV was determined from PET and CT scans using MIM software and reviewed by radiation oncologists. Univariate association and multivariate regression analyses were performed to evaluate the association between mean VAF and total-body TV. Results We analyzed 75 matched blood draws and CT or PET scans from 25 unique patients with SCLC. Univariate analysis revealed a positive association between mean VAF and total-body TV (Spearman’s ρ = 0.292, p < 0.01), and when considering only treatment-naive and pretreatment patients (n = 11), there was an increase in the magnitude of association (ρ = 0.618, p = 0.048). The relationship remained significant when adjusting for treatment status and bone metastases (p = 0.046). In the subgroup of patients with TP53 variants, univariate analysis revealed a significant association (ρ = 0.762, p = 0.037) only when considering treatment-naive and pretreatment patients (n = 8). Conclusions We observed a positive association between mean VAF and total-body TV in patients with SCLC, suggesting mean VAF may represent a dynamic biomarker of tumor burden that could be followed to monitor disease status.
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Affiliation(s)
- Jarrod T Smith
- Department of Medicine, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Aneri Balar
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dhairya A Lakhani
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christien Kluwe
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Zhiguo Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Prasad Kopparapu
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Karinna Almodovar
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anel Muterspaugh
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yingjun Yan
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sally York
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Leora Horn
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sanja Antic
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | | | | | | | - Lee Lim
- Resolution Bioscience, Bellevue, Washington
| | - Evan Osmundson
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Pierre P Massion
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christine M Lovly
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Wade Iams
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
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Beau-Faller M, Pencreach E, Leduc C, Blons H, Merlio JP, Bringuier PP, de Fraipont F, Escande F, Lemoine A, Ouafik L, Denis M, Hofman P, Lacave R, Melaabi S, Langlais A, Missy P, Morin F, Moro-Sibilot D, Barlesi F, Cadranel J. Independent prognostic value of ultra-sensitive quantification of tumor pre-treatment T790M subclones in EGFR mutated non-small cell lung cancer (NSCLC) treated by first/second generation TKI, depends on variant allele frequency (VAF): Results of the French cooperative thoracic intergroup (IFCT) biomarkers France project. Lung Cancer 2019; 140:19-26. [PMID: 31841714 DOI: 10.1016/j.lungcan.2019.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/09/2019] [Accepted: 10/11/2019] [Indexed: 01/12/2023]
Abstract
OBJECTIVES T790M mutations inEGFR-mutated non-small cell lung cancer (NSCLC) account for nearly 50% of acquired resistance mechanisms to EGFR-TKIs. Earlier studies suggested that tumor T790M could also be detected in TKI-naïve EGFR-mutated NSCLC. The aim of the study is to assess the prevalence and clinical significance of quantification of tumor pre-treatment T790M subclones. MATERIALS AND METHODS We analyzed 366 EGFR-mutated NSCLC patients of the real-life IFCT Biomarkers France study with available pre-treatment formalin-fixed paraffin-embedded (FFPE) tumor DNA before treatment by first/second-generation EGFR-TKI. We used ultra-sensitive Droplet Digital Polymerase Chain Reaction (ddPCR) QX200 (BIO-RAD®, Hercules, CA, USA). All samples were tested in duplicate. RESULTS ddPCR identified T790M in 19/240 specimens (8%). T790M-positive and T790M-negative populations were not different for clinical baseline characteristics. T790M Variant Allele Frequency (VAF) was > 0.01% <0.1%, > 0.1% <1%, > 1% <10%, and >10% in five (26.3%), six (31.6%), six (31.6%), and two (10.5%) patients, respectively. T790M VAF was >0.1% in 11/13 (84%) patients with rapid (<3 months) or usual progression (3-20 months) compared to 0/3 with low progression (>20 months) (p = 0.02). In a Cox model, T790M mutation positivity was correlated with overall survival (OS) and progression-free survival (PFS) for 10% > VAF >1% (hazard ratio [HR] = 2.83, 95% confidence interval [CI] 1.13-7.07, p = 0.03; HR=3.62, 95%CI 1.43-4.92, p = 0.007, respectively) and for VAF >10% (HR = 19.14, 95%CI 4.35-84.26, p < 0.001; HR = 17.89, 95%CI 2.21-144.86, p = 0.007, respectively). CONCLUSION Ultra-sensitive detection of tumor T790M mutation concerned 8% of EGFR-mutated TKI-naïve NSCLC patients and has a negative prognostic value only for T790M VAF over 1%.
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MESH Headings
- Adenocarcinoma of Lung/drug therapy
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/pathology
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Carcinoma, Large Cell/drug therapy
- Carcinoma, Large Cell/genetics
- Carcinoma, Large Cell/pathology
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Drug Resistance, Neoplasm
- ErbB Receptors/genetics
- Female
- Follow-Up Studies
- France
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Mutation
- Prognosis
- Protein Kinase Inhibitors/therapeutic use
- Retrospective Studies
- Survival Rate
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Affiliation(s)
- Michèle Beau-Faller
- Laboratory of Biochemistry and Molecular Biology, Centre Hospitalier Universitaire de Strasbourg, Hôpital de Hautepierre, Strasbourg, France; IRFAC UMR-S1113, Inserm, Université de Strasbourg, Strasbourg, France.
| | - Erwan Pencreach
- IRFAC UMR-S1113, Inserm, Université de Strasbourg, Strasbourg, France
| | - Charlotte Leduc
- Chest Department, Centre Hospitalier Universitaire de Strasbourg, Nouvel Hôpital Civil, Strasbourg, France
| | - Hélène Blons
- HEGP, Biochimie UF de Pharmacogénétique et Oncologie Moléculaire, Paris, France
| | - Jean-Philippe Merlio
- Department of Pathology and Tumor Biology, CHU and University Bordeaux, Hôpital Haut-Lévêque, Pessac, France
| | - Pierre-Paul Bringuier
- Centre de Biologie et Pathologie Est, Service d'Anatomie et de Cytologie Pathologique, Hospices Civils de Lyon et Université Claude Bernard Lyon 1, Lyon, France
| | - Florence de Fraipont
- UM de Génétique moléculaire: Maladies Héréditaires et Oncologie, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France; UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences-Université Grenoble Alpes, Grenoble, France
| | - Fabienne Escande
- Laboratoire de Biochimie et Biologie moléculaire, CHRU Lille, LILLE, France
| | - Antoinette Lemoine
- Biochimie et Oncogénétique INSERM UMR-S1193, Hôpital Paul Brousse, Hôpitaux Universitaires Paris-Sud, Villejuif, France
| | - L'Houcine Ouafik
- Aix Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, Faculté de Médecine Secteur Nord, Service de Transfert d'Oncologie Biologique, Marseille, France
| | - Marc Denis
- Laboratoire de Biochimie et Plateforme de Génétique Moléculaire des Cancers, CHU Nantes, Nantes, France
| | - Paul Hofman
- Université Côte d'Azur, and FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Inserm U1081/CNRS 7284, and Hospital-Integrated Biobank (BB-0033-00025) Pasteur Hospital, Nice, France
| | - Roger Lacave
- Faculté de Médecine Sorbonne Université, and Groupe Hospitalier HUEP, Hôpital Tenon, Unité de Génomique des Tumeurs Solides, Assistance Publique-Hôpitaux de Paris, France
| | - Samia Melaabi
- Service de Génétique, Unité de Pharmacogénomique, Institut Curie, Paris, France
| | - Alexandra Langlais
- Department of Biostatistics, French Cooperative Thoracic Intergroup, Paris, France
| | - Pascale Missy
- Clinical Research Unit, French Cooperative Thoracic Intergroup, Paris, France
| | - Franck Morin
- Clinical Research Unit, French Cooperative Thoracic Intergroup, Paris, France
| | - Denis Moro-Sibilot
- Unité d'Oncologie Thoracique, Service Hospitalier Universitaire Pneumologie Physiologie Pôle Thorax et Vaisseaux, CHU Grenoble Alpes, Grenoble, France
| | - Fabrice Barlesi
- Aix Marseille University, CNRS, INSERM, CRCM, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Jacques Cadranel
- AP-HP, Hôpital Tenon, Service de Pneumogie, GRC 04 Theranoscan, Sorbonne Université, Paris, France
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