1
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Park JH, Seo AN, Kim M. Diagnostic Usefulness of p53 Immunostaining in Gastric Cancer and Dysplasia: A Real-world Clinical Experience. In Vivo 2024; 38:1865-1874. [PMID: 38936896 PMCID: PMC11215596 DOI: 10.21873/invivo.13641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND/AIM Gastric cancer and its precancerous lesions represent a significant public health concern. A subset of gastric cancers exhibits mutations in the TP53 gene, often accompanying distinctive morphologic alterations. This study aimed to assess the diagnostic efficacy of p53 immunostaining in real-world clinical settings. PATIENTS AND METHODS A retrospective analysis was conducted on 50 cases of gastric tumors and tumor-like lesions, wherein p53 immunostaining played a pivotal diagnostic role. The staining pattern of p53 was examined in conjunction with clinicopathologic parameters. RESULTS Mutant p53 staining pattern demonstrated a significant association with high-grade nuclear atypia (p<0.001), high-grade dysplasia, and tubular adenocarcinoma (p<0.001), as well as microsatellite instability status (p=0.034). Furthermore, the diagnostic utility of p53 immunostaining was evident in scenarios where: 1) biopsy specimens contained few tumor cells, 2) pathologic evaluation of resection margins was limited by cauterization artifacts, and 3) distinction between low-grade and high-grade gastric dysplasia was challenging. CONCLUSION P53 immunostaining can be helpful for the diagnosis of gastric tumor and tumor-like lesions, and accurate pathologic margin evaluation, particularly in lesions demonstrating intestinal-type differentiation and some degree of nuclear atypia.
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Affiliation(s)
- Ji Hyun Park
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - An Na Seo
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Moonsik Kim
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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2
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Liu Y, Ho C, Yu W, Huang Y, Miller J, Gao Q, Syed M, Ma Y, Wang M, Maciag L, Petrova-Drus K, Zhu M, Yao J, Vanderbilt C, Durham B, Benhamida J, Ewalt MD, Dogan A, Roshal M, Nafa K, Arcila ME. Quantification of Measurable Residual Disease Detection by Next-Generation Sequencing-Based Clonality Testing in B-Cell and Plasma Cell Neoplasms. J Mol Diagn 2024; 26:168-178. [PMID: 38103591 PMCID: PMC10918645 DOI: 10.1016/j.jmoldx.2023.11.009] [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: 07/04/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023] Open
Abstract
Next-generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of various technical aspects of the MRD assays, but more studies are warranted to establish the performance characteristics and enable standardization and broad utilization in routine clinical practice. Here, the authors describe an NGS-based IGH MRD quantification assay, incorporating a spike-in calibrator for monitoring B-cell and plasma cell neoplasms based on their unique IGH rearrangement status. Comparison of MRD status (positive or undetectable) by NGS and flow cytometry (FC) assays showed high concordance (91%, 471/519 cases) and overall good linear correlation in MRD quantitation, particularly for chronic lymphocytic leukemia and B-lymphoblastic leukemia/lymphoma (R = 0.85). Quantitative correlation was lower for plasma cell neoplasms, where underestimation by FC is a known limitation. No significant effects on sequencing efficiency by the spike-in calibrator were observed, with excellent inter- and intra-assay reproducibility within the authors' laboratory, and in comparison to an external laboratory, using the same assay and protocols. Assays performed both at internal and external laboratories showed highly concordant MRD detection (100%) and quantitation (R = 0.97). Overall, this NGS-based MRD assay showed highly reproducible results with quantitation that correlated well with FC MRD assessment, particularly for B-cell neoplasms.
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Affiliation(s)
- Ying Liu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Caleb Ho
- Loxo Oncology, Inc., Stamford, Connecticut
| | - Wayne Yu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ying Huang
- Invivoscribe, Inc., San Diego, California
| | | | - Qi Gao
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mustafa Syed
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuanyuan Ma
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meiyi Wang
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lidia Maciag
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Menglei Zhu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin Durham
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark D Ewalt
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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3
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Benintende G, Pozzo F, Innocenti I, Autore F, Fresa A, D’Arena G, Gattei V, Lurenti L. Measurable residual disease in chronic lymphocytic leukemia. Front Oncol 2023; 13:1112616. [PMID: 36865804 PMCID: PMC9971803 DOI: 10.3389/fonc.2023.1112616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Measurable residual disease (MRD) is defined as the presence of residual cancer cells after treatment in patients with clinically undetectable disease, who would otherwise be considered in complete remission. It is a highly sensitive parameter which indicates the disease burden and predicts survival in this setting of patients. In recent years, MRD has gained a role in many hematological malignancies as a surrogate endpoint for clinical trials: undetectable MRD has been correlated to longer progression free survival (PFS) and overall survival (OS). New drugs and combinations have been developed with the aim to achieve MRD negativity, which would indicate favorable prognosis. Different methods to measure MRD have also been devised, which include flow cytometry, polymerase chain reaction (PCR) and next generation sequencing (NGS), with different sensitivity and accuracy in evaluating deep remission after treatment. In this review, we will analyze the current recommendations for the detection of MRD, with particular focus on its role in Chronic Lymphocytic Leukemia (CLL), as well as the different detection methods. Moreover, we will discuss the results of clinical trials and the role of MRD in new therapeutic schemes with inhibitors and monoclonal antibodies. MRD is not currently used in the clinical practice to evaluate response to treatment, due to technical and economical limitations, but it's gaining more and more interest in trials settings, especially since the introduction of venetoclax. The use of MRD in trials will likely be followed by a broader practical application in the future. The aim of this work is to provide a reader-friendly summary of the state of art in the field, as MRD will soon become an accessible tool to evaluate our patients, predict their survival and guide physician's therapeutic choices and preferences.
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Affiliation(s)
- Giulia Benintende
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, Rome, Italy,*Correspondence: Giulia Benintende,
| | - Federico Pozzo
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Idanna Innocenti
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesco Autore
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Alberto Fresa
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Giovanni D’Arena
- “San Luca” Hospital, Azienda Sanitaria Locale (ASL) Salerno, Salerno, Italy
| | - Valter Gattei
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico di Aviano (CRO) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Luca Lurenti
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, Rome, Italy
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4
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Dogliotti I, Jiménez C, Varettoni M, Talaulikar D, Bagratuni T, Ferrante M, Pérez J, Drandi D, Puig N, Gilestro M, García-Álvarez M, Owen R, Jurczak W, Tedeschi A, Leblond V, Kastritis E, Kersten MJ, D’Sa S, Kaščák M, Willenbacher W, Roccaro AM, Poulain S, Morel P, Kyriakou C, Fend F, Vos JMI, Dimopoulos MA, Buske C, Ferrero S, García-Sanz R. Diagnostics in Waldenström's macroglobulinemia: a consensus statement of the European Consortium for Waldenström's Macroglobulinemia. Leukemia 2023; 37:388-395. [PMID: 36435884 PMCID: PMC9898035 DOI: 10.1038/s41375-022-01762-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/28/2022]
Abstract
The diagnosis of Waldenström's macroglobulinemia (WM), an IgM-associated lymphoplasmacytic lymphoma, can be challenging due to the different forms of disease presentation. Furthermore, in recent years, WM has witnessed remarkable progress on the diagnostic front, as well as a deeper understanding of the disease biology, which has affected clinical practice. This, together with the increasing variety of tools and techniques available, makes it necessary to have a practical guidance for clinicians to perform the initial evaluation of patients with WM. In this paper, we present the consensus recommendations and laboratory requirements for the diagnosis of WM developed by the European Consortium of Waldenström's Macroglobulinemia (ECWM), for both clinical practice as well as the research/academical setting. We provide the procedures for multiparametric flow cytometry, fluorescence in situ hybridization and molecular tests, and with this offer guidance for a standardized diagnostic work-up and methodological workflow of patients with IgM monoclonal gammopathy of uncertain significance, asymptomatic and symptomatic WM.
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Affiliation(s)
- Irene Dogliotti
- grid.7605.40000 0001 2336 6580Unit of Hematology, Department of Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Cristina Jiménez
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain.
| | - Marzia Varettoni
- grid.419425.f0000 0004 1760 3027Division of Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Dipti Talaulikar
- grid.1001.00000 0001 2180 7477Canberra Health Services, College of Medicine, Biology and Environment Australian National University, Canberra ACT, Australia
| | - Tina Bagratuni
- grid.5216.00000 0001 2155 0800Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Martina Ferrante
- grid.7605.40000 0001 2336 6580Unit of Hematology, Department of Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - José Pérez
- grid.411258.bHematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain
| | - Daniela Drandi
- grid.7605.40000 0001 2336 6580Unit of Hematology, Department of Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Noemí Puig
- grid.411258.bHematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain
| | - Milena Gilestro
- grid.7605.40000 0001 2336 6580Unit of Hematology, Department of Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - María García-Álvarez
- grid.411258.bHematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain
| | - Roger Owen
- grid.415967.80000 0000 9965 1030The Leeds Teaching Hospitals National Health Service Trust, Leeds, UK
| | - Wojciech Jurczak
- grid.418165.f0000 0004 0540 2543Maria Sklodowska-Curie National Research Institute of Oncology, Krakow, Poland
| | - Alessandra Tedeschi
- grid.416200.1ASST Grande Ospedale Metropolitano Niguarda Hospital, Milan, Italy
| | - Veronique Leblond
- grid.462844.80000 0001 2308 1657Département d’Hématologie Hôpital Pitié-Salpêtrière APHP, UPMC Université Paris, Paris, France
| | - Efstathios Kastritis
- grid.5216.00000 0001 2155 0800Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece ,grid.5216.00000 0001 2155 0800National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Marie José Kersten
- grid.509540.d0000 0004 6880 3010Department of Hematology, Amsterdam UMC, Location University of Amsterdam, Cancer Center Amsterdam and LYMMCARE (Lymphoma and Myeloma Center Amsterdam), Amsterdam, The Netherlands
| | - Shirley D’Sa
- grid.439749.40000 0004 0612 2754Centre for Waldenströms Macroglobulinaemia and Related Conditions, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Michal Kaščák
- grid.412684.d0000 0001 2155 4545Department of Haematooncology, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Wolfgang Willenbacher
- grid.410706.4Department of Haematology and Oncology, Internal Medicine V, Innsbruck University Hospital & Syndena GmbH, Connect to Cure, Innsbruck, Austria
| | - Aldo M. Roccaro
- grid.412725.7Clinical Research Development and Phase I Unit, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Stephanie Poulain
- grid.410463.40000 0004 0471 8845Laboratory of Hematology, Biology and Pathology Center, CHU of Lille, INSERM UMR-S 1277, Team 4, Oncolille, Lille, France
| | - Pierre Morel
- grid.134996.00000 0004 0593 702XService d’Hematologie Clinique et Therapie Cellulaire, Centre Hospitalier Universitaire d’Amiens-Picardie, Amiens, France
| | - Charalampia Kyriakou
- grid.439749.40000 0004 0612 2754Centre for Waldenströms Macroglobulinaemia and Related Conditions, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Falko Fend
- grid.411544.10000 0001 0196 8249Institute of Pathology and Comprehensive Cancer Centre, Eberhard-Karls-University, University Hospital Tübingen, Tübingen, Germany
| | - Josephine M. I. Vos
- grid.509540.d0000 0004 6880 3010Department of Hematology, Amsterdam UMC, Location University of Amsterdam, Cancer Center Amsterdam and LYMMCARE (Lymphoma and Myeloma Center Amsterdam), Amsterdam, The Netherlands
| | - Meletios A. Dimopoulos
- grid.5216.00000 0001 2155 0800Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece ,grid.5216.00000 0001 2155 0800National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Christian Buske
- grid.410712.10000 0004 0473 882XInstitute of Experimental Cancer Research, Comprehensive Cancer Center Ulm, University Hospital of Ulm, Ulm, Germany
| | - Simone Ferrero
- grid.7605.40000 0001 2336 6580Unit of Hematology, Department of Biotechnology and Health Sciences, University of Torino, Torino, Italy ,Hematology Division 1U, “AOU Città della Salute e della Scienza di Torino”, Torino, Italy
| | - Ramón García-Sanz
- grid.411258.bHematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain
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5
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Kim SJ, Kim YJ, Yoon SE, Ryu KJ, Park B, Park D, Cho D, Kim HY, Cho J, Ko YH, Park WY, Kim WS. Circulating Tumor DNA-Based Genotyping and Monitoring for Predicting Disease Relapses of Patients with Peripheral T-Cell Lymphomas. Cancer Res Treat 2023; 55:291-303. [PMID: 35240014 PMCID: PMC9873338 DOI: 10.4143/crt.2022.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/23/2022] [Indexed: 02/04/2023] Open
Abstract
PURPOSE Plasma circulating tumor DNA (ctDNA) could reflect the genetic alterations present in tumor tissues. However, there is little information about the clinical relevance of cell-free DNA genotyping in peripheral T-cell lymphoma (PTCL). MATERIALS AND METHODS After targeted sequencing plasma cell-free DNA of patients with various subtypes of PTCL (n=94), we analyzed the mutation profiles of plasma ctDNA samples and their predictive value of dynamic ctDNA monitoring for treatment outcomes. RESULTS Plasma ctDNA mutations were detected in 53 patients (56%, 53/94), and the detection rate of somatic mutations was highest in angioimmunoblastic T-cell lymphoma (24/31, 77%) and PTCL, not otherwise specified (18/29, 62.1%). Somatic mutations were detected in 51 of 66 genes that were sequenced, including the following top 10 ranked genes: RHOA, CREBBP, KMT2D, TP53, IDH2, ALK, MEF2B, SOCS1, CARD11, and KRAS. In the longitudinal assessment of ctDNA mutation, the difference in ctDNA mutation volume after treatment showed a significant correlation with disease relapse or progression. Thus, a ≥ 1.5-log decrease in genome equivalent (GE) between baseline and the end of treatment showed a significant association with better survival outcomes than a < 1.5-log decrease in GE. CONCLUSION Our results suggest the clinical relevance of plasma ctDNA analysis in patients with PTCL. However, our findings should be validated by a subsequent study with a larger study population and using a broader gene panel.
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Affiliation(s)
- Seok Jin Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul,
Korea,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute Samsung Medical Center, Seoul,
Korea
| | - Sang Eun Yoon
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | - Kyung Ju Ryu
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | - Bon Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | | | - Duck Cho
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | - Hyun-Young Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | - Junhun Cho
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | - Young Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul,
Korea
| | - Woong-Yang Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul,
Korea,Samsung Genome Institute Samsung Medical Center, Seoul,
Korea
| | - Won Seog Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul,
Korea,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul,
Korea
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6
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Digital PCR as a New Method for Minimal Residual Disease Monitoring and Treatment Free Remission Management in Chronic Myeloid Leukemia Patients: Is It Reliable? HEMATO 2022. [DOI: 10.3390/hemato4010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effective and sensitive monitoring of Minimal Residual Disease or Measurable Residual Disease (MRD) is a very important aspect in the management of patients affected by hematologic malignancies. The recent availability of new technologies has opened to the improvement of MRD monitoring. It is particularly relevant in patients affected by Chronic Myeloid Leukemia (CML). MRD monitoring is key in the management of CML patients thanks to the efficacy of TKIs therapy. Moreover, the policies of TKIs discontinuation aimed at treatment free remission are strongly based on the good selection of patients eligible for stopping TKIs therapy. The recently described application of digital PCR in CML patients monitoring seems to improve the accuracy and precision in the identification of optimal responders. The present review reports an overview on the application of digital PCR in the monitoring of MRD in CML and its impact on TKIs discontinuation trials and, consequently, on TFR success.
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7
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Hussaini MO, Srivastava J, Lee LW, Nishihori T, Shah BD, Alsina M, Pinilla-Ibarz J, Shain KH. Assessment of Clonotypic Rearrangements and Minimal Residual Disease in Lymphoid Malignancies: A Large Cancer Center Experience Using clonoSEQ. Arch Pathol Lab Med 2021; 146:485-493. [PMID: 34343238 DOI: 10.5858/arpa.2020-0457-oa] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Measurable (minimal) residual disease (MRD) is an independent prognostic factor for survival outcomes in patients with lymphoid and plasma cell malignancies and has been incorporated into consensus criteria regarding treatment response, strategy, and clinical trial endpoints. clonoSEQ (a next-generation sequencing [NGS]-MRD assay) uses multiplex polymerase chain reaction and NGS to identify clonotypic rearrangements at the immunoglobulin (Ig) H, IgK, IgL, T-cell receptor (TCR)-β, and TCR-γ loci, and translocated B-cell lymphoma 1/IgH and 2/IgH sequences for MRD assessment. Additionally, it can be used to confirm diagnoses of cutaneous T-cell lymphoma (CTCL). OBJECTIVE.— To review the technical aspects of our experience using the clonoSEQ Assay in routine clinical practice. DESIGN.— In this single-center experience, 390 patients with lymphoid and plasma cell malignancies were assessed with the NGS-MRD Assay at a central laboratory. RESULTS.— Median time from arrival of the shipment to initiation of the assay (defined as captured in Adaptive's secure tracking system) was 2.1 hours. Overall, 317 patients had 1 or more samples submitted for sequence identification. Of these, 290 (91.5%) had trackable sequences identified. The median calibration rate of samples by malignancy (where n ≥ 10 samples, excluding CTCL samples) was 88.1%, across a variety of fresh and archived sample sources (177 of 201 samples). TCR-β and/or TCR-γ clonotypes were identified in 40 of 95 samples (42.1%) from 66 patients with suspected CTCL. CONCLUSIONS.— This NGS-MRD Assay is a valuable and sensitive tool for monitoring MRD in patients with plasma cell and lymphoid malignancies and assisting in the diagnosis of CTCL.
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Affiliation(s)
- Mohammad O Hussaini
- From Hematopathology and Laboratory Medicine (Hussaini), Moffitt Cancer Center, Tampa, Florida
| | - Jaya Srivastava
- Medical Affairs, Adaptive Biotechnologies, Seattle, Washington (Srivastava, Lee)
| | - Lik Wee Lee
- Medical Affairs, Adaptive Biotechnologies, Seattle, Washington (Srivastava, Lee)
| | - Taiga Nishihori
- Blood and Bone Marrow Transplantation (Nishihori, Alsina), Moffitt Cancer Center, Tampa, Florida
| | - Bijal D Shah
- Malignant Hematology (Shah, Pinilla-Ibarz, Shain), Moffitt Cancer Center, Tampa, Florida
| | - Melissa Alsina
- Blood and Bone Marrow Transplantation (Nishihori, Alsina), Moffitt Cancer Center, Tampa, Florida
| | - Javier Pinilla-Ibarz
- Malignant Hematology (Shah, Pinilla-Ibarz, Shain), Moffitt Cancer Center, Tampa, Florida
| | - Kenneth H Shain
- Malignant Hematology (Shah, Pinilla-Ibarz, Shain), Moffitt Cancer Center, Tampa, Florida
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8
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Genuardi E, Klous P, Mantoan B, Drandi D, Ferrante M, Cavallo F, Alessandria B, Dogliotti I, Grimaldi D, Ragaini S, Clerico M, Lo Schirico M, Saraci E, Yilmaz M, Zaccaria GM, Cortelazzo S, Vitolo U, Luminari S, Federico M, Boccadoro M, van Min M, Splinter E, Ladetto M, Ferrero S. Targeted locus amplification to detect molecular markers in mantle cell and follicular lymphoma. Hematol Oncol 2021; 39:293-303. [PMID: 33742718 PMCID: PMC8451873 DOI: 10.1002/hon.2864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/22/2021] [Accepted: 03/06/2021] [Indexed: 11/16/2022]
Abstract
Minimal residual disease (MRD) monitoring by PCR methods is a strong and standardized predictor of clinical outcome in mantle cell lymphoma (MCL) and follicular lymphoma (FL). However, about 20% of MCL and 40% of FL patients lack a reliable molecular marker, being thus not eligible for MRD studies. Recently, targeted locus amplification (TLA), a next‐generation sequencing (NGS) method based on the physical proximity of DNA sequences for target selection, identified novel gene rearrangements in leukemia. The aim of this study was to test TLA in MCL and FL diagnostic samples lacking a classical, PCR‐detectable, t(11; 14) MTC (BCL1/IGH), or t(14; 18) major breakpoint region and minor cluster region (BCL2/IGH) rearrangements. Overall, TLA was performed on 20 MCL bone marrow (BM) or peripheral blood (PB) primary samples and on 20 FL BM, identifying a novel BCL1 or BCL2/IGH breakpoint in 16 MCL and 8 FL patients (80% and 40%, respectively). These new breakpoints (named BCL1‐TLA and BCL2‐TLA) were validated by ASO primers design and compared as MRD markers to classical IGH rearrangements in eight MCL: overall, MRD results by BCL1‐TLA were superimposable (R Pearson = 0.76) to the standardized IGH‐based approach. Moreover, MRD by BCL2‐TLA reached good sensitivity levels also in FL and was predictive of a primary refractory case. In conclusion, this study offers the proof of principle that TLA is a promising and reliable NGS‐based technology for the identification of novel molecular markers, suitable for further MRD analysis in previously not traceable MCL and FL patients.
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Affiliation(s)
- Elisa Genuardi
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | | | - Barbara Mantoan
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Daniela Drandi
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Martina Ferrante
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Federica Cavallo
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Beatrice Alessandria
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Irene Dogliotti
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Daniele Grimaldi
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Simone Ragaini
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Michele Clerico
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Mariella Lo Schirico
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | | | | | - Gian Maria Zaccaria
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | | | - Umberto Vitolo
- Department of Oncology, Division of Hematology, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Stefano Luminari
- Hematology Unit, Azienda USL IRCCS di Reggio Emilia, Reggio Emilia, Modena, Italy.,Medical Oncology, CHIMOMO department, University of Modena and Reggio Emilia, Modena, Italy
| | - Massimo Federico
- Medical Oncology, CHIMOMO department, University of Modena and Reggio Emilia, Modena, Italy
| | - Mario Boccadoro
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | | | | | - Marco Ladetto
- Division of Hematology, Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Simone Ferrero
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
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9
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Huggett JF. The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. Clin Chem 2021; 66:1012-1029. [PMID: 32746458 DOI: 10.1093/clinchem/hvaa125] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.
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10
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Juelg P, Kipf E, Specht M, Fillies M, Eckert C, Paust N, Zengerle R, Lehnert M, Hutzenlaub T. The MRD disk: automated minimal residual disease monitoring by highly sensitive centrifugal microfluidic multiplex qPCR. LAB ON A CHIP 2021; 21:558-570. [PMID: 33319895 DOI: 10.1039/d0lc00945h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a proof-of-principle study on automated, highly sensitive and multiplexed qPCR quantification by centrifugal microfluidics. The MRD disk can be used for standardisation of repetitive, longitudinal assays with high requirements on reproducibility and sensitivity, such as cancer monitoring. In contrast to high-throughput qPCR automation by bulky and expensive robotic workstations we employ a small centrifugal microfluidic instrument, addressing the need of low- to mid-throughput applications. As a potential application we demonstrate automated minimum residual disease (MRD) monitoring of prognostic markers in patients with acute lymphoblastic leukaemia (ALL). The disk-workflow covers all aspects of clinical gold standard MRD quantification: generation of standard curves, specificity controls, no template controls and quantification of the ALL patient sample. We integrated a highly sensitive, colorimetric 2-plex analysis of MRD targets, as well as a 2-plex analysis of reference genes, both in parallel and in a single LabDisk cartridge. For this purpose, a systematic procedure for crosstalk- and signal-to-noise-optimisation is introduced, providing a guideline for efficient multiplex readout inside microfluidic platforms. The qPCR standard curves (n = 12/12) generated on-disk reach clinically required linearity (R2 = 98.1% to R2 = 99.8%). In three consecutive MRD disk runs with an ALL patient sample containing the two representative MRD targets VH3D3D5JH3 and VkIkde, we observe high accordance between the on-disk quantifications (48 ± 6 copies/reaction and 69 ± 6 copies/reaction) and the expected concentrations (57 copies/reaction for both targets). In comparison to the clinical gold standard of manually pipetted, singleplex assays, the MRD disk yields comparable limit of quantification (1 × 10-4) in n = 6/6 analyses (vs. n = 4/4 in gold standard) and a limit of detection (1 × 10-5) in n = 6/6 analysis (vs. n = 2/4 in gold standard). The automation reduces the risk of manual liquid handling errors, making the MRD disk an attractive solution to assure reproducibility in moderate-throughput, longitudinal gene quantification applications.
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Affiliation(s)
- Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Elena Kipf
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Mara Specht
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Marion Fillies
- Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Cornelia Eckert
- Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nils Paust
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. and Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. and Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Tobias Hutzenlaub
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. and Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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11
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Gholipour E, Sarvarian P, Samadi P, Talebi M, Movassaghpour A, Motavalli R, Hojjat-Farsangi M, Yousefi M. Exosome: From leukemia progression to a novel therapeutic approach in leukemia treatment. Biofactors 2020; 46:698-715. [PMID: 32797698 DOI: 10.1002/biof.1669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022]
Abstract
Exosomes, as small vesicles, are released by tumor cells and tumor microenvironment (cells and function as key intercellular mediators and effects on different processes including tumorigenesis, angiogenesis, drug resistance, and evasion from immune system. These functions are due to exosomes' biomolecules which make them as efficient markers in early diagnosis of the disease. Also, exosomes have been recently applied in vaccination. The potential role of exosomes in immune response toward leukemic cells makes them efficient immunotherapeutic agents treating leukemia. Furthermore, variations in exosomes contents make them beneficial to be used in treating different diseases. This review introduces the role of exosomes in the development of hematological malignancies and evaluates their functional role in the treatment of these malignancies.
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Affiliation(s)
- Elham Gholipour
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Sarvarian
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Samadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Talebi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aliakbar Movassaghpour
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roza Motavalli
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hojjat-Farsangi
- Immune and Gene Therapy Lab, Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institute, Stockholm, Sweden
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Aging Research Institute, Tabriz university of Medical Sciences, Tabriz, Iran
- Endocrine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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12
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Beck RC, Kim AS, Goswami RS, Weinberg OK, Yeung CCS, Ewalt MD. Molecular/Cytogenetic Education for Hematopathology Fellows. Am J Clin Pathol 2020; 154:149-177. [PMID: 32444878 DOI: 10.1093/ajcp/aqaa038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES At a discussion on molecular/cytogenetic education for hematopathology fellows at the 2018 Society for Hematopathology Program Directors Meeting, consensus was that fellows should understand basic principles and indications for and limitations of molecular/cytogenetic testing used in routine practice. Fellows should also be adept at integrating results of such testing for rendering a final diagnosis. To aid these consensus goals, representatives from the Society for Hematopathology and the Association for Molecular Pathology formed a working group to devise a molecular/cytogenetic curriculum for hematopathology fellow education. CURRICULUM SUMMARY The curriculum includes a primer on cytogenetics and molecular techniques. The bulk of the curriculum reviews the molecular pathology of individual malignant hematologic disorders, with applicable molecular/cytogenetic testing for each and following the 2017 World Health Organization classification of hematologic neoplasms. Benign hematologic disorders and bone marrow failure syndromes are also discussed briefly. Extensive tables are used to summarize genetics of individual disorders and appropriate methodologies. CONCLUSIONS This curriculum provides an overview of the current understanding of the molecular biology of hematologic disorders and appropriate ancillary testing for their evaluation. The curriculum may be used by program directors for training hematopathology fellows or by practicing hematopathologists.
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Affiliation(s)
- Rose C Beck
- Department of Pathology, University Hospitals of Cleveland, Case Western Reserve University, Cleveland, OH (Society for Hematopathology Representative)
| | - Annette S Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA (Association for Molecular Pathology Representative)
| | - Rashmi S Goswami
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Olga K Weinberg
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Cecilia C S Yeung
- Department of Pathology, University of Washington, and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Mark D Ewalt
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora
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13
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Analytical evaluation of the clonoSEQ Assay for establishing measurable (minimal) residual disease in acute lymphoblastic leukemia, chronic lymphocytic leukemia, and multiple myeloma. BMC Cancer 2020; 20:612. [PMID: 32605647 PMCID: PMC7325652 DOI: 10.1186/s12885-020-07077-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/15/2020] [Indexed: 01/02/2023] Open
Abstract
Background The clonoSEQ® Assay (Adaptive Biotechnologies Corporation, Seattle, USA) identifies and tracks unique disease-associated immunoglobulin (Ig) sequences by next-generation sequencing of IgH, IgK, and IgL rearrangements and IgH-BCL1/2 translocations in malignant B cells. Here, we describe studies to validate the analytical performance of the assay using patient samples and cell lines. Methods Sensitivity and specificity were established by defining the limit of detection (LoD), limit of quantitation (LoQ) and limit of blank (LoB) in genomic DNA (gDNA) from 66 patients with multiple myeloma (MM), acute lymphoblastic leukemia (ALL), or chronic lymphocytic leukemia (CLL), and three cell lines. Healthy donor gDNA was used as a diluent to contrive samples with specific DNA masses and malignant-cell frequencies. Precision was validated using a range of samples contrived from patient gDNA, healthy donor gDNA, and 9 cell lines to generate measurable residual disease (MRD) frequencies spanning clinically relevant thresholds. Linearity was determined using samples contrived from cell line gDNA spiked into healthy gDNA to generate 11 MRD frequencies for each DNA input, then confirmed using clinical samples. Quantitation accuracy was assessed by (1) comparing clonoSEQ and multiparametric flow cytometry (mpFC) measurements of ALL and MM cell lines diluted in healthy mononuclear cells, and (2) analyzing precision study data for bias between clonoSEQ MRD results in diluted gDNA and those expected from mpFC based on original, undiluted samples. Repeatability of nucleotide base calls was assessed via the assay’s ability to recover malignant clonotype sequences across several replicates, process features, and MRD levels. Results LoD and LoQ were estimated at 1.903 cells and 2.390 malignant cells, respectively. LoB was zero in healthy donor gDNA. Precision ranged from 18% CV (coefficient of variation) at higher DNA inputs to 68% CV near the LoD. Variance component analysis showed MRD results were robust, with expected laboratory process variations contributing ≤3% CV. Linearity and accuracy were demonstrated for each disease across orders of magnitude of clonal frequencies. Nucleotide sequence error rates were extremely low. Conclusions These studies validate the analytical performance of the clonoSEQ Assay and demonstrate its potential as a highly sensitive diagnostic tool for selected lymphoid malignancies.
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14
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Al-Katib AM, Ebrahim AS, Kandouz M, Zaiem F, Raufi A, Ebrahim S, Mohamed A, Emara N, Gabali AM. Isolation and characterization of a CD34 + sub-clone in B-cell lymphoma. Oncotarget 2020; 11:148-160. [PMID: 32010428 PMCID: PMC6968783 DOI: 10.18632/oncotarget.27415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Non-Hodgkin's lymphoma (NHL) is the most common hematological malignancy in the US. Many types remain incurable despite response to initial therapy and achievement of complete remission (CR). Advanced laboratory techniques like multicolor flow cytometry (FCM) and polymerase chain reaction (PCR) have demonstrated persistence of rare malignant cell population post therapy. However, the functional and biological characteristics of this population have not been elucidated. Established B-lymphoma cell lines (B-NHL) and patient-derived samples (PDS) were analyzed using 8-color FCM. CD34+ sub-population was enriched using in vitro exposure to 2-chlorodeoxyadenosine (2-CdA) and by CD34 magnetic beads. Genetic analysis of cell fractions was done by karyotyping and array comparative genomic hybridization (aCGH). Sensitivity to chemotherapy was assayed by short-term in vitro exposure to chemotherapy. Clonogenicity was determined by soft agar colony formation assay, and proliferation was determined using DNA staining with propidium iodide and FCM. FCM demonstrated the presence of a minute sub-clone of monotypic B-cells that express CD34 in B-NHL cell lines (3 of 3) and in PDS (8 of 8). This sub-population enriched up to 50 fold in vitro by exposure to 2-CdA and up to 80% purity by CD34 magnetic bead column isolation. Except for CD34 expression, this population expressed identical phenotype and genotype to parent cells, but was more proliferative, Hoechst 33342-positive, clonogenic, and resistant to chemotherapy compared with the CD34- population. The isolated CD34+ monotypic B-cells may contribute to resistance of certain NHL to treatment and should be targeted by potential new drugs for NHL.
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Affiliation(s)
- Ayad M. Al-Katib
- Lymphoma Research Laboratory, Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Abdul Shukkur Ebrahim
- Lymphoma Research Laboratory, Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Mustapha Kandouz
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Feras Zaiem
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Ali Raufi
- Lymphoma Research Laboratory, Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Salah Ebrahim
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Anwar Mohamed
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Nada Emara
- Lymphoma Research Laboratory, Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Ali M. Gabali
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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15
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Sánchez R, Ayala R, Martínez-López J. Minimal Residual Disease Monitoring with Next-Generation Sequencing Methodologies in Hematological Malignancies. Int J Mol Sci 2019; 20:ijms20112832. [PMID: 31185671 PMCID: PMC6600313 DOI: 10.3390/ijms20112832] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/15/2022] Open
Abstract
Ultra-deep next-generation sequencing has emerged in recent years as an important diagnostic tool for the detection and follow-up of tumor burden in most of the known hematopoietic malignancies. Meticulous and high-throughput methods for the lowest possible quantified disease are needed to address the deficiencies of more classical techniques. Precision-based approaches will allow us to correctly stratify each patient based on the minimal residual disease (MRD) after a treatment cycle. In this review, we consider the most prominent ways to approach next-generation sequencing methodologies to follow-up MRD in hematological neoplasms.
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Affiliation(s)
- Ricardo Sánchez
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
| | - Rosa Ayala
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Joaquín Martínez-López
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
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Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019; 17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023] Open
Abstract
Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biological experiments, variant calling can be significantly affected by outside factors including those used to prepare, store, and analyze samples. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing, alongside diverse biological and clinical variables, and evaluate their effect on variant caller selection and optimization.
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17
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Advantage of Next-Generation Sequencing in Dynamic Monitoring of Circulating Tumor DNA over Droplet Digital PCR in Cetuximab Treated Colorectal Cancer Patients. Transl Oncol 2018; 12:426-431. [PMID: 30562681 PMCID: PMC6297189 DOI: 10.1016/j.tranon.2018.11.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 12/24/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) blockade resistance is common in the treatment of RAS wide type colorectal cancer (CRC). During the treatment of cetuximab, acquired resistant genomic alterations always occurs earlier than disease progression observed by medical images. Identification of genomic alterations dynamically might have certain clinical significance. Because of the limitation of repeated tissue biopsy, liquid biopsy is increasingly recognized. Droplet digital polymerase chain reaction (ddPCR) is the main detection methods for circulating tumor DNA (ctDNA), however, the application of next-generation sequencing (NGS) for ctDNA detection becomes more and more popular. Here we develop a NGS-based ctDNA assay and evaluated its sensitivity and specificity while using ddPCR as control. These two technologies were both used for genomic alteration detection for the peripheral blood samples from cetuximab-treated colorectal cancer patients dynamically. Fifteen patients were enrolled in this study, including eight males and seven females. The sensitivity and specificity of our NGS assay were 87.5% and 100% respectively, and liner regression analysis comparing variant allele frequency (VAF) revealed high concordance between NGS and ddPCR (R2 = 0.98). NGS actually found more mutation information than ddPCR such as the additional dynamic changes of TP53 which were observed in the disease progression patients. Moreover, the variant allele fraction of TP53 was also found by NGS to be changed along with the clinical efficacy evaluation dynamically during the whole treatment process. In conclusion, our newly developed NGS-based ctDNA assay shows similar performance with ddPCR but have more advantages of its high throughput of multigenetic detection for the dynamic monitoring during the treatment of cetuximab in metastasis CRC patients.
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