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Diagnostics
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Advances in Lymphoma Molecular Diagnostics
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Advances in Lymphoma Molecular Diagnostics

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 21264

Special Issue Editor

Dr. Richard Flavin

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Guest Editor
Director of Histopathology, St James's Hospital, Trinity College Dublin, Dublin, Ireland
Interests: genitourinary; gynaecological; haematopathology; cancer molecular diagnostics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, there have been rapid advances in the molecular diagnostics of malignancy, including lymphoma. This has led to the publication of an integrated WHO classification system for lymphoid malignancy incorporating clinical, morphological, immunophenotypic and molecular genetic data. This Special Issue seeks expert review and primary research articles on recent advances in the molecular diagnostics of lymphoma which include future perspectives/directions.

Dr. Richard Flavin
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • B-cell lymphoma
  • T-cell lymphoma
  • clonality testing
  • next generation sequencing
  • FISH
  • mutational analysis
  • cell of origin
  • gene expression profiling
  • genetics
  • cytogenetics
  • flow cytometry
  • array CGH
  • SNP analysis

Related Special Issue

Published Papers (7 papers)

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Research

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12 pages, 2582 KiB  
Article
Deep Learning Approach to Automatize TMTV Calculations Regardless of Segmentation Methodology for Major FDG-Avid Lymphomas
by Wendy Revailler, Anne Ségolène Cottereau, Cedric Rossi, Rudy Noyelle, Thomas Trouillard, Franck Morschhauser, Olivier Casasnovas, Catherine Thieblemont, Steven Le Gouill, Marc André, Herve Ghesquieres, Romain Ricci, Michel Meignan and Salim Kanoun
Diagnostics 2022, 12(2), 417; https://doi.org/10.3390/diagnostics12020417 - 06 Feb 2022
Cited by 9 | Viewed by 2366
Abstract
The total metabolic tumor volume (TMTV) is a new prognostic factor in lymphomas that could benefit from automation with deep learning convolutional neural networks (CNN). Manual TMTV segmentations of 1218 baseline 18FDG-PET/CT have been used for training. A 3D V-NET model has been [...] Read more.
The total metabolic tumor volume (TMTV) is a new prognostic factor in lymphomas that could benefit from automation with deep learning convolutional neural networks (CNN). Manual TMTV segmentations of 1218 baseline 18FDG-PET/CT have been used for training. A 3D V-NET model has been trained to generate segmentations with soft dice loss. Ground truth segmentation has been generated using a combination of different thresholds (TMTVprob), applied to the manual region of interest (Otsu, relative 41% and SUV 2.5 and 4 cutoffs). In total, 407 and 405 PET/CT were used for test and validation datasets, respectively. The training was completed in 93 h. In comparison with the TMTVprob, mean dice reached 0.84 in the training set, 0.84 in the validation set and 0.76 in the test set. The median dice scores for each TMTV methodology were 0.77, 0.70 and 0.90 for 41%, 2.5 and 4 cutoff, respectively. Differences in the median TMTV between manual and predicted TMTV were 32, 147 and 5 mL. Spearman’s correlations between manual and predicted TMTV were 0.92, 0.95 and 0.98. This generic deep learning model to compute TMTV in lymphomas can drastically reduce computation time of TMTV. Full article
(This article belongs to the Special Issue Advances in Lymphoma Molecular Diagnostics)
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12 pages, 2848 KiB  
Communication
Deep Sequencing of Immunoglobulin Genes Identifies a Very Low Percentage of Monoclonal B Cells in Primary Cutaneous Marginal Zone Lymphomas with CD30-Positive Hodgkin/Reed–Sternberg-like Cells
by Arianna Di Napoli, Evelina Rogges, Niccolò Noccioli, Anna Gazzola, Gianluca Lopez, Severino Persechino, Rita Mancini and Elena Sabattini
Diagnostics 2022, 12(2), 290; https://doi.org/10.3390/diagnostics12020290 - 24 Jan 2022
Cited by 3 | Viewed by 2085
Abstract
The spectrum of cutaneous CD30-positive lymphoproliferative disorders encompasses both inflammatory and neoplastic conditions. CD30+ Hodgkin and Reed–Sternberg-like cells have been occasionally reported in primary cutaneous marginal zone lymphoma, where they are thought to represent a side neoplastic component within a dominant background of [...] Read more.
The spectrum of cutaneous CD30-positive lymphoproliferative disorders encompasses both inflammatory and neoplastic conditions. CD30+ Hodgkin and Reed–Sternberg-like cells have been occasionally reported in primary cutaneous marginal zone lymphoma, where they are thought to represent a side neoplastic component within a dominant background of lymphomatous small B cells. Herein, we describe the histological and molecular findings of three cases of primary cutaneous marginal zone lymphomas with CD30+ H/RS cells, in which next-generation sequencing analysis revealed the clonal population to consist in less than 5% of the cutaneous B-cell infiltrate, providing a thought-provoking focus on a possible main role for CD30+ cells in primary cutaneous marginal zone lymphoproliferations. Full article
(This article belongs to the Special Issue Advances in Lymphoma Molecular Diagnostics)
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Review

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16 pages, 3541 KiB  
Review
Molecular Diagnostic Review of Diffuse Large B-Cell Lymphoma and Its Tumor Microenvironment
by Robert Ta, David Yang, Christian Hirt, Thomas Drago and Richard Flavin
Diagnostics 2022, 12(5), 1087; https://doi.org/10.3390/diagnostics12051087 - 27 Apr 2022
Cited by 3 | Viewed by 4790
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma. It is a clinically and morphologically heterogeneous entity that has continued to resist complete subtyping. Molecular subtyping efforts emerged in earnest with the advent of gene expression profiling (GEP). This molecular subtyping [...] Read more.
Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma. It is a clinically and morphologically heterogeneous entity that has continued to resist complete subtyping. Molecular subtyping efforts emerged in earnest with the advent of gene expression profiling (GEP). This molecular subtyping approach has continued to evolve simultaneously with others including immunohistochemistry and more modern genomic approaches. Recently, the veritable explosion of genomic data availability and evolving computational methodologies have provided additional avenues, by which further understanding and subclassification of DBLCLs is possible. The goal of this review is to provide a historical overview of the major classification timepoints in the molecular subtyping of DLBCL, from gene expression profiling to present day understanding. Full article
(This article belongs to the Special Issue Advances in Lymphoma Molecular Diagnostics)
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34 pages, 2695 KiB  
Review
Nucleic Acid Biomarkers in Waldenström Macroglobulinemia and IgM-MGUS: Current Insights and Clinical Relevance
by Daniela Drandi, Philippe Decruyenaere, Martina Ferrante, Fritz Offner, Jo Vandesompele and Simone Ferrero
Diagnostics 2022, 12(4), 969; https://doi.org/10.3390/diagnostics12040969 - 12 Apr 2022
Cited by 6 | Viewed by 3935
Abstract
Waldenström Macroglobulinemia (WM) is an indolent lymphoplasmacytic lymphoma, characterized by the production of excess immunoglobulin M monoclonal protein. WM belongs to the spectrum of IgM gammopathies, ranging from asymptomatic IgM monoclonal gammopathy of undetermined significance (IgM-MGUS), through IgM-related disorders and asymptomatic WM to [...] Read more.
Waldenström Macroglobulinemia (WM) is an indolent lymphoplasmacytic lymphoma, characterized by the production of excess immunoglobulin M monoclonal protein. WM belongs to the spectrum of IgM gammopathies, ranging from asymptomatic IgM monoclonal gammopathy of undetermined significance (IgM-MGUS), through IgM-related disorders and asymptomatic WM to symptomatic WM. In recent years, its complex genomic and transcriptomic landscape has been extensively explored, hereby elucidating the biological mechanisms underlying disease onset, progression and therapy response. An increasing number of mutations, cytogenetic abnormalities, and molecular signatures have been described that have diagnostic, phenotype defining or prognostic implications. Moreover, cell-free nucleic acid biomarkers are increasingly being investigated, benefiting the patient in a minimally invasive way. This review aims to provide an extensive overview of molecular biomarkers in WM and IgM-MGUS, considering current shortcomings, as well as potential future applications in a precision medicine approach. Full article
(This article belongs to the Special Issue Advances in Lymphoma Molecular Diagnostics)
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24 pages, 1321 KiB  
Review
Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine
by Ka-Hei (Murphy) Sun, Yin-Ting (Heylie) Wong, Ka-Man (Carmen) Cheung, Carmen (Michelle) Yuen, Yun-Tat (Ted) Chan, Wing-Yan (Jennifer) Lai, Chun (David) Chao, Wing-Sum (Katie) Fan, Yuen-Kiu (Karen) Chow, Man-Fai Law and Ho-Chi (Tommy) Tam
Diagnostics 2022, 12(2), 409; https://doi.org/10.3390/diagnostics12020409 - 05 Feb 2022
Cited by 6 | Viewed by 3093
Abstract
Natural killer (NK)/T-cell lymphoma (NKTCL) is an aggressive malignancy with unique epidemiological, histological, molecular, and clinical characteristics. It occurs in two pathological forms, namely, extranodal NKTCL (ENKTCL) and aggressive NK leukemia, according to the latest World Health Organization (WHO) classification. Epstein–Barr virus (EBV) [...] Read more.
Natural killer (NK)/T-cell lymphoma (NKTCL) is an aggressive malignancy with unique epidemiological, histological, molecular, and clinical characteristics. It occurs in two pathological forms, namely, extranodal NKTCL (ENKTCL) and aggressive NK leukemia, according to the latest World Health Organization (WHO) classification. Epstein–Barr virus (EBV) infection has long been proposed as the major etiology of lymphomagenesis. The adoption of high-throughput sequencing has allowed us to gain more insight into the molecular mechanisms of ENKTCL, which largely involve chromosome deletion and aberrations in Janus kinase (JAK)-signal transducer and activator of transcription (STAT), programmed cell death protein-1 (PD-1)/PD-ligand 1 (PD-L1) pathways, as well as mutations in tumor suppressor genes. The molecular findings could potentially influence the traditional chemoradiotherapy approach, which is known to be associated with significant toxicity. This article will review the latest molecular findings in NKTCL and recent advances in the field of molecular diagnosis in NKTCL. Issues of quality control and technical difficulties will also be discussed, along with future prospects in the molecular diagnosis and treatment of NKTCL. Full article
(This article belongs to the Special Issue Advances in Lymphoma Molecular Diagnostics)
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18 pages, 352 KiB  
Review
Advances in Lymphoma Molecular Diagnostics
by Igor Age Kos, Lorenz Thurner, Joerg Thomas Bittenbring, Konstantinos Christofyllakis and Dominic Kaddu-Mulindwa
Diagnostics 2021, 11(12), 2174; https://doi.org/10.3390/diagnostics11122174 - 23 Nov 2021
Cited by 2 | Viewed by 2050
Abstract
Lymphomas encompass a diverse group of malignant lymphoid neoplasms. Over recent years much scientific effort has been undertaken to identify and understand molecular changes in lymphomas, resulting in a wide range of genetic alterations that have been reported across all types of lymphomas. [...] Read more.
Lymphomas encompass a diverse group of malignant lymphoid neoplasms. Over recent years much scientific effort has been undertaken to identify and understand molecular changes in lymphomas, resulting in a wide range of genetic alterations that have been reported across all types of lymphomas. As many of these changes are now incorporated into the World Health Organization’s defined criteria for the diagnostic evaluation of patients with lymphoid neoplasms, their accurate identification is crucial. Even if many alterations are not routinely evaluated in daily clinical practice, they may still have implications in risk stratification, treatment, prognosis or disease monitoring. Moreover, some alterations can be used for targeted treatment. Therefore, these advances in lymphoma molecular diagnostics in some cases have led to changes in treatment algorithms. Here, we give an overview of and discuss advances in molecular techniques in current clinical practice, as well as highlight some of them in a clinical context. Full article
(This article belongs to the Special Issue Advances in Lymphoma Molecular Diagnostics)

Other

Jump to: Research, Review

12 pages, 580 KiB  
Systematic Review
The Need for Standardization in Next-Generation Sequencing Studies for Classic Hodgkin Lymphoma: A Systematic Review
by Antonio Santisteban-Espejo, Irene Bernal-Florindo, Jose Perez-Requena, Lidia Atienza-Cuevas, Julia Moran-Sanchez, María del Carmen Fernandez-Valle, Raquel Romero-Garcia and Marcial Garcia-Rojo
Diagnostics 2022, 12(4), 963; https://doi.org/10.3390/diagnostics12040963 - 12 Apr 2022
Cited by 5 | Viewed by 1870
Abstract
Classic Hodgkin lymphoma (cHL) constitutes a B cell-derived neoplasm defined by a scarce tumoral population, termed Hodgkin and Reed–Sternberg (HRS) cells, submerged into a histologically heterogeneous microenvironment. The paucity of HRS cells has historically hampered genetic studies, rendering the identification of the recurrent [...] Read more.
Classic Hodgkin lymphoma (cHL) constitutes a B cell-derived neoplasm defined by a scarce tumoral population, termed Hodgkin and Reed–Sternberg (HRS) cells, submerged into a histologically heterogeneous microenvironment. The paucity of HRS cells has historically hampered genetic studies, rendering the identification of the recurrent genetic lesions and molecular pathways deregulated in this lymphoma difficult. The advent of high-throughput sequencing methods such as next-generation sequencing (NGS) could sensibly optimize the identification of the mutational landscape of cHL. However, there is no current consensus either in the design of panels for targeted NGS or in its most relevant clinical applications. In this work, we systematically review the current state of NGS studies of cHL, stressing the need for standardization both in the candidate genes to be analyzed and the bioinformatic pipelines. As different institutions have developed and implemented their own customized NGS-based protocols, to compare and systematically review the major findings of this ongoing research area could be of added value for centers that routinely perform diagnostic, monitoring and genotyping strategies in cHL samples. The results of this systematic review should contribute to the interdepartmental harmonization and achievement of a consensus in the current clinical applications of NGS studies of cHL. Full article
(This article belongs to the Special Issue Advances in Lymphoma Molecular Diagnostics)
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