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Zeng Y, Wei R, Bao L, Xue T, Qin Y, Ren M, Bai Q, Yao Q, Yu C, Chen C, Wei P, Yu B, Cao J, Li X, Zhang Q, Zhou X. Characteristics and Clinical Value of MYC , BCL2, and BCL6 Rearrangement Detected by Next-generation Sequencing in DLBCL. Am J Surg Pathol 2024; 48:919-929. [PMID: 38937822 PMCID: PMC11251499 DOI: 10.1097/pas.0000000000002258] [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] [Indexed: 06/29/2024]
Abstract
MYC , BCL2, and BCL6 rearrangements are clinically important events of diffuse large B-cell lymphoma (DLBCL). The ability and clinical value of targeted next-generation sequencing (NGS) in the detection of these rearrangements in DLBCL have not been fully determined. We performed targeted NGS (481-gene-panel) and break-apart FISH of MYC , BCL2, and BCL6 gene regions in 233 DLBCL cases. We identified 88 rearrangements (16 MYC ; 20 BCL2 ; 52 BCL6 ) using NGS and 96 rearrangements (28 MYC ; 20 BCL2 ; 65 BCL6 ) using FISH. The consistency rates between FISH and targeted NGS for the detection of MYC , BCL2, and BCL6 rearrangements were 93%, 97%, and 89%, respectively. FISH-cryptic rearrangements (NGS+/FISH-) were detected in 7 cases (1 MYC ; 3 BCL2 ; 2 BCL6 ; 1 MYC::BCL6 ), mainly caused by small chromosomal insertions and inversions. NGS-/FISH+ were detected in 38 cases (14 MYC ; 4 BCL2 ; 20 BCL6 ).To clarify the cause of the inconsistencies, we selected 17 from the NGS-/FISH+ rearrangements for further whole genome sequencing (WGS), and all 17 rearrangements were detected with break points by WGS. These break points were all located outside the region covered by the probe of targeted NGS, and most (16/17) were located in the intergenic region. These results indicated that targeted NGS is a powerful clinical diagnostics tool for comprehensive MYC , BCL2, and BCL6 rearrangement detection. Compared to FISH, it has advantages in describing the break point distribution, identifying uncharacterized partners, and detecting FISH-cryptic rearrangements. However, the lack of high-sensitivity caused by insufficient probe coverage is the main limitation of the current technology.
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Affiliation(s)
- Yupeng Zeng
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Ran Wei
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Longlong Bao
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Tian Xue
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Yulan Qin
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu
| | - Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Qianming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Qianlan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Chengli Yu
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Chen Chen
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Ping Wei
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Baohua Yu
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Junning Cao
- Department of Oncology, Shanghai Medical College
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoqiu Li
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
| | - Qunling Zhang
- Department of Oncology, Shanghai Medical College
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center
- Department of Oncology, Shanghai Medical College
- Institute of Pathology, Fudan University
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Yan Z, Yao ZH, Yao SN, Zhao S, Wang HY, Chu JF, Xu YL, Zhang JY, Wei B, Zheng JW, Xia QX, Wu DY, Luo XF, Zhou WP, Liu YY. [A consistency comparison between next-generation sequencing and the FISH method for gene rearrangement detection in B-cell lymphomas]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2024; 45:561-565. [PMID: 39134487 PMCID: PMC11310812 DOI: 10.3760/cma.j.cn121090-20231225-00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Indexed: 12/06/2024]
Abstract
Objective: To compare the consistency of lymphoma multigene detection panels based on next-generation sequencing (NGS) with FISH detection of B-cell lymphoma gene rearrangement. Methods: From January 2019 to May 2023, fusion genes detected by lymphoma-related 413 genes that targeted capture sequencing of 489 B-cell lymphoma tissues embedded in paraffin were collected from Henan Cancer Hospital, and the results were compared with simultaneous FISH detection of four break/fusion genes: BCL2, BCL6, MYC, and CCND1. Consistency was defined as both methods yielding positive or negative results for the same sample. The relationship between fusion mutation abundance in NGS and the positivity rate of cells in FISH was also analyzed. Results: Kappa consistency analysis revealed high consistency between NGS and FISH in detecting the four B-cell lymphoma-related gene rearrangement (P<0.001 for all) ; however, the detection rates of positive individuals differed for the four genes. Compared with FISH, NGS demonstrated a higher detection rate for BCL2 rearrangement, a lower detection rate for BCL6 and MYC rearrangement, and a similar detection rate for CCND1 rearrangement. No correlation was found between fusion mutation abundance in NGS and the positivity rate of cells in FISH. Conclusions: NGS and FISH detection of B-cell lymphoma gene rearrangement demonstrate overall good consistency. NGS is superior to FISH in detecting BCL2 rearrangement, inferior in detecting MYC rearrangement, and comparable in detecting CCND1 rearrangement.
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Affiliation(s)
- Z Yan
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - Z H Yao
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - S N Yao
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - S Zhao
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - H Y Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - J F Chu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - Y L Xu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - J Y Zhang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - B Wei
- Department of Molecular Pathology, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - J W Zheng
- Department of Molecular Pathology, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - Q X Xia
- Department of Pathology, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - D Y Wu
- Department of Pathology, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - X F Luo
- Department of Clinical Research Management, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - W P Zhou
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
| | - Y Y Liu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou 450008, China
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Menke JR, Aypar U, Bangs CD, Cook SL, Gupta S, Hasserjian RP, Kong CS, Lin O, Long SR, Ly A, Menke JAS, Natkunam Y, Ruiz-Cordero R, Spiteri E, Ye J, Zadeh SL, Gratzinger DA. Performance of MYC, BCL2, and BCL6 break-apart FISH in small biopsies with large B-cell lymphoma: a retrospective Cytopathology Hematopathology Interinstitutional Consortium study. Front Oncol 2024; 14:1408238. [PMID: 38903717 PMCID: PMC11187077 DOI: 10.3389/fonc.2024.1408238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Fluorescence in situ hybridization (FISH) is an essential ancillary study used to identify clinically aggressive subsets of large B-cell lymphomas that have MYC, BCL2, or BCL6 rearrangements. Small-volume biopsies such as fine needle aspiration biopsy (FNAB) and core needle biopsy (CNB) are increasingly used to diagnose lymphoma and obtain material for ancillary studies such as FISH. However, the performance of FISH in small biopsies has not been thoroughly evaluated or compared to surgical biopsies. Methods We describe the results of MYC, BCL2, and BCL6 FISH in a series of 222 biopsy specimens, including FNAB with cell blocks, CNBs, and surgical excisional or incisional biopsies from 208 unique patients aggregated from 6 academic medical centers. A subset of patients had FNAB followed by a surgical biopsy (either CNB or excisional biopsy) obtained from the same or contiguous anatomic site as part of the same clinical workup; FISH results were compared for these paired specimens. Results FISH had a low hybridization failure rate of around 1% across all specimen types. FISH identified concurrent MYC and BCL2 rearrangements in 20 of 197 (10%) specimens and concurrent MYC and BCL6 rearrangements in 3 of 182 (1.6%) specimens. The paired FNAB and surgical biopsy specimens did not show any discrepancies for MYC or BCL2 FISH; of the 17 patients with 34 paired cytology and surgical specimens, only 2 of the 49 FISH probes compared (4% of all comparisons) showed any discrepancy and both were at the BCL6 locus. One discrepancy was due to necrosis of the CNB specimen causing a false negative BCL6 FISH result when compared to the FNAB cell block that demonstrated a BCL6 rearrangement. Discussion FISH showed a similar hybridization failure rate in all biopsy types. Ultimately, MYC, BCL2, or BCL6 FISH showed 96% concordance when compared across paired cytology and surgical specimens, suggesting FNAB with cell block is equivalent to other biopsy alternatives for evaluation of DLBCL or HGBCL FISH testing.
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Affiliation(s)
- Joshua R. Menke
- Division of Hematopathology, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Umut Aypar
- Division of Cytogenetics, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Charles D. Bangs
- Division of Cytogenetics, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Stephen L. Cook
- Department of Laboratory Medicine, San Francisco Veterans Administration Health Care System, San Francisco, CA, United States
| | - Srishti Gupta
- Division of Hematopathology, Department of Pathology, Stanford University, Stanford, CA, United States
- Division of Hematopathology, Department of Laboratory Medicine, San Francisco, CA, United States
| | - Robert P. Hasserjian
- Division of Hematopathology, Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | - Christina S. Kong
- Division of Cytopathology, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Oscar Lin
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Steven R. Long
- Division of Cytopathology, Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Amy Ly
- Division of Cytopathology, Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | | | - Yasodha Natkunam
- Division of Hematopathology, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Roberto Ruiz-Cordero
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Divisons of Molecular Genetic Pathology, Cytopathology, and Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, FL, United States
| | - Elizabeth Spiteri
- Division of Cytogenetics, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Julia Ye
- Division of Cytopathology, Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Sara L. Zadeh
- Division of Cytopathology, Department of Pathology, University of Virginia, Charlottesville, VA, United States
| | - Dita A. Gratzinger
- Division of Hematopathology, Department of Pathology, Stanford University, Stanford, CA, United States
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Allahyar A, Pieterse M, Swennenhuis J, Los-de Vries GT, Yilmaz M, Leguit R, Meijers RWJ, van der Geize R, Vermaat J, Cleven A, van Wezel T, Diepstra A, van Kempen LC, Hijmering NJ, Stathi P, Sharma M, Melquiond ASJ, de Vree PJP, Verstegen MJAM, Krijger PHL, Hajo K, Simonis M, Rakszewska A, van Min M, de Jong D, Ylstra B, Feitsma H, Splinter E, de Laat W. Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing. Nat Commun 2021; 12:3361. [PMID: 34099699 PMCID: PMC8184748 DOI: 10.1038/s41467-021-23695-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/10/2021] [Indexed: 12/03/2022] Open
Abstract
In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens.
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Affiliation(s)
- Amin Allahyar
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark Pieterse
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - G Tjitske Los-de Vries
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | - Roos Leguit
- University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands
| | - Ruud W J Meijers
- University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands
| | | | - Joost Vermaat
- Leiden University Medical Centre, Department of Hematology, Leiden, the Netherlands
| | - Arjen Cleven
- Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands
| | - Tom van Wezel
- Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands
| | - Arjan Diepstra
- University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands
| | - Léon C van Kempen
- University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands
| | - Nathalie J Hijmering
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Phylicia Stathi
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Milan Sharma
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Adrien S J Melquiond
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paula J P de Vree
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | | | - Daphne de Jong
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | | | - Wouter de Laat
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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Wang X, Johnson V, Johnson L, Cook JR. RNA-Based next generation sequencing complements but does not replace fluorescence in situ hybridization studies for the classification of aggressive B-Cell lymphomas. Cancer Genet 2020; 252-253:43-47. [PMID: 33360122 DOI: 10.1016/j.cancergen.2020.12.004] [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: 08/27/2020] [Revised: 10/22/2020] [Accepted: 12/04/2020] [Indexed: 01/18/2023]
Abstract
Aggressive B-cell lymphomas are currently classified based in part upon the presence or absence of translocations involving BCL2, BCL6, and MYC. Most clinical laboratories employ fluorescence in situ hybridization (FISH) analysis for the detection of these rearrangements. The potential role of RNA-based sequencing approaches in the evaluation of malignant lymphoma is currently unclear. In this study, we performed RNA sequencing (RNAseq) in 37 cases of aggressive B-cell lymphomas using a commercially available next generation sequencing assay and compared results to previously performed FISH studies. RNAseq detected 1/7 MYC (14%), 3/8 BCL2 (38%) and 4/8 BCL6 (50%) translocations identified by FISH. RNAseq also detected 1 MYC/IGH fusion in a case not initially tested by FISH due to low MYC protein expression and 2 BCL6 translocations that were not detected by FISH. RNAseq identified the partner gene in each detected rearrangement, including a novel EIF4G1-BCL6 rearrangement. In summary, RNAseq complements FISH for the detection of rearrangements of BCL2, BCL6 and MYC in the evaluation and classification of aggressive B-cell lymphomas by detecting rearrangements that may be cryptic by FISH methods and by identifying the rearrangement partner genes. Detection of these clinically important translocations may be optimized by combined use of FISH and RNAseq.
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Affiliation(s)
- Xiaoqiong Wang
- Department of Laboratory Medicine, Robert J Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, United States
| | | | | | - James R Cook
- Department of Laboratory Medicine, Robert J Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, United States.
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Evolving insights into the genomic complexity and immune landscape of diffuse large B-cell lymphoma: opportunities for novel biomarkers. Mod Pathol 2020; 33:2422-2436. [PMID: 32620919 DOI: 10.1038/s41379-020-0616-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 12/18/2022]
Abstract
Recently, comprehensive genomic analyses have allowed a better molecular characterization of diffuse large B-cell lymphoma (DLBCL), offering novel opportunities in patient risk stratification and management. In the era of precision medicine, this has allowed us to move closer toward a more promising therapeutic outcome in the setting of DLBCL. In this review, we highlight the newly reported heterogeneous mutational landscapes of DLBCL (from two whole-exome sequencing studies, and from a more recent work targeting a 293-gene of a hematologic malignancy-designed panel. Altogether, these studies provide further evidence of the clinical applicability of genomic tests. We also briefly review established biomarkers in DLBCL (e.g., MYC and TP53), and our understanding of the germinal center cell reaction, including its epigenetic regulation, emphasizing some of the key epigenetic modifiers that play a role in lymphomagenesis, with available therapeutic targets. In addition, we present current data regarding the role of immune landscapes in DLBCL (inflamed versus non-inflamed), how the recently defined molecular DLBCL subtypes may affect the cellular composition of the tumor microenvironment and the function of the immune cells, and how this new knowledge may result in promising therapeutic approaches in the near future.
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