1
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Gagnon MF, Bruehl FK, Sill DR, Meyer RG, Greipp PT, Hoppman NL, Xu X, Baughn LB, Peterson JF, McPhail ED, Ketterling RP, King RL. Cytogenetic and pathologic characterization of MYC-rearranged B-cell lymphomas in pediatric and young adult patients. J Hematop 2024; 17:51-61. [PMID: 38561469 PMCID: PMC11127862 DOI: 10.1007/s12308-024-00579-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
MYC-rearranged B-cell lymphoma (BCL) in the pediatric/young adult (YA) age group differs substantially in disease composition from adult cohorts. However, data regarding the partner genes, concurrent rearrangements, and ultimate diagnoses in these patients is scarce compared to that in adult cohorts. We aimed to characterize the spectrum of MYC-rearranged (MYC-R) mature, aggressive BCL in the pediatric/YA population. A retrospective study of morphologic, immunophenotypic, and fluorescence in situ hybridization (FISH) results of patients age ≤ 30 years with suspected Burkitt lymphoma (BL), diffuse large B-cell lymphoma (DLBCL) or high-grade B-cell lymphoma (HGBCL), and a MYC-R by FISH between 2013-2022 was performed. Two-hundred fifty-eight cases (129 (50%) pediatric (< 18 years) and 129 (50%) YA (18-30 years)) were included. Most MYC-R BCL in pediatric (89%) and YA (66%) cases were BL. While double-hit (DH) cytogenetics (MYC with BCL2 and/or BCL6-R, HGBCL-DH) was rare in the pediatric population (2/129, 2%), HGBCL-DH increased with age and was identified in 17/129 (13%) of YA cases. Most HGBCL-DH had MYC and BCL6-R, while BCL2-R were rare in both groups (3/258, 1%). MYC-R without an IG partner was more common in the YA group (14/116 (12%) vs 2/128 (2%), p = 0.001). The pediatric to YA transition is characterized by decreasing frequency in BL and increasing genetic heterogeneity of MYC-R BCL, with emergence of DH-BCL with MYC and BCL6-R. FISH to evaluate for BCL2 and BCL6 rearrangements is likely not warranted in the pediatric population but should continue to be applied in YA BCL.
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Affiliation(s)
- Marie-France Gagnon
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Frido K Bruehl
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Daniel R Sill
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Reid G Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen D McPhail
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rebecca L King
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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2
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Koduru P, Chen W, Fuda F, Kaur G, Awan F, John S, Garcia R, Gagan J. RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241230262. [PMID: 38371338 PMCID: PMC10874141 DOI: 10.1177/2632010x241230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
Background Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.
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Affiliation(s)
- Prasad Koduru
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weina Chen
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Franklin Fuda
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gurbakhash Kaur
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Farrukh Awan
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel John
- Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rolando Garcia
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey Gagan
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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3
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Coccaro N, Anelli L, Zagaria A, Tarantini F, Cumbo C, Tota G, Minervini CF, Minervini A, Conserva MR, Redavid I, Parciante E, Macchia MG, Specchia G, Musto P, Albano F. Feasibility of Optical Genome Mapping in Cytogenetic Diagnostics of Hematological Neoplasms: A New Way to Look at DNA. Diagnostics (Basel) 2023; 13:diagnostics13111841. [PMID: 37296693 DOI: 10.3390/diagnostics13111841] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Optical genome mapping (OGM) is a new genome-wide technology that can reveal both structural genomic variations (SVs) and copy number variations (CNVs) in a single assay. OGM was initially employed to perform genome assembly and genome research, but it is now more widely used to study chromosome aberrations in genetic disorders and in human cancer. One of the most useful OGM applications is in hematological malignancies, where chromosomal rearrangements are frequent and conventional cytogenetic analysis alone is insufficient, necessitating further confirmation using ancillary techniques such as fluorescence in situ hybridization, chromosomal microarrays, or multiple ligation-dependent probe amplification. The first studies tested OGM efficiency and sensitivity for SV and CNV detection, comparing heterogeneous groups of lymphoid and myeloid hematological sample data with those obtained using standard cytogenetic diagnostic tests. Most of the work based on this innovative technology was focused on myelodysplastic syndromes (MDSs), acute myeloid leukemia (AML), and acute lymphoblastic leukemia (ALL), whereas little attention was paid to chronic lymphocytic leukemia (CLL) or multiple myeloma (MM), and none was paid to lymphomas. The studies showed that OGM can now be considered as a highly reliable method, concordant with standard cytogenetic techniques but able to detect novel clinically significant SVs, thus allowing better patient classification, prognostic stratification, and therapeutic choices in hematological malignancies.
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Affiliation(s)
- Nicoletta Coccaro
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luisa Anelli
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Antonella Zagaria
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Tarantini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Cosimo Cumbo
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giuseppina Tota
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Crescenzio Francesco Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Angela Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Maria Rosa Conserva
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Immacolata Redavid
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Elisa Parciante
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Maria Giovanna Macchia
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giorgina Specchia
- School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Albano
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari "Aldo Moro", 70124 Bari, Italy
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Tang G, Li S, Toruner GA, Jain P, Tang Z, Hu S, Xu J, Cheng J, Robinson M, Vega F, Medeiros LJ. Clinical impact of 5 'MYC or 3 'MYC gain/loss detected by FISH in patients with aggressive B-cell lymphomas. Cancer Genet 2023; 272-273:1-8. [PMID: 36566629 DOI: 10.1016/j.cancergen.2022.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/07/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
FISH analysis using MYC break-apart probes is a widely used technique to assess for MYC rearrangement (MYC-R). Occasionally, FISH results in atypical signal patterns, such as gain or loss of 5'MYC or 3'MYC. The clinical impact and/or relationship of these atypical signal patterns to MYC-R are unknown. In this study, we assessed 35 patients who had aggressive B-cell lymphomas and exhibited atypical FISH signal patterns: 3'MYC deletion (n = 16) or 3'MYC deletion plus 5'MYC amplification (n = 5), 5'MYC gain (n = 10), 5'MYC deletion (n = 3), and 3'MYC gain (n = 1). For comparison, we also included 9 patients who showed an unbalanced MYC-R. Patients with 5'MYC gain showed MYC expression and were often refractory to chemotherapy (n = 7) or had early relapse (n = 2). By contrast, lymphomas with 3'MYC deletion were negative or had low expression of MYC (16 of 18), and patients often responded to chemotherapy (16 of 19). The median event-free survival was 24, 6, and 4 months for patients with 3'MYC deletion, 5'MYC gain and unbalanced MYC-R, respectively (p = 0.0048). We conclude that 5'MYC gain is associated with MYC expression and a poorer prognosis and likely represents an unbalanced MYC-R. By contrast, 3'MYC deletions are not associated with MYC expression or a poorer prognosis and this finding may be unrelated to MYC-R.
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Affiliation(s)
- Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Shaoying Li
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Preetesh Jain
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shimin Hu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Xu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joanne Cheng
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melissa Robinson
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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5
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Pitel BA, Zuckerman EZ, Baughn LB. Mate Pair Sequencing: Next-Generation Sequencing for Structural Variant Detection. Methods Mol Biol 2023; 2621:127-149. [PMID: 37041444 DOI: 10.1007/978-1-0716-2950-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Structural variant detection by next-generation sequencing (NGS) methods have a higher molecular resolution than conventional cytogenetic techniques (Aypar et al., Eur J Haematol 102(1):87-96, 2019; Smadbeck et al., Blood Cancer J 9(12):103, 2019) and are particularly helpful in characterizing genomic rearrangements. Mate pair sequencing (MPseq) leverages a unique library preparation chemistry involving circularization of long DNA fragments, allowing for a unique application of paired-end sequencing of reads that are expected to map 2-5 kb apart in the genome. The unique orientation of the reads allows the user to estimate the location of breakpoints involved in a structural variant either within the sequenced reads or between the two reads. The precision of structural variant and copy number detection by this method allows for characterization of cryptic and complex rearrangements that may be otherwise undetectable by conventional cytogenetic methods (Singh et al., Leuk Lymphoma 60(5):1304-1307, 2019; Peterson et al., Blood Adv 3(8):1298-1302, 2019; Schultz et al., Leuk Lymphoma 61(4):975-978, 2020; Peterson et al., Mol Case Studies 5(2), 2019; Peterson et al., Mol Case Studies 5(3), 2019).
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Affiliation(s)
- Beth A Pitel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | | | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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6
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García R, Hussain A, Chen W, Wilson K, Koduru P. An artificial intelligence system applied to recurrent cytogenetic aberrations and genetic progression scores predicts
MYC
rearrangements in large B‐cell lymphoma. EJHAEM 2022; 3:707-721. [PMID: 36051032 PMCID: PMC9421965 DOI: 10.1002/jha2.451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/05/2022] [Accepted: 04/09/2022] [Indexed: 11/20/2022]
Abstract
Diffuse large B‐cell lymphoma (DLBCL), the most common type of non‐Hodgkin lymphoma, is characterized by MYC rearrangements (MYC R) in up to 15% of cases, and these have unfavorable prognosis. Due to cryptic rearrangements and variations in MYC breakpoints, MYC R may be undetectable by conventional methods in up to 10%–15% of cases. In this study, a retrospective proof of concept study, we sought to identify recurrent cytogenetic aberrations (RCAs), generate genetic progression scores (GP) from RCAs and apply these to an artificial intelligence (AI) algorithm to predict MYC status in the karyotypes of published cases. The developed AI algorithm is validated for its performance on our institutional cases. In addition, cytogenetic evolution pattern and clinical impact of RCAs was performed. Chromosome losses were associated with MYC‐, while partial gain of chromosome 1 was significant in MYC R tumors. MYC R was the sole driver alteration in MYC‐rearranged tumors, and evolution patterns revealed RCAs associated with gene expression signatures. A higher GPS value was associated with MYC R tumors. A subsequent AI algorithm (composed of RCAs + GPS) obtained a sensitivity of 91.4 and specificity of 93.8 at predicting MYC R. Analysis of an additional 59 institutional cases with the AI algorithm showed a sensitivity and specificity of 100% and 87% each with positive predictive value of 92%, and a negative predictive value of 100%. Cases with a MYC R showed a shorter survival.
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Affiliation(s)
- Rolando García
- Department of Pathology UT Southwestern Medical Center Dallas Texas USA
| | - Anas Hussain
- Deccan College of Medical Sciences Hyderabad India
| | - Weina Chen
- Department of Pathology UT Southwestern Medical Center Dallas Texas USA
| | - Kathleen Wilson
- Department of Pathology UT Southwestern Medical Center Dallas Texas USA
| | - Prasad Koduru
- Department of Pathology UT Southwestern Medical Center Dallas Texas USA
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7
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Akkari YM, Baughn LB, Dubuc AM, Smith AC, Mallo M, Dal Cin P, Diez Campelo M, Gallego MS, Granada Font I, Haase DT, Schlegelberger B, Slavutsky I, Mecucci C, Levine RL, Hasserjian RP, Solé F, Levy B, Xu X. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood 2022; 139:2273-2284. [PMID: 35167654 PMCID: PMC9710485 DOI: 10.1182/blood.2021014309] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Cytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been shown to drive tumorigenesis, define diseases, and guide treatment. Technological innovations in sequencing have ushered in our present-day clinical genomics era. With recent publications highlighting novel sequencing technologies as alternatives to conventional cytogenetic approaches, we, an international consortium of laboratory geneticists, pathologists, and oncologists, describe herein the advantages and limitations of both conventional chromosome banding and novel sequencing technologies and share our considerations on crucial next steps to implement these novel technologies in the global clinical setting for a more accurate cytogenetic evaluation, which may provide improved diagnosis and treatment management. Considering the clinical, logistic, technical, and financial implications, we provide points to consider for the global evolution of cytogenetic testing.
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Affiliation(s)
- Yassmine M.N. Akkari
- Departments of Cytogenetics and Molecular Pathology, Legacy Health, Portland, OR
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Adam C. Smith
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Mar Mallo
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Maria Diez Campelo
- Hematology Department University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Marta S. Gallego
- Laboratory of Cytogenetics and Molecular Cytogenetics, Department of Clinical Pathology, Italian Hospital, Buenos Aires, Argentina
| | - Isabel Granada Font
- Hematology Laboratory, Germans Trias i Pujol University Hospital–Catalan Institute of Oncology, Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Detlef T. Haase
- Clinics of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Irma Slavutsky
- Laboratory Genetics of Lymphoid Malignancies, Institute of Experimental Medicine, Buenos Aires, Argentina
| | - Cristina Mecucci
- Laboratory of Cytogenetics and Molecular Medicine, Hematology University of Perugia, Perugia, Italy
| | - Ross L. Levine
- Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Francesc Solé
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Brynn Levy
- College of Physicians and Surgeons, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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8
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Cryptic MYC insertions in Burkitt lymphoma: New data and a review of the literature. PLoS One 2022; 17:e0263980. [PMID: 35167621 PMCID: PMC8846522 DOI: 10.1371/journal.pone.0263980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022] Open
Abstract
The occurrence of MYC-negative Burkitt lymphoma (BL) has been discussed for many years. The real frequency of the MYC insertion in MYC-negative BL is still unknown. Fine-needle aspiration biopsies of 108 consecutive patients with clinicopathologically suspected BL (suspBL) were evaluated by flow cytometry, classical cytogenetics, and fluorescence in situ hybridization (FISH). We found 12 cases (11%) without the MYC rearrangement by FISH with a MYC breakapart probe: two patients (1.9%) with cryptic MYC/IGH fusion (finally diagnosed as BL) and 10 patients (9.3%) with 11q gain/loss (finally diagnosed as Burkitt-like lymphoma with 11q aberration). The exact breakpoints of the cryptic MYC/IGH were investigated by next-generation sequencing. The MYC insertions’ breakpoints were identified in PVT1 in the first case, and 42 kb upstream of 5′MYC in the second case. To date, a molecular characterization of the MYC insertion in BL has only been reported in one case. Detailed descriptions of our MYC insertions in a routinely and consecutively diagnosed suspBL cohort will contribute to resolving the issue of MYC negativity in BL. In our opinion, the presence of the MYC insertions in BL and other lymphomas might be underestimated, because routine genetic diagnostics are usually based on FISH only, without karyotyping.
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9
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Sharma P, Singal S, Costello P, Krishnan K. Burkitt lymphoma: interpreting FISH testing for MYC gene rearrangements. BMJ Case Rep 2022; 15:e246687. [PMID: 35135797 PMCID: PMC8830099 DOI: 10.1136/bcr-2021-246687] [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] [Accepted: 01/13/2022] [Indexed: 11/04/2022] Open
Abstract
Burkitt lymphoma is a highly aggressive B cell non-Hodgkin's lymphoma characterised by translocation of MYC gene on chromosome 8. This translocation is usually detected by fluorescent in-situ hybridisation (FISH) studies as part of routine diagnostic work-up and prognostication. FISH testing is commonly done with the break-apart probe (BAP). This case illustrates how this testing can be falsely negative. This patient is a young male diagnosed with Stage I low-risk Burkitt with FISH negative for MYC translocation initially on BAP testing. Additional testing with dual FISH probe detected MYC/IGH translocation. FISH testing using BAPs alone may be falsely negative for MYC translocations creating a diagnostic challenge and compromising the treatment approach and assessment of prognosis.
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Affiliation(s)
- Purva Sharma
- Department of Medical Oncology, East Tennessee State University, Johnson City, Tennessee, USA
| | - Sakshi Singal
- Department of Medical Oncology, East Tennessee State University, Johnson City, Tennessee, USA
| | - Patrick Costello
- Department of Watauga Pathology, East Tennessee State University, Johnson City, Tennessee, USA
| | - Koyamangalath Krishnan
- Division of Medical Oncology, Department of Internal Medicine, East Tennessee State University, Johnson City, Tennessee, USA
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10
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Sharma N, Smadbeck JB, Abdallah N, Zepeda-Mendoza C, Binder M, Pearce KE, Asmann YW, Peterson JF, Ketterling RP, Greipp PT, Leif Bergsagel P, Vincent Rajkumar S, Kumar SK, Baughn LB. The Prognostic Role of MYC Structural Variants Identified by NGS and FISH in Multiple Myeloma. Clin Cancer Res 2021; 27:5430-5439. [PMID: 34233962 PMCID: PMC8738776 DOI: 10.1158/1078-0432.ccr-21-0005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/16/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Structural variants (SV) of the MYC gene region are common in multiple myeloma and influence disease progression. However, the prognostic significance of different MYC SVs in multiple myeloma has not been clearly established. EXPERIMENTAL DESIGN We conducted a retrospective study of multiple myeloma comparing MYC SV subtypes identified by next-generation sequencing (NGS) and FISH to MYC expression and disease survival using 140 cases from Mayo Clinic and 658 cases from the MMRF CoMMpass study. RESULTS MYC SVs were found in 41% of cases and were classified into nine subtypes. A correlation between the presence of a MYC SV and increased MYC expression was identified. Among the nine MYC subtypes, the non-immunoglobulin (non-Ig) insertion subtype was independently associated with improved outcomes, while the Ig insertion subtype, specifically involving the IgL gene partner, was independently associated with poorer outcomes compared with other MYC SV subtypes. Although the FISH methodology failed to detect approximately 70% of all MYC SVs, those detected by FISH were associated with elevated MYC gene expression and poor outcomes suggesting a different pathogenic role for FISH-detected MYC subtypes compared with other MYC subtypes. CONCLUSIONS Understanding the impact of different MYC SVs on disease outcome is necessary for the reliable interpretation of MYC SVs in multiple myeloma. NGS approaches should be considered as a replacement technique for a more comprehensive evaluation of the multiple myeloma clone.
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Affiliation(s)
- Neeraj Sharma
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Nadine Abdallah
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | | | - Moritz Binder
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Kathryn E. Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Yan W. Asmann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL
| | - Jess F. Peterson
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rhett P. Ketterling
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Patricia T. Greipp
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - P. Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ
| | - S. Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Shaji K. Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Linda B. Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN,Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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11
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Guenzel AJ, Smadbeck JB, Golden CL, Williamson CM, Benevides Demasi JC, Vasmatzis G, Pearce KE, Olteanu H, Xu X, Hoppman NL, Greipp PT, Baughn LB, Ketterling RP, Peterson JF. Clinical utility of next generation sequencing to detect IGH/IL3 rearrangements [t(5;14)(q31.1;q32.1)] in B-lymphoblastic leukemia/lymphoma. Ann Diagn Pathol 2021; 53:151761. [PMID: 33991782 DOI: 10.1016/j.anndiagpath.2021.151761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/06/2021] [Indexed: 11/18/2022]
Abstract
The t(5;14)(q31.1;q32.1) associated with B-lymphoblastic leukemia/lymphoma (B-ALL/LBL) is a rare, recurrent genetic abnormality recognized as a distinct entity by the 2017 World Health Organization (WHO) classification. In these cases, the IGH enhancer region (14q32.1) is juxtaposed to the vicinity of the IL3 gene (5q31.1), resulting in increased production of interleukin-3 (IL3) and subsequently a characteristic reactive eosinophilia. B-ALL with t(5;14)(q31.1;q32.1) may have a low lymphoblast count that can complicate detection of t(5;14)(q31.1;q32.1) by conventional chromosome studies. We have identified four patients with IGH/IL3 rearrangements despite normal conventional chromosome studies in each case [one patient had a non-clonal t(5;14)(q31;q32) finding]. Fluorescence in situ hybridization utilizing a laboratory-developed IGH break-apart probe set identified IGH rearrangements in three of four cases, and a next generation sequencing (NGS) based assay, mate-pair sequencing (MPseq), was required to characterize the IGH/IL3 rearrangements in each case. Three patients demonstrated a balanced t(5;14)(q31.1;q32.1) while one patient had a cryptic insertion of the IL3 gene into the IGH region. These results demonstrate that NGS-based assays, such as MPseq, confer an advantage in the detection of IGH/IL3 rearrangements that are otherwise challenging to characterize by traditional cytogenetic methodologies.
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Affiliation(s)
- Adam J Guenzel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - James B Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States of America
| | - Crystal L Golden
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Cynthia M Williamson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Jonna C Benevides Demasi
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States of America
| | - Kathryn E Pearce
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Horatiu Olteanu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Xinjie Xu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Nicole L Hoppman
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Linda B Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Rhett P Ketterling
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America; Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Jess F Peterson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America.
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12
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Shah SI, D’Angelo CR, Kratz JD, Yang DT. Diagnostic challenges in an aggressive case of peripheralizing marginal zone lymphoma. Clin Case Rep 2020; 8:3303-3310. [PMID: 33363923 PMCID: PMC7752602 DOI: 10.1002/ccr3.3395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/07/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022] Open
Abstract
B-cell lymphomas with atypical presentation or immunophenotype pose diagnostic challenges. Conventional ancillary tests (cytogenetics, FISH) can help, but have technical limitations. New technologies such as mate-pair sequencing (MPSeq) offer a route around these technical limitations.
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Affiliation(s)
- Sujal I. Shah
- Department of PathologyUniversity of Wisconsin School of Medicine and Public HealthMadisonWIUSA
| | - Christopher R. D’Angelo
- Department of MedicineSection of Hematology/OncologyUniversity of Wisconsin School of Medicine and Public HealthMadisonWIUSA
| | - Jeremy D. Kratz
- Department of MedicineSection of Hematology/OncologyUniversity of Wisconsin School of Medicine and Public HealthMadisonWIUSA
| | - David T. Yang
- Department of PathologyUniversity of Wisconsin School of Medicine and Public HealthMadisonWIUSA
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13
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A practical approach to FISH testing for MYC rearrangements and brief review of MYC in aggressive B-cell lymphomas. J Hematop 2020. [DOI: 10.1007/s12308-020-00404-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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14
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Lopes JL, Webley M, Pitel BA, Pearce KE, Smadbeck JB, Johnson SH, Vasmatzis G, Sukov WR, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Finn L, Peterson JF. Characterizing false-positive fluorescence in situ hybridization results by mate-pair sequencing in a patient with chronic myeloid leukemia and progression to myeloid blast crisis. Cancer Genet 2020; 243:48-51. [PMID: 32272434 DOI: 10.1016/j.cancergen.2020.02.008] [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] [Received: 11/19/2019] [Revised: 01/23/2020] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
Traditional cytogenetic testing methodologies, including conventional chromosome analysis and fluorescence in situ hybridization (FISH), are invaluable for the detection or recurrent genetic abnormalities in various hematologic malignancies. However, technological advances, including a novel next-generation sequencing technique termed mate-pair sequencing (MPseq), continue to revolutionize the field of cytogenetics by enabling the characterization of structural variants at a significantly higher resolution compared to traditional methodologies. To illustrate the power of MPseq, we present a 27-year-old male diagnosed with chronic myeloid leukemia in myeloid blast crisis with multiple chromosomal abnormalities observed in all 20 metaphases from a peripheral blood specimen, including t(9;22)(q34;q11.2) and t(4;11)(q12;p15). Suspicious of a novel NUP98/PDGFRA fusion [t(4;11)(q12;p15)], break-apart FISH probe sets for the PDGFRA (4q12) and NUP98 (11p15.4) gene regions were performed and were both positive in approximately 86% of 200 interphase nuclei. However, subsequent MPseq testing revealed breakpoints located within the NUP98 gene and within an intergenic region (4q12) located between the CHIC2 and PDGFRA genes, indicating this 4;11 translocation does not result in the predicted NUP98/PDGFRA gene fusion as inferred from FISH and conventional chromosome results. This case demonstrates the clinical utility of MPseq, particularly for characterizing novel gene fusion events which may ultimately identify a false-positive FISH result.
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Affiliation(s)
- Jaime L Lopes
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Matthew Webley
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Beth A Pitel
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Kathryn E Pearce
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - James B Smadbeck
- Mayo Clinic, Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - Sarah H Johnson
- Mayo Clinic, Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - George Vasmatzis
- Mayo Clinic, Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, United States
| | - William R Sukov
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Patricia T Greipp
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Nicole L Hoppman
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Rhett P Ketterling
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Linda B Baughn
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Laura Finn
- Division of Hematology and Bone Marrow Transplant, Department of Internal Medicine, Ochsner Medical Center, New Orleans, LA, United States
| | - Jess F Peterson
- Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States.
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15
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The double-hit signature identifies double-hit diffuse large B-cell lymphoma with genetic events cryptic to FISH. Blood 2020; 134:1528-1532. [PMID: 31527075 DOI: 10.1182/blood.2019002600] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/08/2019] [Indexed: 12/24/2022] Open
Abstract
High-grade B-cell lymphomas with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/THs) include a group of diffuse large B-cell lymphomas (DLBCLs) with inferior outcomes after standard chemoimmunotherapy. We recently described a gene expression signature that identifies 27% of germinal center B-cell DLBCLs (GCB-DLBCLs) as having a double-hit-like expression pattern (DHITsig) and inferior outcomes; however, only half of these cases have both MYC and BCL2 translocations identifiable using standard breakapart fluorescence in situ hybridization (FISH). Here, 20 DHITsig+ GCB-DLBCLs apparently lacking MYC and/or BCL2 rearrangements underwent whole-genome sequencing. This revealed 6 tumors with MYC or BCL2 rearrangements that were cryptic to breakapart FISH. Copy-number analysis identified 3 tumors with MYC and 6 tumors with MIR17HG gains or amplifications, both of which may contribute to dysregulation of MYC and its downstream pathways. Focal deletions of the PVT1 promoter were observed exclusively among DHITsig+ tumors lacking MYC translocations; this may also contribute to MYC overexpression. These results highlight that FISH fails to identify all HGBL-DH/THs, while revealing a range of other genetic mechanisms potentially underlying MYC dysregulation in DHITsig+ DLBCL, suggesting that gene expression profiling is more sensitive for identifying the biology underlying poor outcomes in GCB-DLBCL.
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