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Østergaard S, Schejbel L, Breinholt MF, Pedersen MØ, Hammer T, Munksgaard L, Nørgaard P, Høgdall E, Gjerdrum LMR, Nielsen TH. Mutational landscape in Waldenström macroglobulinemia evaluated using a next-generation sequencing lymphoma panel in routine clinical practice. Leuk Lymphoma 2024; 65:758-767. [PMID: 38340359 DOI: 10.1080/10428194.2024.2313623] [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: 06/26/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Next-generation sequencing (NGS) affords comprehensive insights into the genomic landscape of lymphomas. We examined the mutational pattern in patients with Waldenström macroglobulinemia (WM) or lymphoplasmacytic lymphoma (LPL) as well as the diagnostic and clinical utility of a tailored NGS lymphoma panel. A consecutive series of 45 patients was reviewed and NGS analysis was performed as part of a routine diagnostic setup. The custom designed NGS panel assayed all coding sequences of 59 genes of known clinical significance in lymphoid neoplasms. The most frequently mutated genes were MYD88, CXCR4, BIRC3, CD79B, and ARID1A. Additional somatic mutations were detected in 17 genes with four mutations categorized as pathogenic or likely pathogenic. BIRC3 and TP53 mutations were associated with adverse clinical phenotypes. NGS performance for the MYD88L265P variant was 96% when compared to qPCR. In conclusion, targeted NGS provided important diagnostic and prognostic information in a routine clinical setting.
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Affiliation(s)
- Simon Østergaard
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Lone Schejbel
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Mette Ølgod Pedersen
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Troels Hammer
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Lars Munksgaard
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Peter Nørgaard
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
- Department of Pathology, Hvidovre Hospital, Hvidovre, Denmark
| | - Estrid Høgdall
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lise Mette Rahbek Gjerdrum
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Torsten Holm Nielsen
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Danish Medicines Agency, Copenhagen, Denmark
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Artymiuk CJ, Basu S, Koganti T, Tandale P, Balan J, Dina MA, Barr Fritcher EG, Wu X, Ashworth T, He R, Viswanatha DS. Clinical Validation of a Targeted Next-Generation Sequencing Panel for Lymphoid Malignancies. J Mol Diagn 2024:S1525-1578(24)00077-1. [PMID: 38582399 DOI: 10.1016/j.jmoldx.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/16/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
Lymphoid malignancies are a heterogeneous group of hematological disorders characterized by a diverse range of morphologic, immunophenotypic, and clinical features. Next-generation sequencing (NGS) is increasingly being applied to delineate the complex nature of these malignancies and identify high-value biomarkers with diagnostic, prognostic, or therapeutic benefit. However, there are various challenges in using NGS routinely to characterize lymphoid malignancies, including pre-analytic issues, such as sequencing DNA from formalin-fixed, paraffin-embedded tissue, and optimizing the bioinformatic workflow for accurate variant calling and filtering. This study reports the clinical validation of a custom capture-based NGS panel to test for molecular markers in a range of lymphoproliferative diseases and histiocytic neoplasms. The fully validated clinical assay represents an accurate and sensitive tool for detection of single-nucleotide variants and small insertion/deletion events to facilitate the characterization and management of patients with hematologic cancers specifically of lymphoid origin.
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Affiliation(s)
- Cody J Artymiuk
- Molecular Hematopathology Laboratory, Mayo Clinic, Rochester, Minnesota.
| | - Shubham Basu
- Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Tejaswi Koganti
- Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | | | - Michelle A Dina
- Molecular Hematopathology Laboratory, Mayo Clinic, Rochester, Minnesota
| | | | - Xianglin Wu
- Clinical Genome Sequencing Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Taylor Ashworth
- Clinical Genome Sequencing Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Rong He
- Hematopathology Division, Mayo Clinic, Rochester, Minnesota
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Breinholt MF, Schejbel L, Gang AO, Nielsen TH, Pedersen LM, Høgdall E, Nørgaard P. Next generation sequencing in routine diagnostics of mature non-Hodgkin's B-cell lymphomas. Eur J Haematol 2023; 111:583-591. [PMID: 37452559 DOI: 10.1111/ejh.14048] [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: 04/21/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
INTRODUCTION Integration of molecular characterization of lymphomas in clinical diagnostics may improve subclassification and risk-stratification, and we implemented a next generation sequencing (NGS) analysis as part of routine diagnostic work-up of all mature B-cell non-Hodgkin's lymphoma (B-NHL). Here, we present data of mutational profiles with potential complementary diagnostic, prognostic, and predictive value detected in our consecutive non-selected cohort of B-NHL patients. METHODS NGS results from 298 patients with both newly diagnosed and relapsed/refractory disease were included as a single center study. NGS was performed as routine analysis together with standard diagnostic work-up using a custom-made amplicon PCR-based multiplex NGS panel covering all coding exons and consensus splice sites in 59 genes. RESULTS Mutations were detected in 94% of the 298 samples. Most lymphomas could be classified definitively, but 24 cases were classified as small B-cell lymphomas without defining characteristics. Of these, 50% (12/24 cases) could retrospectively be assigned a likely diagnostic subtype according to mutational findings. CONCLUSION Implementation of a 59 gene exome sequencing panel added diagnostic value to 50% of unclassified cases and provided in 94% of the cases possible biomarkers for disease monitoring as well as potential diagnostic, prognostic, and predictive markers for future studies.
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Affiliation(s)
| | - Lone Schejbel
- Department of Pathology, Herlev-Gentofte Hospital, Herlev, Denmark
| | - Anne Ortved Gang
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Torsten Holm Nielsen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Danish Medicines Agency, Copenhagen, Denmark
| | - Lars Møller Pedersen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev-Gentofte Hospital, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peter Nørgaard
- Department of Pathology, Herlev-Gentofte Hospital, Herlev, Denmark
- Department of Pathology, Hvidovre Hospital, Hvidovre, Denmark
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Fei F, Natkunam Y, Zehnder JL, Stehr H, Gratzinger D. Diagnostic Impact of Next-Generation Sequencing Panels for Lymphoproliferative Neoplasms on Small-Volume Biopsies. Am J Clin Pathol 2022; 158:345-361. [PMID: 35552630 DOI: 10.1093/ajcp/aqac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We investigated the feasibility and utility of next-generation sequencing (NGS)-based targeted somatic mutation panels and IG/TR gene rearrangement assays in the diagnosis of lymphoproliferative disorders (LPDs) in small-volume biopsies. MATERIALS We performed a retrospective, single-institution review of all NGS assays requested over a 3-year period by hematopathologists for diagnostic purposes on small-volume biopsies. RESULTS We identified 59 small-volume biopsies. The TR assay was most commonly requested (42 [71%]), followed by the somatic mutation panel (32 [54%]) and IG assay (26 [44%]). NGS studies were associated with a change in the diagnostic line in about half of cases (28 [47%]) and in a change in the likelihood of a diagnosis in a further 16 cases (27%); there was no diagnostic impact of NGS testing in 15 cases (25%). CONCLUSIONS Implementation of NGS panel somatic mutation or IG/TR gene rearrangement assays on small-volume biopsies contributes to the diagnosis of LPDs in the majority of select cases for diagnostic purposes. The molecular diagnosis is considered in the context of the clinical, histologic, and immunophenotypic findings and does not by itself lead to a definitive diagnosis in small-volume biopsies.
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Affiliation(s)
- Fei Fei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dita Gratzinger
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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Identification of a Cancer-Predisposing Germline POT1 p.Ile49Metfs*7 Variant by Targeted Sequencing of a Splenic Marginal Zone Lymphoma. Genes (Basel) 2022; 13:genes13040591. [PMID: 35456397 PMCID: PMC9028718 DOI: 10.3390/genes13040591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Germline disruptive variants in Protection of Telomeres 1 (POT1) predispose to a wide variety of cancers, including melanoma, chronic lymphocytic leukemia (CLL), Hodgkin lymphoma, myeloproliferative neoplasms, and glioma. We report the first case of splenic marginal zone lymphoma (SMZL) arising in a patient with a germline POT1 variant: a 65-year-old male with an extensive history of cancer, including melanoma and papillary thyroid carcinoma, who presented with circulating atypical lymphocytosis. Bone marrow biopsy revealed 20% involvement by a CD5−CD10− B-cell lymphoma that was difficult to classify. During the clinical workup of his low-grade lymphoma, targeted next-generation sequencing (NGS) identified POT1 p.I49Mfs*7 (NM_015450:c. 147delT) at a variant allele frequency (VAF) of 51%. NGS of skin fibroblasts confirmed the POT1 variant was germline. This likely pathogenic POT1 loss-of-function variant has only been reported once before as a germline variant in a patient with glioma and likely represents one of the most deleterious germline POT1 variants ever linked to familial cancer. The spectrum of cancers associated with germline pathogenic POT1 variants (i.e., autosomal dominant POT1 tumor predisposition syndrome) should potentially be expanded to include SMZL, a disease often associated with the loss of chromosome 7q: the location of the POT1 genetic locus (7q31.33).
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