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Gould C, McBean M, Thompson E, Lickiss J, Tiong IS, Westerman D, Blombery P. Observations from a national sample exchange program for molecular haematology testing. Pathology 2024; 56:540-547. [PMID: 38413254 DOI: 10.1016/j.pathol.2023.12.413] [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: 07/25/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 02/29/2024]
Abstract
External quality assessment programs (EQAP) for molecular haematology generally only assess the analytical phase of laboratory testing or provide limited evaluation of post-analytical components. We incorporated comprehensive post-analytical evaluation into an existing national inter-laboratory sample exchange program for molecular haematology due to the increasing complexity of diagnostic molecular testing and interpretation. We report key findings from four years of longitudinal data using this approach. Eighteen participating laboratories enrolled in an annual reciprocal sample exchange program from 2019-2022, which covered conventional and next-generation sequencing (NGS) assays. Participants submitted results on their laboratory information system-generated reports which then underwent central review. Reports were assessed according to consensus values and relevant national and international reporting standards and guidelines. A total of 680 reports were received. Laboratories had high concordance in the analytical phase of testing, with incorrect variant detection observed in a total of six of 680 (0.9%) reports. In contrast, post-analytical concordance was much lower, with at least one discordance observed in 28.9-57.6% of all conventional reports and 33.3-100% NGS reports. The most frequent post-analytical discordances were: (1) not including key technical information on reports (total 41.9% conventional, 47.2% NGS); (2) not using standard gene and variant nomenclature (total 28.2% conventional, 25.6% NGS). NGS reports also demonstrated discrepancies in variant classification (total 20.4%) and interpretation (total 10.2%). The rate of discrepancies generally improved year-on-year. Inter-laboratory concordance for molecular haematology testing is high in the analytical phase, however opportunities exist for improvement in the post-analytical phase. Given that result interpretation is crucial for clinical decision-making and that molecular testing is a complex and evolving field, we suggest that EQAPs should comprehensively evaluate both analytical and post-analytical components of laboratory performance in order to harmonise reporting and to support the accurate interpretation of molecular haematology tests.
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Affiliation(s)
- Clare Gould
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
| | - Michelle McBean
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Ella Thompson
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Jennifer Lickiss
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Ing Soo Tiong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - David Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
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Murciano-Goroff YR, Uppal M, Chen M, Harada G, Schram AM. Basket Trials: Past, Present, and Future. ANNUAL REVIEW OF CANCER BIOLOGY 2024; 8:59-80. [PMID: 38938274 PMCID: PMC11210107 DOI: 10.1146/annurev-cancerbio-061421-012927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Large-scale tumor molecular profiling has revealed that diverse cancer histologies are driven by common pathways with unifying biomarkers that can be exploited therapeutically. Disease-agnostic basket trials have been increasingly utilized to test biomarker-driven therapies across cancer types. These trials have led to drug approvals and improved the lives of patients while simultaneously advancing our understanding of cancer biology. This review focuses on the practicalities of implementing basket trials, with an emphasis on molecularly targeted trials. We examine the biologic subtleties of genomic biomarker and patient selection, discuss previous successes in drug development facilitated by basket trials, describe certain novel targets and drugs, and emphasize practical considerations for participant recruitment and study design. This review also highlights strategies for aiding patient access to basket trials. As basket trials become more common, steps to ensure equitable implementation of these studies will be critical for molecularly targeted drug development.
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Affiliation(s)
| | - Manik Uppal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Monica Chen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
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Tashkandi H, Younes IE. Advances in Molecular Understanding of Polycythemia Vera, Essential Thrombocythemia, and Primary Myelofibrosis: Towards Precision Medicine. Cancers (Basel) 2024; 16:1679. [PMID: 38730632 PMCID: PMC11083661 DOI: 10.3390/cancers16091679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Myeloproliferative neoplasms (MPNs), including Polycythemia Vera (PV), Essential Thrombocythemia (ET), and Primary Myelofibrosis (PMF), are characterized by the clonal proliferation of hematopoietic stem cells leading to an overproduction of hematopoietic cells. The last two decades have seen significant advances in our understanding of the molecular pathogenesis of these diseases, with the discovery of key mutations in the JAK2, CALR, and MPL genes being pivotal. This review provides a comprehensive update on the molecular landscape of PV, ET, and PMF, highlighting the diagnostic, prognostic, and therapeutic implications of these genetic findings. We delve into the challenges of diagnosing and treating patients with prognostic mutations, clonal evolution, and the impact of emerging technologies like next-generation sequencing and single-cell genomics on the field. The future of MPN management lies in leveraging these molecular insights to develop personalized treatment strategies, aiming for precision medicine that optimizes outcomes for patients. This article synthesizes current knowledge on molecular diagnostics in MPNs, underscoring the critical role of genetic profiling in enhancing patient care and pointing towards future research directions that promise to further refine our approach to these complex disorders.
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Affiliation(s)
- Hammad Tashkandi
- Department of Pathology and Laboratory Medicine, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Ismail Elbaz Younes
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, University of Minnesota, Minneapolis, MN 55455, USA;
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Church AJ, Akkari Y, Deeb K, Kolhe R, Lin F, Spiteri E, Wolff DJ, Shao L. Section E6.7-6.12 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in solid tumors. Genet Med 2024; 26:101070. [PMID: 38376505 DOI: 10.1016/j.gim.2024.101070] [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: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 02/21/2024] Open
Abstract
Clinical cytogenomic studies of solid tumor samples are critical to the diagnosis, prognostication, and treatment selection for cancer patients. An overview of current cytogenomic techniques for solid tumor analysis is provided, including standards for sample preparation, clinical and technical considerations, and documentation of results. With the evolving technologies and their application in solid tumor analysis, these standards now include sequencing technology and optical genome mapping, in addition to the conventional cytogenomic methods, such as G-banded chromosome analysis, fluorescence in situ hybridization, and chromosomal microarray analysis. This updated Section E6.7-6.12 supersedes the previous Section E6.5-6.8 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Alanna J Church
- Department of Pathology, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Kristin Deeb
- Department of Pathology, Emory University, Atlanta, GA
| | - Ravindra Kolhe
- Department of Pathology, Augusta University, Augusta, GA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, University of California at Los Angeles, Los Angeles, CA
| | | | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC
| | - Lina Shao
- Department of Pathology and Pediatrics, University of Michigan, Ann Arbor, MI
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Kwon R, Yeung CCS. Advances in next-generation sequencing and emerging technologies for hematologic malignancies. Haematologica 2024; 109:379-387. [PMID: 37584286 PMCID: PMC10828783 DOI: 10.3324/haematol.2022.282442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/17/2023] [Indexed: 08/17/2023] Open
Abstract
Innovations in molecular diagnostics have often evolved through the study of hematologic malignancies. Examples include the pioneering characterization of the Philadelphia chromosome by cytogenetics in the 1970s, the implementation of polymerase chain reaction for high-sensitivity detection and monitoring of mutations and, most recently, targeted next- generation sequencing to drive the prognostic and therapeutic assessment of leukemia. Hematologists and hematopath- ologists have continued to advance in the past decade with new innovations improving the type, amount, and quality of data generated for each molecule of nucleic acid. In this review article, we touch on these new developments and discuss their implications for diagnostics in hematopoietic malignancies. We review advances in sequencing platforms and library preparation chemistry that can lead to faster turnaround times, novel sequencing techniques, the development of mobile laboratories with implications for worldwide benefits, the current status of sample types, improvements to quality and reference materials, bioinformatic pipelines, and the integration of machine learning and artificial intelligence into mol- ecular diagnostic tools for hematologic malignancies.
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Affiliation(s)
- Regina Kwon
- Department of Laboratory Medicine and Pathology, University of Washington
| | - Cecilia C. S. Yeung
- Department of Laboratory Medicine and Pathology, University of Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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Giudice V, Serio B, Errichiello S, Ferrara I, Galdiero A, Bertolini A, Visconti R, De Novellis D, Guariglia R, Luponio S, Morini D, Della Corte AM, Sessa AM, Verdesca F, Langella M, Izzo B, Selleri C. Subclones with variants of uncertain clinical significance might contribute to ineffective hemopoiesis and leukemia predisposition. Eur J Haematol 2023; 111:729-741. [PMID: 37501402 DOI: 10.1111/ejh.14069] [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: 05/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Splicing modifications, genomic instability, and hypomethylation are central mechanisms promoting myelodysplasia and acute myeloid leukemia (AML). In this real-life retrospective study, to elucidate pathophysiology of clonal hemopoiesis in hematological malignancies, we investigated clinical significance of mutations in leukemia-related genes of known pathogenetic significance and of variants of uncertain clinical significance (VUS) in a cohort of patients with MDS and AML. METHODS A total of 59 consecutive subjects diagnosed with MDS, 48 with AML, and 17 with clonal cytopenia with unknown significance were screened for somatic mutations in AML-related genes by next-generation sequencing. RESULTS We showed that TET2, SETBP1, ASXL1, EZH2, RUNX1, SRSF2, DNMT3A, and IDH1/2 were commonly mutated. MDS patients also showed a high genetic complexity, especially for SETBP1. Moreover, the presence of SETBP1 wild-type or two or more simultaneous VUS variants identified a subgroup of AML and MDS patients with better outcome, while the presence of single SETBP1 VUS variant was related to a worse prognosis, regardless TET2 mutational status. CONCLUSIONS In conclusions, we linked both pathogenic and VUS variants in AML-related genes to clonal hematopoiesis; therefore, we proposed to consider those variants as prognostic markers in leukemia and myelodysplasia. However, further studies in larger prospective cohorts are required to validate our results.
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Affiliation(s)
- Valentina Giudice
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Bianca Serio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Santa Errichiello
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Idalucia Ferrara
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Alessandra Galdiero
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Angela Bertolini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Roberta Visconti
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Danilo De Novellis
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
| | - Roberto Guariglia
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Serena Luponio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Denise Morini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Della Corte
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Anna Maria Sessa
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Francesco Verdesca
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Maddalena Langella
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Barbara Izzo
- Department of Molecular Medicine and Medical Biotechnology, CEINGE-Biotecnologie Avanzate, University of Naples "Federico II", Naples, Italy
| | - Carmine Selleri
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
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