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Krishnamurthy K, Chai J, Liu X, Wang Y, Naeem R, Goldstein DY. Clinical validation of the Ion Torrent Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer as a stand-alone assay for single-nucleotide variants, insertions/deletions, and fusion genes: Challenges, performance, and perspectives. Am J Clin Pathol 2024:aqae063. [PMID: 38823030 DOI: 10.1093/ajcp/aqae063] [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: 03/03/2024] [Accepted: 04/26/2024] [Indexed: 06/03/2024] Open
Abstract
OBJECTIVES Myeloid neoplasms require comprehensive characterization of genetic abnormalities, including single-nucleotide variants, small insertions and deletions, and fusions and translocations for management. The Oncomine Myeloid Assay GX v2 (Thermo Fisher Scientific) analyzes 17 full genes, 28 hotspot genes, 30 fusion driver genes, and 5 expression genes. METHODS The validation set included 192 DNA samples, 28 RNA samples, and 9 cell lines and contrived controls. The DNA and RNA were extracted from both peripheral blood and bone marrow. Library preparation, templating, and sequencing was performed on the fully automated Genexus Integrated Sequencer (Thermo Fisher Scientific). The sequencing data were analyzed by manual curation, default Oncomine filters and the Oncomine Reporter (Thermo Fisher Scientific). RESULTS Of the 600 reference pathogenic DNA variants targeted by the assay, concordance was seen in 98.3% of unfiltered variant call format files. Precision and reproducibility were 100%, and the lower limit of detection was 2% variant allele frequency for DNA. Inability to detect variants in long homopolymer regions intrinsic to the Ion Torrent chemistry led to 7 missed variants; 100% concordance was seen with reference RNA samples. CONCLUSIONS This extensive clinical validation of the Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer with its built-in bioinformatics pipeline and Ion Torrent Oncomine Reporter shows robust performance in terms of variant calling accuracy, precision, and reproducibility, with the advantage of a rapid turnaround time of 2 days. The greatest limitation is the inability to detect variants in long homopolymer regions.
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Affiliation(s)
| | - Jiani Chai
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Xiaowei Liu
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Yanhua Wang
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - Rizwan Naeem
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
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2
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Sadigh S, Kim AS. Molecular Pathology of Myeloid Neoplasms: Molecular Pattern Recognition. Clin Lab Med 2024; 44:339-353. [PMID: 38821648 DOI: 10.1016/j.cll.2023.08.007] [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: 06/02/2024]
Abstract
Despite the apparent complexity of the molecular genetic underpinnings of myeloid neoplasms, most myeloid mutational profiles can be understood within a simple framework. Somatic mutations accumulate in hematopoietic stem cells with aging and toxic insults, termed clonal hematopoiesis. These "old stem cells" mutations, predominantly in the epigenetic and RNA spliceosome pathways, act as "founding" driver mutations leading to a clonal myeloid neoplasm when sufficient in number and clone size. Subsequent mutations can create the genetic flavor of the myeloid neoplasm ("backseat" drivers) due to their enrichment in certain entities or act as progression events ("aggressive" drivers) during clonal evolution.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Annette S Kim
- Division of Diagnostic Genetics and Genomics, Department of Pathology, University of Michigan/Michigan Medicine, 2800 Plymouth Road, NCRC 36-1221-79, Ann Arbor, MI 48109, USA.
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3
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Sadigh S, DeAngelo DJ, Garcia JS, Hasserjian RP, Hergott CB, Lane AA, Lovitch SB, Lucas F, Luskin MR, Morgan EA, Pinkus GS, Pozdnyakova O, Rodig SJ, Shanmugam V, Tsai HK, Winer ES, Zemmour D, Kim AS. Cutaneous Manifestations of Myeloid Neoplasms Exhibit Broad and Divergent Morphologic and Immunophenotypic Features but Share Ancestral Clonal Mutations With Bone Marrow. Mod Pathol 2024; 37:100352. [PMID: 37839675 DOI: 10.1016/j.modpat.2023.100352] [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: 05/10/2023] [Revised: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
In this study, we performed a comprehensive molecular analysis of paired skin and peripheral blood/bone marrow (BM) samples from 17 patients with cutaneous myeloid or cutaneous histiocytic-dendritic neoplasms. The cutaneous manifestations included 10 patients with cutaneous acute myeloid leukemia (c-AML), 2 patients with full or partial Langerhans cell differentiation, 2 patients with blastic plasmacytoid dendritic cell neoplasms (BPDCN), 1 patient with both Langerhans cell differentiation and BPDCN, and 2 patients with full or partial indeterminate dendritic cell differentiation. Seven of the 10 c-AML patients (70%) exhibited concurrent or subsequent marrow involvement by acute myeloid leukemia, with all 7 cases (100%) demonstrating shared clonal mutations in both the skin and BM. However, clonal relatedness was documented in one additional case that never had any BM involvement. Nevertheless, NPM1 mutations were identified in 7 of the 10 (70%) of these c-AML cases while one had KMT2A rearrangement and one showed inv(16). All 3 patients (100%) with Langerhans cell neoplasms, 2 patients with BPDCN (100%), and one of the 2 patients (50%) with other cutaneous dendritic cell neoplasms also demonstrated shared mutations between the skin and concurrent or subsequent myeloid neoplasms. Both BM and c-AML shared identical founding drivers, with a predominance of NPM1, DNMT3A, and translocations associated with monocytic differentiation, with common cutaneous-only mutations involving genes in the signal transduction and epigenetic pathways. Cutaneous histiocytic-dendritic neoplasms shared founding drivers in ASXL1, TET2, and/or SRSF2. However, in the Langerhans cell histiocytosis or histiocytic sarcoma cases, there exist recurrent secondary RAS pathway hits, whereas cutaneous BPDCN cases exhibit copy number or structural variants. These results enrich and broaden our understanding of clonally related cutaneous manifestations of myeloid neoplasms and further illuminate the highly diverse spectrum of morphologic and immunophenotypic features they exhibit.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott B Lovitch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Geraldine S Pinkus
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vignesh Shanmugam
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric S Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David Zemmour
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Now with Department of Pathology, University of Michigan, Ann Arbor, Michigan.
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4
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Nian Q, Li Y, Li J, Zhao L, Rodrigues Lima F, Zeng J, Liu R, Ye Z. U2AF1 in various neoplastic diseases and relevant targeted therapies for malignant cancers with complex mutations (Review). Oncol Rep 2024; 51:5. [PMID: 37975232 PMCID: PMC10688450 DOI: 10.3892/or.2023.8664] [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: 10/03/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
U2 small nuclear RNA auxiliary factor 1 (U2AF1) is a multifunctional protein that plays a crucial role in the regulation of RNA splicing during eukaryotic gene expression. U2AF1 belongs to the SR family of splicing factors and is involved in the removal of introns from mRNAs and exon-exon binding. Mutations in U2AF1 are frequently observed in myelodysplastic syndrome, primary myelofibrosis, chronic myelomonocytic leukaemia, hairy cell leukaemia and other solid tumours, particularly in lung, pancreatic, and ovarian carcinomas. Therefore, targeting U2AF1 for therapeutic interventions may be a viable strategy for treating malignant diseases. In the present review, the pathogenic mechanisms associated with U2AF1 in different malignant diseases were summarized, and the potential of related targeting agents was discussed. Additionally, the feasibility of natural product-based therapies directed against U2AF1 was explored.
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Affiliation(s)
- Qing Nian
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Yihui Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing 100730, P.R. China
| | - Jingwei Li
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Liyun Zhao
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France
| | - Jinhao Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610000, P.R. China
| | - Rongxing Liu
- Department of Pharmacy, The Second Affiliated Hospital, Army Medical University, Chongqing 400000, P.R. China
| | - Zhijun Ye
- Department of Clinical Nutrition, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
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5
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Zbieranski N, Insuasti-Beltran G. Analytical Validation of an Automated Semiconductor-Based Next-Generation Sequencing Assay for Detection of DNA and RNA Alterations in Myeloid Neoplasms. J Mol Diagn 2024; 26:29-36. [PMID: 37879438 DOI: 10.1016/j.jmoldx.2023.09.011] [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: 06/09/2023] [Revised: 08/23/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
Myeloid neoplasms are heterogeneous tumors derived from early hematopoietic progenitors. Most international guidelines, including the European LeukemiaNet 2022 update, recommend testing a comprehensive set of genes, most within a 3- to 5-day period for optimal treatment decisions. Next-generation sequencing gene panels are essential for identifying genetic alterations, risk stratification, and determining targeted therapies for myeloid malignancies. This study describes the analytical validation of the Oncomine Myeloid Assay GX v2 (Myeloid GX v2) in combination with the Ion Torrent Genexus System using commercial controls, 16 variant-negative samples, and 130 clinical samples of myeloid neoplasms. The Myeloid GX v2 panel detected single nucleotide variants (SNVs), insertions/deletions (indels) (allele frequency >5%), and gene fusions (minimum 11 fusion copies/μL) in synthetic controls with a sensitivity of 100%. Specificity for detection of SNVs, indels, or fusions in 16 variant-negative samples was 100%. Sensitivity for detection of SNVs, indels, and gene fusions in 130 clinical samples was 99%, 97%, and 100%, respectively. Overall precision was 100% for SNVs, 96% for indels, and 100% for fusions. The average turnaround time from nucleic acid extraction to results was 2 days. The Myeloid GX v2 panel is highly accurate and reproducible for the detection of SNVs, indels, and gene fusions in myeloid neoplasms. The ability to deliver clinically relevant results in a short time is key to providing personalized treatments.
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Affiliation(s)
- Nora Zbieranski
- Department of Pathology, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
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6
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Stacey SN, Zink F, Halldorsson GH, Stefansdottir L, Gudjonsson SA, Einarsson G, Hjörleifsson G, Eiriksdottir T, Helgadottir A, Björnsdottir G, Thorgeirsson TE, Olafsdottir TA, Jonsdottir I, Gretarsdottir S, Tragante V, Magnusson MK, Jonsson H, Gudmundsson J, Olafsson S, Holm H, Gudbjartsson DF, Sulem P, Helgason A, Thorsteinsdottir U, Tryggvadottir L, Rafnar T, Melsted P, Ulfarsson MÖ, Vidarsson B, Thorleifsson G, Stefansson K. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis. Nat Genet 2023; 55:2149-2159. [PMID: 37932435 PMCID: PMC10703693 DOI: 10.1038/s41588-023-01555-z] [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: 05/09/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.
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Affiliation(s)
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Thorunn A Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Magnus Ö Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Brynjar Vidarsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Hematology, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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7
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Craven KE, Ewalt MD. Premalignant Clonal Hematopoiesis (Clonal Hematopoiesis of Indeterminate Potential and Clonal Cytopenia of Undetermined Significance). Clin Lab Med 2023; 43:565-576. [PMID: 37865503 DOI: 10.1016/j.cll.2023.06.001] [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] [Indexed: 10/23/2023]
Abstract
Premalignant clonal hematopoiesis is the presence of somatic alterations in the blood of otherwise healthy individuals. Although the condition is not considered as a cancer, it carries an increased risk of developing a hematologic malignancy, particularly in those with large neoplastic clones, multiple pathogenic mutations, and high-risk mutations. In addition to the increased risk of malignancy, clonal hematopoiesis carries a markedly increased risk of cardiovascular events and death. Appropriate identification of this entity is critical to mitigate cardiovascular risk factors and ensure appropriate monitoring for the emergence of blood cancer.
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Affiliation(s)
- Kelly E Craven
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 36, New York, NY 10065, USA
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 36, New York, NY 10065, USA.
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8
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Hogg G, Severson EA, Cai L, Hoffmann HM, Holden KA, Fitzgerald K, Kenyon A, Zeng Q, Mooney M, Gardner S, Chen W, Nagan N, Boles D, Parker S, Richman TJ, Letovsky S, Dong H, Anderson SM, Ramkissoon S, Reddy P, Eisenberg M, Chenn A, Jensen TJ. Clinical characterization of the mutational landscape of 24,639 real-world samples from patients with myeloid malignancies. Cancer Genet 2023; 278-279:38-49. [PMID: 37586297 DOI: 10.1016/j.cancergen.2023.07.006] [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: 03/15/2023] [Revised: 06/30/2023] [Accepted: 07/15/2023] [Indexed: 08/18/2023]
Abstract
Myeloid neoplasms represent a broad spectrum of hematological disorders for which somatic mutation status in key driver genes is important for diagnosis, prognosis and treatment. Here we summarize the findings of a targeted, next generation sequencing laboratory developed test in 24,639 clinical myeloid samples. Data were analyzed comprehensively and as part of individual cohorts specific to acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Overall, 48,015 variants were detected, and variants were found in all 50 genes in the panel. The mean number of mutations per patient was 1.95. Mutation number increased with age (Spearman's rank correlation coefficient, ρ = 0.29, P < 0.0001) and was higher in patients with AML than MDS or MPN (Student's t-test, P < 0.0001). TET2 was the most common mutation detected (19.1% of samples; 4,695/24,639) including 7.7% (1,908/24,639) with multi-hit TET2 mutations. Mutation frequency was correlated between patients with cytopenias and MDS (Spearman's, ρ = 0.97, P < 2.2×10-16) with the MDS diagnostic gene SF3B1 being the only notable outlier. This large retrospective study shows the utility of NGS testing to inform clinical decisions during routine clinical care and highlights the mutational landscape of a broad population of myeloid patients.
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Affiliation(s)
| | | | - Li Cai
- Labcorp Durham, Durham, NC, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shakti Ramkissoon
- Labcorp Durham, Durham, NC, USA; Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | | | | | - Taylor J Jensen
- Labcorp San Diego, San Diego, CA, USA; Labcorp Durham, Durham, NC, USA
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9
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Pozdnyakova O, Niculescu RS, Kroll T, Golemme L, Raymond N, Briggs D, Kim A. Beyond the routine CBC: machine learning and statistical analyses identify research CBC parameter associations with myelodysplastic syndromes and specific underlying pathogenic variants. J Clin Pathol 2023; 76:624-631. [PMID: 35577566 DOI: 10.1136/jclinpath-2021-207860] [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: 07/29/2021] [Accepted: 04/16/2022] [Indexed: 11/04/2022]
Abstract
AIMS Given the time, expense and clinical expertise required for a myelodysplastic syndrome (MDS) diagnosis, there is a clear need for a cost-effective screening laboratory test that can rapidly and accurately distinguish patients with cytopenias related to MDS from other causes. METHODS We measured conventional and research use only complete blood cell (CBC) parameters using the Sysmex XN-series haematology analyser in 102 MDS patients (70 patients with active MDS and 32 patients in remission), 43 patients with cytopenia without morphological evidence of MDS and 484 age-adjusted controls. A variety of algorithms, including random forest machine learning, were used to construct parameter-based models to predict the presence of MDS using both CBC and molecular data or CBC data alone and correlated individual pathogenic variants/genetic pathways with CBC parameters changes. RESULTS Using the CBC parameters alone, our predictive model for active MDS showed a 0.86 receiver operating characteristic curve (ROC)/area under the ROC curve (AUC), with 0.87 sensitivity and 0.72 specificity; with the addition of the molecular and demographic status, the ROC/AUC improved to 0.93, sensitivity to 0.89 and specificity to 0.84. The most discriminatory MDS parameters were reflective of dysplastic neutrophil morphology, red cell count fragmentation and degree of platelet immaturity. Specific patterns of parameters were associated with individual gene pathogenic variants or affected pathways. CONCLUSIONS CBC research parameters can be used as an adjunct to the haematological workup of cytopenia(s) to help screen for patients with high likelihood of MDS.
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Affiliation(s)
- Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | - Lisa Golemme
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Nolan Raymond
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Debra Briggs
- Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Annette Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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10
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Demir D. Insights into the New Molecular Updates in Acute Myeloid Leukemia Pathogenesis. Genes (Basel) 2023; 14:1424. [PMID: 37510328 PMCID: PMC10378849 DOI: 10.3390/genes14071424] [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: 04/30/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
As our understanding of the biologic basis of acute myeloid leukemia evolves, so do the classification systems used to describe this group of cancers. Early classification systems focused on the morphologic features of blasts and other cell populations; however, the explosion in genomic technologies has led to rapid growth in our understanding of these diseases and thus the refinement of classification systems. Recently, two new systems, the International Consensus Classification system and the 5th edition of the World Health Organization classification of tumors of hematopoietic and lymphoid tissues, were published to incorporate the latest genomic advances in blood cancer. This article reviews the major updates in acute myeloid leukemia in both systems and highlights the biologic insights that have driven these changes.
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Affiliation(s)
- Derya Demir
- Department of Pathology, Ege University Faculty of Medicine, Izmir 35100, Turkey
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11
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Totiger TM, Ghoshal A, Zabroski J, Sondhi A, Bucha S, Jahn J, Feng Y, Taylor J. Targeted Therapy Development in Acute Myeloid Leukemia. Biomedicines 2023; 11:641. [PMID: 36831175 PMCID: PMC9953553 DOI: 10.3390/biomedicines11020641] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Therapeutic developments targeting acute myeloid leukemia (AML) have been in the pipeline for five decades and have recently resulted in the approval of multiple targeted therapies. However, there remains an unmet need for molecular treatments that can deliver long-term remissions and cure for this heterogeneous disease. Previously, a wide range of small molecule drugs were developed to target sub-types of AML, mainly in the relapsed and refractory setting; however, drug resistance has derailed the long-term efficacy of these as monotherapies. Recently, the small molecule venetoclax was introduced in combination with azacitidine, which has improved the response rates and the overall survival in older adults with AML compared to those of chemotherapy. However, this regimen is still limited by cytotoxicity and is not curative. Therefore, there is high demand for therapies that target specific abnormalities in AML while sparing normal cells and eliminating leukemia-initiating cells. Despite this, the urgent need to develop these therapies has been hampered by the complexities of this heterogeneous disease, spurring the development of innovative therapies that target different mechanisms of leukemogenesis. This review comprehensively addresses the development of novel targeted therapies and the translational perspective for acute myeloid leukemia, including the development of selective and non-selective drugs.
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Affiliation(s)
- Tulasigeri M. Totiger
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Anirban Ghoshal
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jenna Zabroski
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Anya Sondhi
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Saanvi Bucha
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jacob Jahn
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yangbo Feng
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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12
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Abbou N, Piazzola P, Gabert J, Ernest V, Arcani R, Couderc AL, Tichadou A, Roche P, Farnault L, Colle J, Ouafik L, Morange P, Costello R, Venton G. Impact of Molecular Biology in Diagnosis, Prognosis, and Therapeutic Management of BCR::ABL1-Negative Myeloproliferative Neoplasm. Cells 2022; 12:cells12010105. [PMID: 36611899 PMCID: PMC9818322 DOI: 10.3390/cells12010105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
BCR::ABL1-negative myeloproliferative neoplasms (MPNs) include three major subgroups-polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF)-which are characterized by aberrant hematopoietic proliferation with an increased risk of leukemic transformation. Besides the driver mutations, which are JAK2, CALR, and MPL, more than twenty additional mutations have been identified through the use of next-generation sequencing (NGS), which can be involved with pathways that regulate epigenetic modifications, RNA splicing, or DNA repair. The aim of this short review is to highlight the impact of molecular biology on the diagnosis, prognosis, and therapeutic management of patients with PV, ET, and PMF.
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Affiliation(s)
- Norman Abbou
- Molecular Biology Laboratory, North University Hospital, 13015 Marseille, France
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
| | - Pauline Piazzola
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Jean Gabert
- Molecular Biology Laboratory, North University Hospital, 13015 Marseille, France
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
| | - Vincent Ernest
- Hematology Laboratory, Timone University Hospital, 13005 Marseille, France
| | - Robin Arcani
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Department of Internal Medicine, Timone University Hospital, 13005 Marseille, France
| | - Anne-Laure Couderc
- Department of Geriatrics, South University Hospital, 13005 Marseille, France
| | - Antoine Tichadou
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Pauline Roche
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Laure Farnault
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Julien Colle
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - L’houcine Ouafik
- CNRS, INP, Institute of Neurophysiopathol, Aix-Marseille Université, 13005 Marseille, France
- APHM, CHU Nord, Service d’Onco-Biologie, Aix-Marseille Université, 13005 Marseille, France
| | - Pierre Morange
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology Laboratory, Timone University Hospital, 13005 Marseille, France
| | - Régis Costello
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
- TAGC, INSERM, UMR1090, Aix-Marseille University, 13005 Marseille, France
| | - Geoffroy Venton
- INSERM, INRAE, C2VN, Aix-Marseille University, 13005 Marseille, France
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
- TAGC, INSERM, UMR1090, Aix-Marseille University, 13005 Marseille, France
- Correspondence: ; Tel.: +33-4-91-38-41-52
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13
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Zuo Z, Medeiros LJ, Garces S, Routbort MJ, Ok CY, Loghavi S, Kanagal-Shamanna R, Jelloul FZ, Garcia-Manero G, Chien KS, Patel KP, Luthra R, Yin CC. Concurrent Mutations in SF3B1 and PHF6 in Myeloid Neoplasms. BIOLOGY 2022; 12:biology12010013. [PMID: 36671709 PMCID: PMC9855138 DOI: 10.3390/biology12010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
It has been reported that gene mutations in SF3B1 and PHF6 are mutually exclusive. However, this observation has never been rigorously assessed. We report the clinicopathologic and molecular genetic features of 21 cases of myeloid neoplasms with double mutations in SF3B1 and PHF6, including 9 (43%) with myelodysplastic syndrome, 5 (24%) with acute myeloid leukemia, 4 (19%) with myeloproliferative neoplasms, and 3 (14%) with myelodysplastic/myeloproliferative neoplasms. Multilineage dysplasia with ring sideroblasts, increased blasts, and myelofibrosis are common morphologic findings. All cases but one had diploid or non-complex karyotypes. SF3B1 mutations were detected in the first analysis of all the patients. PHF6 mutations occurred either concurrently with SF3B1 mutations or in subsequent follow-up samples and are associated with disease progression and impending death in most cases. Most cases had co-mutations, the most common being ASXL1, RUNX1, TET2, and NRAS. With a median follow-up of 39 months (range, 3-155), 17 (81%) patients died, 3 were in complete remission, and 1 had persistent myelodysplastic syndrome. The median overall survival was 51 months. In summary, concurrent mutations in SF3B1 and PHF6 are rare, but they do exist in a variety of myeloid neoplasms, with roles as early initiating events and in disease progression, respectively.
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Affiliation(s)
- Zhuang Zuo
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (Z.Z.); (C.C.Y.)
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sofia Garces
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark J. Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chi Young Ok
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kelly S. Chien
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (Z.Z.); (C.C.Y.)
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14
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Hergott CB, Kim AS. Molecular Diagnostic Testing for Hematopoietic Neoplasms: Linking Pathogenic Drivers to Personalized Diagnosis. Clin Lab Med 2022; 42:325-347. [PMID: 36150815 DOI: 10.1016/j.cll.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular diagnostics inhabit an increasingly central role in characterizing hematopoietic malignancies. This brief review summarizes the genomic targets important for many major categories of hematopoietic neoplasia by focusing on disease pathogenesis. In myeloid disease, recurrent mutations in key functional classes drive clonal hematopoiesis, on which additional variants can specify clinical presentation and accelerate progression. Lymphoblastic leukemias are frequently initiated by oncogenic fusions that block lymphoid maturation while, in concert with additional mutations, driving proliferation. The links between genetic aberrations and lymphoma patient outcomes have been clarified substantially through the clustering of genomic profiles. Finally, the addition of next-generation sequencing strategies to cytogenetics is refining risk stratification for plasma cell myeloma. In all categories, molecular diagnostics shed light on the unique mechanistic underpinnings of each individual malignancy, thereby empowering more rational, personalized care for these patients.
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Affiliation(s)
- Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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15
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Maddali M, Venkatraman A, Kulkarni UP, Mani S, Raj S, Sigamani E, Korula A, A FN, Lionel SA, Selvarajan S, Manipadam MT, Abraham A, George B, Mathews V, Balasubramanian P. Molecular characterization of triple-negative myeloproliferative neoplasms by next-generation sequencing. Ann Hematol 2022; 101:1987-2000. [PMID: 35840818 DOI: 10.1007/s00277-022-04920-w] [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: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
Abstract
The role of next-generation sequencing (NGS) in identifying mutations in the driver, epigenetic regulator, RNA splicing, and signaling pathway genes in myeloproliferative neoplasms (MPNs) has contributed substantially to our understanding of the disease pathogenesis as well as disease evolution. NGS aids in determining the clonal nature of the disease in a subset of these disorders where mutations in the driver genes are not detected. There is a paucity of real-world data on the utility of this test in the characterization of triple-negative myeloproliferative neoplasms (TN-MPN). In this study, 46 samples of TN-MPN (essential thrombocythemia (ET) = 17; primary myelofibrosis (PMF) = 23; & myeloproliferative neoplasm unclassified (MPN-u) = 6) were screened for markers of clonality using targeted NGS. Among these, 25 (54.3%) patients had mutations that would help determine the clonal nature of the disease. Eight of the 17 TN-ET (47%) and 13 of the 23 TN-PMF (56.5%) patients had noncanonical mutations in the driver genes and mutations in the genes involved in epigenetic regulation. Identification of mutations categorized as high molecular markers (HMR) in 2 patients helped classify them as PMF with high risk according to the MIPSS 70 scoring system. A novel mutation in the MPIG6B (C6orf25) gene associated with childhood myelofibrosis was detected in a 14-year-old girl. The presence of clonal hematopoiesis could be confirmed in four of the six MPN-u patients in this cohort. This study demonstrates the utility of NGS in improving the characterization of TN-MPN by establishing clonality and detecting noncanonical mutations in driver genes, thereby aiding in clinical decision-making.
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Affiliation(s)
- Madhavi Maddali
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Arvind Venkatraman
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Sathya Mani
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Santhosh Raj
- Department of Pathology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Anu Korula
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Fouzia N A
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Sushil Selvarajan
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Aby Abraham
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Biju George
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India
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16
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Bhai P, Hsia CC, Schenkel LC, Hedley BD, Levy MA, Kerkhof J, Santos S, Stuart A, Lin H, Broadbent R, Nan S, Yang P, Xenocostas A, Chin-Yee I, Sadikovic B. Clinical Utility of Implementing a Frontline NGS-Based DNA and RNA Fusion Panel Test for Patients with Suspected Myeloid Malignancies. Mol Diagn Ther 2022; 26:333-343. [PMID: 35381971 DOI: 10.1007/s40291-022-00581-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The use of molecular genetic biomarkers is rapidly advancing to aid diagnosis, prognosis, and clinical management of hematological disorders. We have implemented a next-generation sequencing (NGS) assay for detection of genetic variants and fusions as a frontline test for patients suspected with myeloid malignancy. In this study, we summarize the findings and assess the clinical impact in the first 1613 patients tested. METHODS All patients were assessed using NGS based Oncomine Myeloid Research Assay (ThermoFisher) including 40 genes (17 full genes and 23 genes with clinically relevant "hotspot" regions), along with a panel of 29 fusion driver genes (including over fusion 600 partners). RESULTS Among 1613 patients with suspected myeloid malignancy, 43% patients harbored at least one clinically relevant variant: 91% (90/100) in acute myeloid leukemia patients, 71.7% (160/223) in myelodysplastic syndrome (MDS), 77.5% (308/397) in myeloproliferative neoplasm (MPN), 83% (34/41) in MPN/MDS, and 100% (40/40) in chronic myeloid leukemia patients. Comparison of NGS and cytogenetics results revealed a high degree of concordance in gene fusion detection. CONCLUSIONS Our findings demonstrate clinical utility and feasibility of integrating a NGS-based gene mutation and fusion testing assay as a frontline diagnostic test in a large reported cohort of patients with suspected myeloid malignancy, in a clinical laboratory setting. Overlap with cytogenetic test results provides opportunity for testing reduction and streamlining.
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Affiliation(s)
- Pratibha Bhai
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cyrus C Hsia
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Laila C Schenkel
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Benjamin D Hedley
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael A Levy
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Stephanie Santos
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Alan Stuart
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Robert Broadbent
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Shirley Nan
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Anargyros Xenocostas
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Ian Chin-Yee
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada. .,Victoria Hospital, London Health Sciences Centre, 800 Commissioners Road East, Room E6-211, London, ON, N6A 5W9, Canada.
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada. .,Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada.
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17
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Dermawan JK, Wensel C, Visconte V, Maciejewski JP, Cook JR, Bosler DS. Clinically Significant CUX1 Mutations Are Frequently Subclonal and Common in Myeloid Disorders With a High Number of Co-mutated Genes and Dysplastic Features. Am J Clin Pathol 2022; 157:586-594. [PMID: 34661647 DOI: 10.1093/ajcp/aqab157] [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: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES CUX1 mutations have been reported in myeloid neoplasms. We aimed to characterize the mutational landscape, clonal architecture, and clinical characteristics of myeloid disorders with CUX1 variants. METHODS We reviewed data from a targeted 62-gene panel with CUX1 variants. Variants were classified as of strong or potential clinical significance (tier I/tier II) or of unknown significance (VUS). RESULTS CUX1 variants were identified in 169 cases. The 49 tier I/tier II variants were found in older patients (mean age, 71 vs 60 years old) and predominantly inactivating alterations, while the 120 VUS cases were missense mutations. Monosomy 7/deletion 7q was more common in tier I/tier II cases. Co-mutations were detected in 96% of tier I/tier II cases (average, 3.7/case) but in only 61% of VUS cases (average, 1.5/case). Tier I/tier II CUX1 variants tend to be subclonal to co-mutations (ASXL1, SF3B1, SRSF2, TET2). Among myeloid disorders, tier I/tier II cases were more frequently diagnosed with myelodysplastic syndromes and had a higher number of bone marrow dysplastic lineages. CONCLUSIONS CUX1 mutations are seen with adverse prognostic features and could be a late clonal evolutional event of myeloid disorders. The differences between CUX1 tier I/tier II and VUS underscore the importance of accurate variant classification in reporting of multigene panels.
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Affiliation(s)
- Josephine K Dermawan
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Christine Wensel
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James R Cook
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - David S Bosler
- Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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18
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Enjeti AK, Agarwal R, Blombery P, Chee L, Chua CC, Grigg A, Hamad N, Iland H, Lane S, Perkins A, Singhal D, Tate C, Tiong IS, Ross DM. Panel-based gene testing in myelodysplastic/myeloproliferative neoplasm- overlap syndromes: Australasian Leukaemia and Lymphoma Group (ALLG) consensus statement. Pathology 2022; 54:389-398. [DOI: 10.1016/j.pathol.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
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19
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Zhao F, Bosler DS, Cook JR. Designing Myeloid Gene Panels. Arch Pathol Lab Med 2021; 146:1004-1011. [PMID: 34784413 DOI: 10.5858/arpa.2021-0124-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing studies are increasingly used in the evaluation of suspected chronic myeloid neoplasms (CMNs), but there is wide variability among laboratories in the genes analyzed for this purpose. Recently, the Association for Molecular Pathology CMN working group recommended a core 34-gene set as a minimum target list for evaluation of CMNs. This list was recommended based on literature review, and its diagnostic yield in clinical practice is unknown. OBJECTIVE.— To determine the diagnostic yield of the core 34 genes and assess the potential impact of including selected additional genes. DESIGN.— We retrospectively reviewed 185 patients with known or suspected CMNs tested using a 62-gene next-generation sequencing panel that included all 34 core genes. RESULTS.— The Association for Molecular Pathology's core 34 genes had a diagnostic yield of 158 of 185 (85.4%) to detect at least 1 variant with strong/potential clinical significance and 107 of 185 (57.8%) to detect at least 2 such variants. The 62-gene panel had a diagnostic yield of 160 of 185 (86.5%) and 112 of 185 (60.5%), respectively. Variants of unknown significance were identified in 49 of 185 (26.5%) using the core 34 genes versus 76 of 185 (41.1%) using the 62-gene panel. CONCLUSIONS.— This study demonstrates that the Association for Molecular Pathology-recommended core 34-gene set has a high diagnostic yield in CMNs. Inclusion of selected additional genes slightly increases the rate of abnormal results, while also increasing the detection of variants of unknown significance. We recommend inclusion of CUX1, DDX41, ETNK1, RIT1, and SUZ12 in addition to the Association for Molecular Pathology's 34-gene core set for routine evaluation of CMNs.
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Affiliation(s)
- Fang Zhao
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio.,Zhao is currently located at the Center for Clinical Informatics Research and Education and Department of Pathology, The MetroHealth System/Case Western Reserve University, Cleveland, Ohio
| | - David S Bosler
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - James R Cook
- From the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
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20
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Abstract
Chronic myelomonocytic leukemia (CMML) is a rare and challenging type of myeloproliferative neoplasm. Poor prognosis and high mortality, associated predominantly with progression to secondary acute myeloid leukemia (sAML), is still an unsolved problem. Despite a growing body of knowledge about the molecular repertoire of this disease, at present, the prognostic significance of CMML-associated mutations is controversial. The absence of available CMML cell lines and the small number of patients with CMML make pre-clinical testing and clinical trials complicated. Currently, specific therapy for CMML has not been approved; most of the currently available therapeutic approaches are based on myelodysplastic syndrome (MDS) and other myeloproliferative neoplasm (MNP) studies. In this regard, the development of the robust CMML animal models is currently the focus of interest. This review describes important studies concerning animal models of CMML, examples of methodological approaches, and the obtained hematologic phenotypes.
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21
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Hanbazazh M, Harada S, Reddy V, Mackinnon AC, Harbi D, Morlote D. The Interpretation of Sequence Variants in Myeloid Neoplasms. Am J Clin Pathol 2021; 156:728-748. [PMID: 34155503 DOI: 10.1093/ajcp/aqab039] [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: 11/12/2022] Open
Abstract
OBJECTIVES To provide an overview of the challenges encountered during the interpretation of sequence variants detected by next-generation sequencing (NGS) in myeloid neoplasms, as well as the limitations of the technology with the goal of preventing the over- or undercalling of alterations that may have a significant effect on patient management. METHODS Review of the peer-reviewed literature on the interpretation, reporting, and technical challenges of NGS assays for myeloid neoplasms. RESULTS NGS has been integrated widely and rapidly into the standard evaluating of myeloid neoplasms. Review of the literature reveals that myeloid sequence variants are challenging to detect and interpret. Large insertions and guanine-cytosine-heavy areas prove technically challenging while frameshift and truncating alterations may be classified as variants of uncertain significance by tertiary analysis informatics pipelines due to their absence in the literature and databases. CONCLUSIONS The analysis and interpretation of NGS results in myeloid neoplasia are challenging due to the varied number of detectable gene alterations. Familiarity with the genomic landscape of myeloid malignancies and knowledge of the tools available for the interpretation of sequence variants are essential to facilitate translation into clinical and therapy decisions.
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Affiliation(s)
- Mehenaz Hanbazazh
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shuko Harada
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishnu Reddy
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alexander Craig Mackinnon
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Djamel Harbi
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Diana Morlote
- Department of Pathology, Division of Genomic Diagnostics and Bioinformatics, University of Alabama at Birmingham, Birmingham, AL, USA
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22
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Hammond D, Montalban-Bravo G. Management and Outcomes of Blast Transformed Chronic Myelomonocytic Leukemia. Curr Hematol Malig Rep 2021; 16:405-417. [PMID: 34499330 DOI: 10.1007/s11899-021-00643-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE OF REVIEW Despite recent advances in the treatment of de novo acute myeloid leukemia (AML), AML arising from antecedent chronic myelomonocytic leukemia (CMML) continues to have dismal outcomes. While the unique biological drivers of CMML and subsequent leukemic transformation (LT) have been revealed with advances in molecular characterization, this has not yet translated to the bedside. Here, we review these biologic drivers, outcomes with current therapies, and rationale avenues of future investigation specifically in blast phase CMML (CMML-BP). RECENT FINDINGS CMML-BP outcomes are studied as an aggregate with more common categories of AML with myelodysplasia-related changes (AML-MRCs) or the even broader category of secondary AML (sAML), which illustrates the crux of the problem. While a modest survival advantage with allogeneic hematopoietic stem cell transplant exists, the difficulty is bridging patients to transplant and managing patients that require an allograft-sparing approach. Limited data suggest that short-lived remissions can be obtained employing CPX-351 or venetoclax-based lower intensity combination therapy. Promising future strategies include repurposing cladribine, exploiting the supportive role of dendritic cell subsets with anti-CD123 therapies, MCL-1 inhibition, dual MEK/PLK1 inhibition, FLT3 inhibition in RAS-mutated and CBL-mutated subsets, and immune therapies targeting novel immune checkpoint molecules such as the leukocyte immunoglobulin-like receptor B4 (LILRB4), an immune-modulatory transmembrane protein restrictively expressed on monocytic cells. The successful management of an entity as unique as CMML-BP will require a cooperative, concerted effort to design and conduct clinical trials dedicated to this rare form of sAML.
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Affiliation(s)
- Danielle Hammond
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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23
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Sadigh S, Kim AS. Molecular Pathology of Myeloid Neoplasms: Molecular Pattern Recognition. Surg Pathol Clin 2021; 14:517-528. [PMID: 34373100 DOI: 10.1016/j.path.2021.05.013] [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: 10/20/2022]
Abstract
Despite the apparent complexity of the molecular genetic underpinnings of myeloid neoplasms, most myeloid mutational profiles can be understood within a simple framework. Somatic mutations accumulate in hematopoietic stem cells with aging and toxic insults, termed clonal hematopoiesis. These "old stem cells" mutations, predominantly in the epigenetic and RNA spliceosome pathways, act as "founding" driver mutations leading to a clonal myeloid neoplasm when sufficient in number and clone size. Subsequent mutations can create the genetic flavor of the myeloid neoplasm ("backseat" drivers) due to their enrichment in certain entities or act as progression events ("aggressive" drivers) during clonal evolution.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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Jajosky AN, Havens NP, Sadri N, Oduro KA, Moore EM, Beck RC, Meyerson HJ. Clinical Utility of Targeted Next-Generation Sequencing in the Evaluation of Low-Grade Lymphoproliferative Disorders. Am J Clin Pathol 2021; 156:433-444. [PMID: 33712839 DOI: 10.1093/ajcp/aqaa255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES We investigated the usefulness of a custom-designed 31-gene next-generation sequencing (NGS) panel implemented on a routine basis for the evaluation of low-grade lymphoproliferative disorders (LPDs). METHODS In total, 147 blood, bone marrow, and tissue specimens were sequenced, including 81% B-cell, 15% T-cell, and 3% natural killer (NK)-cell neoplasms. RESULTS Of the cases, 92 (63%) of 147 displayed at least one pathogenic variant while 41 (28%) of 147 had two or more. Low mutation rates were noted in monoclonal B-cell lymphocytoses and samples with small T- and NK-cell clones of uncertain significance. Pathogenic molecular variants were described in specific disorders and classified according to their diagnostic, prognostic, and potential therapeutic value. Diagnostically, in addition to confirming the diagnosis of 15 of 15 lymphoplasmacytic lymphomas, 10 of 12 T large granular lymphocytic leukemias, and 2 of 2 hairy cell leukemias (HCLs), the panel helped resolve the diagnosis of 10 (62.5%) of 16 challenging cases lacking a specified diagnosis based on standard morphology, phenotype, and genetic analysis. CONCLUSIONS Overall, implementation of this targeted lymphoid NGS panel as part of regular hematopathology practice was found to be a beneficial adjunct in the evaluation of low-grade LPDs.
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Affiliation(s)
- Audrey N Jajosky
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nathaniel P Havens
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Navid Sadri
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kwadwo A Oduro
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Erika M Moore
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rose C Beck
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Howard J Meyerson
- Department of Pathology, University Hospitals Cleveland Medical Center/Case Western Reserve University School of Medicine, Cleveland, OH, USA
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25
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Mutational analysis of hematologic neoplasms in 164 paired peripheral blood and bone marrow samples by next-generation sequencing. Blood Adv 2021; 4:4362-4365. [PMID: 32926123 DOI: 10.1182/bloodadvances.2020002306] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/07/2020] [Indexed: 01/30/2023] Open
Abstract
Key Points
Findings support use of PB samples for chronic myeloid neoplasms and for acute leukemias with sufficient circulating disease. In acute leukemias, BM appears to be superior to PB for monitoring measurable residual disease, even in the absence of BM excess blasts.
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26
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BCOR gene alterations in hematological diseases. Blood 2021; 138:2455-2468. [PMID: 33945606 DOI: 10.1182/blood.2021010958] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
The BCL6 co-repressor (BCOR) is a transcription factor involved in the control of embryogenesis, mesenchymal stem cells function, hematopoiesis and lymphoid development. Recurrent somatic clonal mutations of the BCOR gene and its homologue BCORL1 have been detected in several hematological malignancies and aplastic anemia. They are scattered across the whole gene length and mostly represent frameshifts (deletions, insertions), nonsense and missence mutations. These disruptive events lead to the loss of full-length BCOR protein and to the lack or low expression of a truncated form of the protein, both consistent with the tumor suppressor role of BCOR. BCOR and BCORL1 mutations are similar to those causing two rare X-linked diseases: the oculo-facio-cardio-dental (OFCD) and the Shukla-Vernon syndromes, respectively. Here, we focus on the structure and function of normal BCOR and BCORL1 in normal hematopoietic and lymphoid tissues and review the frequency and clinical significance of the mutations of these genes in malignant and non-malignant hematological diseases. Moreover, we discuss the importance of mouse models to better understand the role of Bcor loss, alone and combined with alterations of other genes (e.g. Dnmt3a and Tet2), in promoting hematological malignancies and in providing a useful platform for the development of new targeted therapies.
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27
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Rosenthal SH, Gerasimova A, Ma C, Li HR, Grupe A, Chong H, Acab A, Smolgovsky A, Owen R, Elzinga C, Chen R, Sugganth D, Freitas T, Graham J, Champion K, Bhattacharya A, Racke F, Lacbawan F. Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms. PLoS One 2021; 16:e0243683. [PMID: 33909614 PMCID: PMC8081174 DOI: 10.1371/journal.pone.0243683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. Various NGS based in-house developed and commercial myeloid neoplasm panels have been integrated into routine clinical practice. However, some genes frequently mutated in myeloid malignancies are particularly difficult to sequence with NGS panels (e.g., CEBPA, CARL, and FLT3). We report development and validation of a 48-gene NGS panel that includes genes that are technically challenging for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies ≥5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n = 2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9-99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n = 2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms even in technically challenging genes.
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Affiliation(s)
- Sun Hee Rosenthal
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Anna Gerasimova
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Charles Ma
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hai-Rong Li
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Andrew Grupe
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hansook Chong
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Allan Acab
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Alla Smolgovsky
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Renius Owen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Christopher Elzinga
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Rebecca Chen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Daniel Sugganth
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Tracey Freitas
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Jennifer Graham
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Kristen Champion
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Anindya Bhattacharya
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Frederick Racke
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Felicitas Lacbawan
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
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28
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Ross DM, Thomson C, Hamad N, Lane SW, Manos K, Grigg AP, Guo B, Erber WN, Scott A, Viiala N, Chee L, Latimer M, Tate C, Grove C, Perkins AC, Blombery P. Myeloid somatic mutation panel testing in myeloproliferative neoplasms. Pathology 2021; 53:339-348. [PMID: 33674147 DOI: 10.1016/j.pathol.2021.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 12/22/2022]
Abstract
Myeloproliferative neoplasms are characterised by somatic mutations in pathways that regulate cell proliferation, epigenetic modifications, RNA splicing or DNA repair. Assessment of the mutational profile assists diagnosis and classification, but also aids assessment of prognosis, and may guide the use of emerging targeted therapies. The most practical way to provide information on numerous genetic variants is by using massively parallel sequencing, commonly in the form of disease specific next generation sequencing (NGS) panels. This review summarises the diagnostic and prognostic value of somatic mutation testing in Philadelphia-negative myeloproliferative neoplasms: polycythaemia vera, essential thrombocythaemia, primary myelofibrosis, chronic neutrophilic leukaemia, systemic mastocytosis, and chronic eosinophilic leukaemia. NGS panel testing is increasing in routine practice and promises to improve the accuracy and efficiency of pathological diagnosis and prognosis.
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Affiliation(s)
- David M Ross
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Haematology and Bone Marrow Transplantation, Royal Adelaide Hospital, University of Adelaide, Adelaide, SA, Australia; Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia; Department of Haematology and Genetic Pathology, Flinders University and Medical Centre, Adelaide, SA, Australia.
| | - Candice Thomson
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Haematology and Bone Marrow Transplantation, Royal Adelaide Hospital, University of Adelaide, Adelaide, SA, Australia
| | - Nada Hamad
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Haematology Department, St Vincent's Hospital, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Steven W Lane
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Haematology and Bone Marrow Transplantation, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia; QIMR Berghofer Medical Research Institute, University of Queensland, Brisbane, Qld, Australia
| | - Kate Manos
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Clinical Haematology, Austin Health, Heidelberg, Vic, Australia
| | - Andrew P Grigg
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Clinical Haematology, Austin Health, Heidelberg, Vic, Australia
| | - Belinda Guo
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Wendy N Erber
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia; Haematology Department, PathWest Laboratory Medicine, Perth, WA, Australia
| | - Ashleigh Scott
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Haematology and Bone Marrow Transplantation, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Nick Viiala
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Haematology, Liverpool Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Lynette Chee
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Clinical Haematology, Royal Melbourne Hospital, Peter MacCallum Cancer Centre, Department of Medicine, The University of Melbourne, Melbourne, Vic, Australia
| | - Maya Latimer
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; ACT Pathology and Canberra Hospital, Australian National University, Canberra, ACT, Australia
| | - Courtney Tate
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Haematology Department, Gold Coast University Hospital, University of Queensland, Southport, Qld, Australia
| | - Carolyn Grove
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia; Haematology Department, PathWest Laboratory Medicine, Perth, WA, Australia; Haematology Department, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Andrew C Perkins
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Haematology, Alfred Hospital, Monash University, Melbourne, Vic, Australia
| | - Piers Blombery
- Myeloproliferative Neoplasms Working Party, Australasian Leukaemia and Lymphoma Group, Melbourne, Vic, Australia; Department of Clinical Haematology, Royal Melbourne Hospital, Peter MacCallum Cancer Centre, Department of Medicine, The University of Melbourne, Melbourne, Vic, Australia
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Applications of next-generation sequencing in hematologic malignancies. Hum Immunol 2021; 82:859-870. [PMID: 33648805 DOI: 10.1016/j.humimm.2021.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/21/2022]
Abstract
In the last decade, next-generation sequencing (NGS) has rapidly progressed from a research method to a core component of standard-of-care clinical testing. In oncology, tumor sequencing provides a critical tool to detect somatic driver mutations that not only characterize disease but also impact therapeutic decision-making. Here, we review the important role of NGS in the evaluation of hematopoietic neoplasms. We discusstechnical and practical considerations relevant in somatic mutation testing, emphasizing issues unique to blood cancers. Then, we describe how NGS data is being used to facilitate diagnosis, inform prognosis, guide therapy selection, and even monitor disease. This broad overview highlights the transformative impacts NGS data provides throughout the clinical course of patients with hematologic malignancies.
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30
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Jajosky AN, Sadri N, Meyerson HJ, Oduro KA, Kelkar A, Fitzgerald B, Tomlinson B, Moore EM, Beck RC. Clonal cytopenia of undetermined significance (CCUS) with dysplasia is enriched for MDS-type molecular findings compared to CCUS without dysplasia. Eur J Haematol 2021; 106:500-507. [PMID: 33386622 DOI: 10.1111/ejh.13574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Although morphologic dysplasia is not typically considered a feature of CCUS, we have consistently observed low-level bone marrow (BM) dysplasia among CCUS patients. We sought to determine whether sub-diagnostic BM dysplasia in CCUS patients is associated with other clinico-pathologic findings of myelodysplastic syndrome (MDS). METHODS We identified 49 CCUS patients, 25 with sub-diagnostic dysplasia (CCUS-D), and 24 having no dysplasia (CCUS-ND). We compared the clinical, histologic, and laboratory findings of CCUS-D and CCUS-ND patients to 49 MDS patients, including blood cell counts, BM morphology, flow cytometry, cytogenetics, and results of next-generation sequencing. RESULTS No statistically significant differences were observed between CCUS-D and CCUS-ND patients in the degree of cytopenias, BM cellularity, myeloid-to-erythroid ratio, or the presence of flow cytometric abnormalities. However, compared to CCUS-ND, CCUS-D patients exhibited increased mutations in myeloid malignancy-associated genes, including non-TET2/DNMT3A/ASXL1 variants, spliceosome (SF3B1, SRSF2, ZRSR2, or U2AF1) variants, and IDH2/RUNX1/CBL variants. CCUS-D patients were also enriched for higher variant allele frequencies and co-mutation of TET2/DNMT3A/ASXL1 with other genes. CONCLUSIONS CCUS-D patients exhibit a molecular (but not clinical) profile more similar to MDS patients than CCUS-ND, suggesting CCUS-D may represent a more immediate precursor to MDS and may warrant closer clinical follow-up.
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Affiliation(s)
- Audrey N Jajosky
- Department of Pathology and Laboratory Medicine, University Hospitals of Cleveland/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Navid Sadri
- Department of Pathology and Laboratory Medicine, University Hospitals of Cleveland/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Howard J Meyerson
- Department of Pathology and Laboratory Medicine, University Hospitals of Cleveland/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kwadwo A Oduro
- Department of Pathology and Laboratory Medicine, University Hospitals of Cleveland/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ashwin Kelkar
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Brynn Fitzgerald
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Benjamin Tomlinson
- Division of Hematology and Oncology, Department of Medicine, University Hospitals of Cleveland/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Erika M Moore
- Department of Pathology and Laboratory Medicine, University Hospitals of Cleveland/Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rose C Beck
- Department of Pathology and Laboratory Medicine, University Hospitals of Cleveland/Case Western Reserve University School of Medicine, Cleveland, OH, USA
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31
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Yee MEM, Batsuli G, Chonat S, Park S. Thrombocytosis with acquired von Willebrand disease in an adolescent with sickle cell disease. Clin Case Rep 2021; 9:457-460. [PMID: 33489197 PMCID: PMC7813102 DOI: 10.1002/ccr3.3556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 11/08/2022] Open
Abstract
Thrombocytosis is common in sickle cell disease and may contribute to vaso-occlusion. Hydroxyurea treats extreme thrombocytosis. Acquired von Willebrand disease should be considered prior to aspirin therapy.
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Affiliation(s)
- Marianne E. M. Yee
- Aflac Cancer and Blood Disorders CenterChildren's Healthcare of AtlantaAtlantaGAUSA
- Department of PediatricsDivision of Hematology/OncologyEmory University School of MedicineAtlantaGAUSA
| | - Glaivy Batsuli
- Aflac Cancer and Blood Disorders CenterChildren's Healthcare of AtlantaAtlantaGAUSA
- Department of PediatricsDivision of Hematology/OncologyEmory University School of MedicineAtlantaGAUSA
| | - Satheesh Chonat
- Aflac Cancer and Blood Disorders CenterChildren's Healthcare of AtlantaAtlantaGAUSA
- Department of PediatricsDivision of Hematology/OncologyEmory University School of MedicineAtlantaGAUSA
| | - Sunita Park
- Department of Pathology and Laboratory MedicineChildren's Healthcare of AtlantaAtlantaGAUSA
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32
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Patel JL, Abedi M, Cogle CR, Erba HP, Foucar K, Garcia-Manero G, Grinblatt DL, Komrokji RS, Kurtin SE, Maciejewski JP, Pollyea DA, Revicki DA, Roboz GJ, Savona MR, Scott BL, Sekeres MA, Steensma DP, Thompson MA, Dawn Flick E, Kiselev P, Louis CU, Nifenecker M, Swern AS, George TI. Real-world diagnostic testing patterns for assessment of ring sideroblasts and SF3B1 mutations in patients with newly diagnosed lower-risk myelodysplastic syndromes. Int J Lab Hematol 2020; 43:426-432. [PMID: 33220019 PMCID: PMC8247031 DOI: 10.1111/ijlh.13400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 01/01/2023]
Abstract
Introduction The presence of ring sideroblasts (RS) and mutation of the SF3B1 gene are diagnostic of lower‐risk (LR) myelodysplastic syndromes (MDS) and are correlated with favorable outcomes. However, information on testing and reporting in community‐based clinical settings is scarce. This study from the Connect® MDS/AML Disease Registry aimed to compare the frequency of RS and SF3B1 reporting for patients with LR‐MDS, before and after publication of the 2016 World Health Organization (WHO) MDS classification criteria. Methods Ring sideroblasts assessment and molecular testing data were collected from patients with LR‐MDS at enrollment in the Registry. Patients enrolled between December 2013 and the data cutoff of March 2020 were included in this analysis. Results Among 489 patients with LR‐MDS, 434 (88.8%) underwent RS assessment; 190 were assessed prior to the 2016 WHO guidelines (Cohort A), and 244 after (Cohort B). In Cohort A, 87 (45.8%) patients had RS identified; 29 (33.3%) patients had RS < 15%, none of whom underwent molecular testing for SF3B1. In Cohort B, 96 (39.3%) patients had RS identified; 31 (32.3%) patients had < 15% RS, with 13 undergoing molecular testing of which 10 were assessed for SF3B1. Conclusions In the Connect® MDS/AML Registry, only 32% of patients with <15% RS underwent SF3B1 testing after the publication of the WHO 2016 classification criteria. There was no change in RS assessment frequency before and after publication, despite the potential impact on diagnostic subtyping and therapy selection, suggesting an unmet need for education to increase testing rates for SF3B1 mutations.
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Affiliation(s)
- Jay L Patel
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Mehrdad Abedi
- University of California, Davis, Sacramento, CA, USA
| | | | | | - Kathryn Foucar
- University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | | | | | | | | | | | | | - Gail J Roboz
- Weill Cornell Medicine and The New York Presbyterian Hospital, New York, NY, USA
| | - Michael R Savona
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bart L Scott
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | - Tracy I George
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
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33
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Sportoletti P, Sorcini D, Guzman AG, Reyes JM, Stella A, Marra A, Sartori S, Brunetti L, Rossi R, Papa BD, Adamo FM, Pianigiani G, Betti C, Scialdone A, Guarente V, Spinozzi G, Tini V, Martelli MP, Goodell MA, Falini B. Bcor deficiency perturbs erythro-megakaryopoiesis and cooperates with Dnmt3a loss in acute erythroid leukemia onset in mice. Leukemia 2020; 35:1949-1963. [PMID: 33159179 PMCID: PMC8257496 DOI: 10.1038/s41375-020-01075-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/19/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022]
Abstract
Recurrent loss-of-function mutations of BCL6 co-repressor (BCOR) gene are found in about 4% of AML patients with normal karyotype and are associated with DNMT3a mutations and poor prognosis. Therefore, new anti-leukemia treatments and mouse models are needed for this combinatorial AML genotype. For this purpose, we first generated a Bcor-/- knockout mouse model characterized by impaired erythroid development (macrocytosis and anemia) and enhanced thrombopoiesis, which are both features of myelodysplasia/myeloproliferative neoplasms. We then created and characterized double Bcor-/-/Dnmt3a-/- knockout mice. Interestingly, these animals developed a fully penetrant acute erythroid leukemia (AEL) characterized by leukocytosis secondary to the expansion of blasts expressing c-Kit+ and the erythroid marker Ter119, macrocytic anemia and progressive reduction of the thrombocytosis associated with loss of Bcor alone. Transcriptomic analysis of double knockout bone marrow progenitors revealed that aberrant erythroid skewing was induced by epigenetic changes affecting specific transcriptional factors (GATA1-2) and cell-cycle regulators (Mdm2, Tp53). These findings prompted us to investigate the efficacy of demethylating agents in AEL, with significant impact on progressive leukemic burden and mice overall survival. Information gained from our model expands the knowledge on the biology of AEL and may help designing new rational treatments for patients suffering from this high-risk leukemia.
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Affiliation(s)
- Paolo Sportoletti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy.
| | - Daniele Sorcini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Anna G Guzman
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jaime M Reyes
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arianna Stella
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Andrea Marra
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Sara Sartori
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Lorenzo Brunetti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Roberta Rossi
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Beatrice Del Papa
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Francesco Maria Adamo
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Giulia Pianigiani
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Camilla Betti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Annarita Scialdone
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Valerio Guarente
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Giulio Spinozzi
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Valentina Tini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Maria Paola Martelli
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy
| | - Margaret A Goodell
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brunangelo Falini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, Perugia, 06132, Italy.
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Yao H, Wu C, Chen Y, Guo L, Chen W, Pan Y, Fu X, Wang G, Ding Y. Spectrum of gene mutations identified by targeted next-generation sequencing in Chinese leukemia patients. Mol Genet Genomic Med 2020; 8:e1369. [PMID: 32638549 PMCID: PMC7507579 DOI: 10.1002/mgg3.1369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Despite targeted sequencing have identified several mutations for leukemia, there is still a limit of mutation screening for Chinese leukemia. Here, we used targeted next-generation sequencing for testing the mutation patterns of Chinese leukemia patients. METHODS We performed targeted sequencing of 504 tumor-related genes in 109 leukemia samples to identify single-nucleotide variants (SNVs) and insertions and deletions (INDELs). Pathogenic variants were assessed based on the American College of Medical Genetics and Genomics (ACMG) guidelines. The functional impact of pathogenic genes was explored through gene ontology (GO), pathway analysis, and protein-protein interaction network in silico. RESULTS We identified a total of 4,655 SNVs and 614 INDELs in 419 genes, in which PDE4DIP, NOTCH2, FANCA, BCR, and ROS1 emerged as the highly mutated genes. Of note, we were the first to demonstrate an association of PDE4DIP mutation and leukemia. Based on ACMG guidelines, 39 pathogenic and likely pathogenic mutations in 27 genes were found. GO annotation showed that the biological process including gland development, leukocyte differentiation, respiratory system development, myeloid leukocyte differentiation, mesenchymal to epithelial transition, and so on were involved. CONCLUSION Our study provided a map of gene mutations in Chinese patients with leukemia and gave insights into the molecular pathogenesis of leukemia.
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Affiliation(s)
- Hongxia Yao
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Congming Wu
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yueqing Chen
- Hainan General Hospital, University of South China, Haikou, Hainan, China
| | - Li Guo
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Wenting Chen
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yanping Pan
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Xiangjun Fu
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Guyun Wang
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
| | - Yipeng Ding
- Department of General Practice, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, P.R. China
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35
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Beck RC, Kim AS, Goswami RS, Weinberg OK, Yeung CCS, Ewalt MD. Molecular/Cytogenetic Education for Hematopathology Fellows. Am J Clin Pathol 2020; 154:149-177. [PMID: 32444878 DOI: 10.1093/ajcp/aqaa038] [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] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES At a discussion on molecular/cytogenetic education for hematopathology fellows at the 2018 Society for Hematopathology Program Directors Meeting, consensus was that fellows should understand basic principles and indications for and limitations of molecular/cytogenetic testing used in routine practice. Fellows should also be adept at integrating results of such testing for rendering a final diagnosis. To aid these consensus goals, representatives from the Society for Hematopathology and the Association for Molecular Pathology formed a working group to devise a molecular/cytogenetic curriculum for hematopathology fellow education. CURRICULUM SUMMARY The curriculum includes a primer on cytogenetics and molecular techniques. The bulk of the curriculum reviews the molecular pathology of individual malignant hematologic disorders, with applicable molecular/cytogenetic testing for each and following the 2017 World Health Organization classification of hematologic neoplasms. Benign hematologic disorders and bone marrow failure syndromes are also discussed briefly. Extensive tables are used to summarize genetics of individual disorders and appropriate methodologies. CONCLUSIONS This curriculum provides an overview of the current understanding of the molecular biology of hematologic disorders and appropriate ancillary testing for their evaluation. The curriculum may be used by program directors for training hematopathology fellows or by practicing hematopathologists.
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Affiliation(s)
- Rose C Beck
- Department of Pathology, University Hospitals of Cleveland, Case Western Reserve University, Cleveland, OH (Society for Hematopathology Representative)
| | - Annette S Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA (Association for Molecular Pathology Representative)
| | - Rashmi S Goswami
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Olga K Weinberg
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Cecilia C S Yeung
- Department of Pathology, University of Washington, and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Mark D Ewalt
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora
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Ong J, Lin JI, Mitchell H, Morgan S, Perkins AC. Clinical acceleration of JAK2 p.V617F driven myeloproliferative disease due to a new uncommon homozygous MPL p.Y591D mutation. Haematologica 2020; 105:e428-e431. [PMID: 32499240 DOI: 10.3324/haematol.2020.250969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jeremy Ong
- Department of Pathology, Alfred Health, Melbourne, Australia.,Department of Clinical Haematology, Alfred Health, Melbourne, Australia
| | - Jane I Lin
- Department of Pathology, Alfred Health, Melbourne, Australia
| | - Helen Mitchell
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia
| | - Susan Morgan
- Department of Clinical Haematology, Alfred Health, Melbourne, Australia
| | - Andrew C Perkins
- Australian Centre for Blood Diseases, Monash University, Melbourne, Australia .,Department of Clinical Haematology, Alfred Health, Melbourne, Australia
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Luskin MR, Kim AS, Patel SS, Wright K, LeBoeuf NR, Lane AA. Evidence for separate transformation to acute myeloid leukemia and blastic plasmacytoid dendritic cell neoplasm from a shared ancestral hematopoietic clone. Leuk Lymphoma 2020; 61:2258-2261. [PMID: 32366145 DOI: 10.1080/10428194.2020.1755856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sanjay S Patel
- Division of Hematopathology, Department of Pathology, Weill Cornell Medical College, New York, NY, USA
| | - Kyle Wright
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicole R LeBoeuf
- Department of Dermatology, Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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38
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Clinical Validation of a Myeloid Next-Generation Sequencing Panel for Single-Nucleotide Variants, Insertions/Deletions, and Fusion Genes. J Mol Diagn 2020; 22:208-219. [DOI: 10.1016/j.jmoldx.2019.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
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39
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Keegan A, Bridge JA, Lindeman NI, Long TA, Merker JD, Moncur JT, Montgomery ND, Nagarajan R, Rothberg PG, Routbort MJ, Vasalos P, Xian R, Kim AS. Proficiency Testing of Standardized Samples Shows High Interlaboratory Agreement for Clinical Next Generation Sequencing-Based Hematologic Malignancy Assays With Survey Material-Specific Differences in Variant Frequencies. Arch Pathol Lab Med 2020; 144:959-966. [PMID: 31986076 DOI: 10.5858/arpa.2019-0352-cp] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— As laboratories increasingly turn from single-analyte testing in hematologic malignancies to next-generation sequencing-based panel testing, there is a corresponding need for proficiency testing to ensure adequate performance of these next-generation sequencing assays for optimal patient care. OBJECTIVE.— To report the performance of laboratories on proficiency testing from the first 4 College of American Pathologists Next-Generation Sequencing Hematologic Malignancy surveys. DESIGN.— College of American Pathologists proficiency testing results for 36 different engineered variants and/or allele fractions as well as a sample with no pathogenic variants were analyzed for accuracy and associated assay performance characteristics. RESULTS.— The overall sensitivity observed for all variants was 93.5% (2190 of 2341) with 99.8% specificity (22 800 of 22 840). The false-negative rate was 6.5% (151 of 2341), and the largest single cause of these errors was difficulty in identifying variants in the sequence of CEBPA that is rich in cytosines and guanines. False-positive results (0.18%; 40 of 22 840) were most likely the result of preanalytic or postanalytic errors. Interestingly, the variant allele fractions were almost uniformly lower than the engineered fraction (as measured by digital polymerase chain reaction). Extensive troubleshooting identified a multifactorial cause for the low variant allele fractions, a result of an interaction between the linearized nature of the plasmid and the Illumina TruSeq chemistry. CONCLUSIONS.— Laboratories demonstrated an overall accuracy of 99.2% (24 990 of 25 181) with 99.8% specificity and 93.5% sensitivity when examining 36 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 10% or greater. The data also highlight an issue with artificial linearized plasmids as survey material for next-generation sequencing.
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Affiliation(s)
- Alissa Keegan
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Julia A Bridge
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Neal I Lindeman
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Thomas A Long
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Jason D Merker
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Joel T Moncur
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Nathan D Montgomery
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Rakesh Nagarajan
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Paul G Rothberg
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Mark J Routbort
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Patricia Vasalos
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Rena Xian
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Annette S Kim
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
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40
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Clinical utility of targeted next-generation sequencing–based screening of peripheral blood in the evaluation of cytopenias. Blood 2019; 134:2222-2225. [DOI: 10.1182/blood.2019001610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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41
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Zehnbauer BA. The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice. J Mol Diagn 2019; 21:938-942. [PMID: 31635797 DOI: 10.1016/j.jmoldx.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023] Open
Abstract
This editorial highlights 20 years of JMD defining professional practice.
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Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
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42
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Palomo L, Ibáñez M, Abáigar M, Vázquez I, Álvarez S, Cabezón M, Tazón-Vega B, Rapado I, Fuster-Tormo F, Cervera J, Benito R, Larrayoz MJ, Cigudosa JC, Zamora L, Valcárcel D, Cedena MT, Acha P, Hernández-Sánchez JM, Fernández-Mercado M, Sanz G, Hernández-Rivas JM, Calasanz MJ, Solé F, Such E. Spanish Guidelines for the use of targeted deep sequencing in myelodysplastic syndromes and chronic myelomonocytic leukaemia. Br J Haematol 2019; 188:605-622. [PMID: 31621063 PMCID: PMC7064979 DOI: 10.1111/bjh.16175] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/04/2019] [Accepted: 07/06/2019] [Indexed: 12/20/2022]
Abstract
The landscape of medical sequencing has rapidly changed with the evolution of next generation sequencing (NGS). These technologies have contributed to the molecular characterization of the myelodysplastic syndromes (MDS) and chronic myelomonocytic leukaemia (CMML), through the identification of recurrent gene mutations, which are present in >80% of patients. These mutations contribute to a better classification and risk stratification of the patients. Currently, clinical laboratories include NGS genomic analyses in their routine clinical practice, in an effort to personalize the diagnosis, prognosis and treatment of MDS and CMML. NGS technologies have reduced the cost of large-scale sequencing, but there are additional challenges involving the clinical validation of these technologies, as continuous advances are constantly being made. In this context, it is of major importance to standardize the generation, analysis, clinical interpretation and reporting of NGS data. To that end, the Spanish MDS Group (GESMD) has expanded the present set of guidelines, aiming to establish common quality standards for the adequate implementation of NGS and clinical interpretation of the results, hoping that this effort will ultimately contribute to the benefit of patients with myeloid malignancies.
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Affiliation(s)
- Laura Palomo
- Josep Carreras Leukaemia Research Institute, ICO Badalona-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Sadalona, Spain
| | - Mariam Ibáñez
- Department of Haematology, Hospital Universitari i Politècnic La Fe, València, Spain.,Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain.,Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, València, Spain
| | - María Abáigar
- Institute of Biomedical Research of Salamanca (IBSAL), Cancer Research Centre (IBMCC-CIC; Univ. of Salamanca-CSIC), Salamanca, Spain
| | - Iria Vázquez
- Haematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Sara Álvarez
- NIMGenetics, Genómica y Medicina, S.L., Madrid, Spain
| | - Marta Cabezón
- Haematology Service, ICO Badalona-Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Bárbara Tazón-Vega
- Department of Haematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain.,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Inmaculada Rapado
- Haematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Haematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,Centro de investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Francisco Fuster-Tormo
- Josep Carreras Leukaemia Research Institute, ICO Badalona-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Sadalona, Spain
| | - José Cervera
- Department of Haematology, Hospital Universitari i Politècnic La Fe, València, Spain.,Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain.,Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Rocío Benito
- Institute of Biomedical Research of Salamanca (IBSAL), Cancer Research Centre (IBMCC-CIC; Univ. of Salamanca-CSIC), Salamanca, Spain
| | - María J Larrayoz
- Haematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | | | - Lurdes Zamora
- Haematology Service, ICO Badalona-Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - David Valcárcel
- Department of Haematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain.,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María T Cedena
- Haematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.,Haematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain.,Centro de investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Pamela Acha
- Josep Carreras Leukaemia Research Institute, ICO Badalona-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Sadalona, Spain
| | - Jesús M Hernández-Sánchez
- Institute of Biomedical Research of Salamanca (IBSAL), Cancer Research Centre (IBMCC-CIC; Univ. of Salamanca-CSIC), Salamanca, Spain.,University of Salamanca (USAL), Salamanca, Spain
| | - Marta Fernández-Mercado
- Haematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain.,Advanced Genomics Laboratory, Centre for Applied Medical Research (CIMA), University of Navarra, Haemato-Oncology, Pamplona, Spain.,Biomedical Engineering Department, School of Engineering, University of Navarra, San Sebastian, Spain
| | - Guillermo Sanz
- Department of Haematology, Hospital Universitari i Politècnic La Fe, València, Spain.,Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Jesús M Hernández-Rivas
- Institute of Biomedical Research of Salamanca (IBSAL), Cancer Research Centre (IBMCC-CIC; Univ. of Salamanca-CSIC), Salamanca, Spain.,University of Salamanca (USAL), Salamanca, Spain.,Hospital Universitario de Salamanca, Salamanca, Spain
| | - María J Calasanz
- Haematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Francesc Solé
- Josep Carreras Leukaemia Research Institute, ICO Badalona-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Sadalona, Spain
| | - Esperanza Such
- Department of Haematology, Hospital Universitari i Politècnic La Fe, València, Spain.,Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain.,Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, València, Spain
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Soma LA, Kovach AE, Siddon AJ, Beck R, Gibson SE, Swerdlow SH, Kim AS, Wu D, Jones D, Cook JR, Prakash S, Rosado F, Crane G, Bradley K, Weinberg OK, Sargent RL. Molecular and Cytogenetic Education in Hematopathology Fellowship. Am J Clin Pathol 2019; 152:438-445. [PMID: 31141139 DOI: 10.1093/ajcp/aqz048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Given the increased complexity of molecular and cytogenetic testing (MOL-CG), the Society for Hematopathology Education Committee (SH-EC) was interested in determining what the current expectations are for MOL-CG education in hematopathology (HP) fellowship training. METHODS The SH-EC sent a questionnaire to HP fellowship program directors (HP-PDs) covering MOL-CG training curricula, test menus, faculty background, teaching, and sign-out roles. These findings were explored via a panel-based discussion at the 2018 SH-EC meeting for HP-PDs. RESULTS HP fellows are expected to understand basic principles, nomenclature, and indications for and limitations of testing. Interpretation of common assays is within that scope, but not necessarily proficiency in technical troubleshooting of testing or analysis of complex raw data. CONCLUSIONS The consensus was that HP fellows should understand the components of MOL-CG testing necessary to incorporate those results into an accurate, clinically relevant, and integrated HP report.
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Affiliation(s)
- Lorinda A Soma
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle
| | - Alexandra E Kovach
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center and Monroe Carell Jr Children’s Hospital at Vanderbilt, Nashville, TN
| | - Alexa J Siddon
- Department of Laboratory Medicine, Yale University, New Haven, CT
| | - Rose Beck
- Department of Pathology, University Hospitals of Cleveland/Case Western Reserve University, Cleveland, OH
| | - Sarah E Gibson
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix
| | - Steven H Swerdlow
- Department of Anatomic and Clinical Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Annette S Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - David Wu
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle
| | - Dan Jones
- Department of Pathology, The Ohio State University, Columbus
| | - James R Cook
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Sonam Prakash
- Department of Laboratory Medicine, University of California, San Francisco
| | - Flavia Rosado
- Department of Pathology, University of Texas Southwestern, Dallas
| | - Genevieve Crane
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Kyle Bradley
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA
| | - Olga K Weinberg
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Rachel L Sargent
- Oncology Diagnostics, Janssen Research and Development, Spring House, PA
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Affinity Purification of NF1 Protein-Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners. Genes (Basel) 2019; 10:genes10090650. [PMID: 31466283 PMCID: PMC6770187 DOI: 10.3390/genes10090650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022] Open
Abstract
Neurofibromatosis Type 1 (NF1) is caused by pathogenic variants in the NF1 gene encoding neurofibromin. Definition of NF1 protein–protein interactions (PPIs) has been difficult and lacks replication, making it challenging to define binding partners that modulate its function. We created a novel tandem affinity purification (TAP) tag cloned in frame to the 3’ end of the full-length murine Nf1 cDNA (mNf1). We show that this cDNA is functional and expresses neurofibromin, His-Tag, and can correct p-ERK/ERK ratios in NF1 null HEK293 cells. We used this affinity tag to purify binding partners with Strep-Tactin®XT beads and subsequently, identified them via mass spectrometry (MS). We found the tagged mNf1 can affinity purify human neurofibromin and vice versa, indicating that neurofibromin oligomerizes. We identify 21 additional proteins with high confidence of interaction with neurofibromin. After Metacore network analysis of these 21 proteins, eight appear within the same network, primarily keratins regulated by estrogen receptors. Previously, we have shown that neurofibromin levels negatively regulate keratin expression. Here, we show through pharmacological inhibition that this is independent of Ras signaling, as the inhibitors, selumetinib and rapamycin, do not alter keratin expression. Further characterization of neurofibromin oligomerization and binding partners could aid in discovering new neurofibromin functions outside of Ras regulation, leading to novel drug targets.
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Baer C, Walter W, Hutter S, Twardziok S, Meggendorfer M, Kern W, Haferlach T, Haferlach C. "Somatic" and "pathogenic" - is the classification strategy applicable in times of large-scale sequencing? Haematologica 2019; 104:1515-1520. [PMID: 31273095 PMCID: PMC6669162 DOI: 10.3324/haematol.2019.218917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022] Open
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