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Zheng G, Chen P, Pallavajjalla A, Haley L, Gondek L, Dezern A, Ling H, De Marchi F, Lin MT, Gocke C. The diagnostic utility of targeted gene panel sequencing in discriminating etiologies of cytopenia. Am J Hematol 2019; 94:1141-1148. [PMID: 31350794 PMCID: PMC9162094 DOI: 10.1002/ajh.25592] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 01/03/2023]
Abstract
The diagnostic utility of somatic mutations in the context of cytopenias is unclear: clonal hematopoiesis can be found in healthy individuals, patients with aplastic anemia (AA), clonal cytopenia of undetermined significance (CCUS) and myelodysplastic syndrome (MDS). We examined a cohort of 207 well-characterized cytopenic patients with a 640-gene next generation sequencing (NGS) panel and compared its diagnostic utility with a "virtual" 41 gene panel. The TET2, SF3B1, ASXL1, and TP53 were the most commonly mutated genes (frequency > 10%). Mutations in the 640-gene panel show high sensitivity (98.3%) but low specificity (47.6%) for diagnosis of MDS. Notably, mutations of splicing factors and genes in the RAS pathway are relatively specific to MDS. Furthermore, high variant allele frequency (VAF) predicts MDS: when the VAF is set at 20%, the positive predictive value (PPV) for MDS is 95.9%, with a specificity of 95.3%. The presence of two or more somatic mutations with ≥10% VAF showed a PPV of 95.2%. While the "virtual" 41-gene panel showed a mild decrease in sensitivity (95.7% vs 98.3%), 100% specificity was observed when either VAF was set at ≥20% (100% vs 95.3%), or two or more somatic mutations had VAFs ≥ 10%. Our study shows targeted gene panel sequencing improves the diagnostic approach and accuracy for unexplained cytopenia, with its high sensitivity and high PPV for MDS when applying VAF cutoffs. Furthermore, a 41-gene panel was shown to have at least comparable performance characteristics to the large 640-gene panel.
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Affiliation(s)
- Gang Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, Minnesota
| | - Ping Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Hematology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Aparna Pallavajjalla
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lisa Haley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lukasz Gondek
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Amy Dezern
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Federico De Marchi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Chokr N, Pine AB, Bewersdorf JP, Shallis RM, Stahl M, Zeidan AM. Getting personal with myelodysplastic syndromes: is now the right time? Expert Rev Hematol 2019; 12:215-224. [PMID: 30977414 PMCID: PMC6540985 DOI: 10.1080/17474086.2019.1592673] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/06/2019] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Commonly used scoring systems rely on blood counts, histological and cytological examination of bone marrow and peripheral blood as well as cytogenetic assessments to estimate prognosis of patients with myelodysplastic syndromes (MDS) and guide therapy decisions. Next-generation sequencing (NGS) has identified recurrent genetic abnormalities in up to 90% of patients with MDS and may provide important information regarding the pathogenesis of the disease, diagnostic and prognostic evaluation, and therapy selection. Areas covered: Herein, the authors review the role of NGS in diagnosis, treatment, and prognosis of MDS at various disease stages, and discuss advantages and caveats of incorporating molecular genetics in routine management of MDS. While a vast majority of patients harbor recurrent mutations implicated in MDS pathogenesis, similar mutations can be detected in otherwise healthy individuals with other hematologic malignancies. Besides establishing a diagnosis, NGS may be used to monitor minimal residual disease following treatment. Expert opinion: As more targeted therapies become available, assessment of genetic mutations will become central to individualized therapy selection and may improve diagnostic accuracy and further guide management for each patient. However, multiple challenges remain before NGS can be incorporated into routine clinical practice.
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Affiliation(s)
- Nora Chokr
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA
| | - Alexander B. Pine
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA
| | - Jan Philipp Bewersdorf
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA
| | - Rory M. Shallis
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA
| | - Maximilian Stahl
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA
| | - Amer M. Zeidan
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA
- Cancer Outcomes, Public Policy, and Effectiveness Research (COPPER) Center, Yale University, New Haven, USA
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How I use molecular genetic tests to evaluate patients who have or may have myelodysplastic syndromes. Blood 2018; 132:1657-1663. [PMID: 30185432 DOI: 10.1182/blood-2018-06-860882] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/30/2018] [Indexed: 11/20/2022] Open
Abstract
Myelodysplastic syndromes (MDS) can be difficult to diagnose, especially when morphological changes in blood and marrow cells are minimal, myeloblast proportion is not increased, and the karyotype is normal. The discovery of >40 genes that are recurrently somatically mutated in MDS patients raised hope that molecular genetic testing for these mutations might help clarify the diagnosis in ambiguous cases where patients present with cytopenias and nondiagnostic marrow morphological findings. However, many older healthy individuals also harbor somatic mutations in leukemia-associated driver genes, especially in DNMT3A, TET2, and ASXL1, and detection of common aging-associated mutations in a cytopenic patient can cause diagnostic uncertainty. Despite this potential confounding factor, certain somatic mutation patterns when observed in cytopenic patients confer a high likelihood of disease progression and may allow a provisional diagnosis of MDS even if morphologic dysplasia and other diagnostic criteria are absent. A subset of acquired mutations also influences risk stratification of patients with an established MDS diagnosis and can inform treatment selection. Many unanswered questions remain about the implications of specific mutations, and clinicians also vary widely in their comfort with interpreting sequencing results. Here, I review the use of molecular genetic assays in patients with possible MDS or diagnosed MDS.
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Wang K, Chao HY, Wu P, He C, Zhang R, Shen HJ, Chen SN. [High throughput sequencing combined with DNA-PCR for detection of 51 kinds of hematologic malignancy related gene mutations in patients with myelodysplastic syndromes]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2018; 39:431-434. [PMID: 29779357 PMCID: PMC7342906 DOI: 10.3760/cma.j.issn.0253-2727.2018.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | - R Zhang
- Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou 215006, China
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