1
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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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2
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Cross NCP, Ernst T, Branford S, Cayuela JM, Deininger M, Fabarius A, Kim DDH, Machova Polakova K, Radich JP, Hehlmann R, Hochhaus A, Apperley JF, Soverini S. European LeukemiaNet laboratory recommendations for the diagnosis and management of chronic myeloid leukemia. Leukemia 2023; 37:2150-2167. [PMID: 37794101 PMCID: PMC10624636 DOI: 10.1038/s41375-023-02048-y] [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: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
From the laboratory perspective, effective management of patients with chronic myeloid leukemia (CML) requires accurate diagnosis, assessment of prognostic markers, sequential assessment of levels of residual disease and investigation of possible reasons for resistance, relapse or progression. Our scientific and clinical knowledge underpinning these requirements continues to evolve, as do laboratory methods and technologies. The European LeukemiaNet convened an expert panel to critically consider the current status of genetic laboratory approaches to help diagnose and manage CML patients. Our recommendations focus on current best practice and highlight the strengths and pitfalls of commonly used laboratory tests.
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Affiliation(s)
| | - Thomas Ernst
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Susan Branford
- Centre for Cancer Biology and SA Pathology, Adelaide, SA, Australia
| | - Jean-Michel Cayuela
- Laboratory of Hematology, University Hospital Saint-Louis, AP-HP and EA3518, Université Paris Cité, Paris, France
| | | | - Alice Fabarius
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | | | | | - Rüdiger Hehlmann
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
- ELN Foundation, Weinheim, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Jane F Apperley
- Centre for Haematology, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Simona Soverini
- Department of Medical and Surgical Sciences, Institute of Hematology "Lorenzo e Ariosto Seràgnoli", University of Bologna, Bologna, Italy
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3
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Zhao D, Zhou Q, Zarif M, Eladl E, Wei C, Atenafu EG, Schuh A, Tierens A, Yeung YWT, Minden MD, Chang H. AML with CEBPA mutations: A comparison of ICC and WHO-HAEM5 criteria in patients with 20% or more blasts. Leuk Res 2023; 134:107376. [PMID: 37690321 DOI: 10.1016/j.leukres.2023.107376] [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: 07/13/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
AML with CEBPA mutation and AML with in-frame bZIP CEBPA mutations define favorable-risk disease entities in the proposed 5th edition of the World Health Organization Classification (WHO-HAEM5) and the International Consensus Classification (ICC), respectively. However, the impact of these new classifications on clinical practice remains unclear. We sought to assess the differences between the ICC and WHO-HAEM5 for AML with CEBPA mutation. 741 AML patients were retrospectively analyzed. Cox proportional-hazard regression was used to identify factors predictive of outcome. A validation cohort from the UK-NCRI clinical trials was used to confirm our findings. 81 (11%) AML patients had CEBPA mutations. 39 (48%) patients met WHO-HAEM5 criteria for AML with CEBPA mutation, among which 30 (77%) had biallelic CEBPA mutations and 9 (23%) had a single bZIP mutation. Among the 39 patients who met WHO-HAEM5 criteria, 25 (64%) also met ICC criteria. Compared to patients only meeting WHO-HAEM5 criteria, patients with in-frame bZIP CEBPA mutations (ie. meeting both WHO-HAEM5 and ICC criteria) were younger, had higher bone marrow blast percentages and CEBPA mutation burden, infrequently harboured 2022 ELN high-risk genetic features and co-mutations in other genes, and had superior outcomes. The associations in clinicopathological features and outcomes between the CEBPA-mutated groups were validated in the UK-NCRI cohort. Our study indicates that in-frame bZIP CEBPA mutations are the critical molecular aberrations associated with favorable outcomes in AML patients treated with curative intent chemotherapy. Compared to WHO-HAEM5, the ICC identifies a more homogenous group of CEBPA-mutated AML patients with favorable outcomes.
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Affiliation(s)
- Davidson Zhao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Qianghua Zhou
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Mojgan Zarif
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Entsar Eladl
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Cuihong Wei
- Department of Clinical Laboratory Genetics, Genome Diagnostics & Cancer Cytogenetics, University Health Network, Toronto, ON, Canada
| | - Eshetu G Atenafu
- Department of Biostatistics, University Health Network, Toronto, ON, Canada
| | - Andre Schuh
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Anne Tierens
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Yu Wing Tony Yeung
- Department of Laboratory Medicine, St. Michael's Hospital, Toronto, ON, Canada
| | - Mark D Minden
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Hong Chang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada.
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4
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Zhao D, Zarif M, Zhou Q, Capo-Chichi JM, Schuh A, Minden MD, Atenafu EG, Kumar R, Chang H. TP53 Mutations in AML Patients Are Associated with Dismal Clinical Outcome Irrespective of Frontline Induction Regimen and Allogeneic Hematopoietic Cell Transplantation. Cancers (Basel) 2023; 15:3210. [PMID: 37370821 DOI: 10.3390/cancers15123210] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
TP53 mutations are associated with extremely poor outcomes in acute myeloid leukemia (AML). The outcomes of patients with TP53-mutated (TP53MUT) AML after different frontline treatment modalities are not well established. Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative procedure for AML; however, long-term outcomes among patients with TP53MUT AML after allo-HCT are dismal, and the benefit of allo-HCT remains controversial. We sought to evaluate the outcomes of patients with TP53MUT AML after treatment with different frontline induction therapies and allo-HCT. A total of 113 patients with TP53MUT AML were retrospectively evaluated. Patients with TP53MUT AML who received intensive or azacitidine-venetoclax induction had higher complete remission rates compared to patients treated with other hypomethylating-agent-based induction regimens. However, OS and EFS were not significantly different among the induction regimen groups. Allo-HCT was associated with improved OS and EFS among patients with TP53MUT AML; however, allo-HCT was not significantly associated with improved OS or EFS in time-dependent or landmark analysis. While the outcomes of all patients were generally poor irrespective of therapeutic strategy, transplanted patients with lower TP53MUT variant allele frequency (VAF) at the time of diagnosis had superior outcomes compared to transplanted patients with higher TP53 VAF. Our study provides further evidence that the current standards of care for AML confer limited therapeutic benefit to patients with TP53 mutations.
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Affiliation(s)
- Davidson Zhao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Mojgan Zarif
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Qianghua Zhou
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - José-Mario Capo-Chichi
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Andre Schuh
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Mark D Minden
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Eshetu G Atenafu
- Department of Biostatistics, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Rajat Kumar
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Hans Messner Allogeneic Blood and Marrow Transplantation Program, Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Hong Chang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Laboratory Hematology, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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5
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Zhao D, Eladl E, Zarif M, Capo‐Chichi J, Schuh A, Atenafu E, Minden M, Chang H. Molecular characterization of
AML‐MRC
reveals
TP53
mutation as an adverse prognostic factor irrespective of
MRC
‐defining criteria,
TP53
allelic state, or
TP53
variant allele frequency. Cancer Med 2022; 12:6511-6522. [PMID: 36394085 PMCID: PMC10067127 DOI: 10.1002/cam4.5421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/30/2022] [Accepted: 10/23/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) generally confers poor prognosis, however, patient outcomes are heterogeneous. The impact of TP53 allelic state and variant allele frequency (VAF) in AML-MRC remains poorly defined. METHODS We retrospectively evaluated 266 AML-MRC patients who had NGS testing at our institution from 2014 to 2020 and analyzed their clinical outcomes based on clinicopathological features. RESULTS TP53 mutations were associated with cytogenetic abnormalities in 5q, 7q, 17p, and complex karyotype. Prognostic evaluation of TP53MUT AML-MRC revealed no difference in outcome between TP53 double/multi-hit state and single-hit state. Patients with high TP53MUT variant allele frequency (VAF) had inferior outcomes compared to patients with low TP53MUT VAF. When compared to TP53WT patients, TP53MUT patients had inferior outcomes regardless of MRC-defining criteria, TP53 allelic state, or VAF. TP53 mutations and elevated serum LDH were independent predictors for inferior OS and EFS, while PHF6 mutations and transplantation were independent predictors for favorable OS and EFS. NRAS mutation was an independent predictor for favorable EFS. CONCLUSIONS Our study suggests that TP53MUT AML-MRC defines a very-high-risk subentity of AML in which novel therapies should be explored.
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Affiliation(s)
- Davidson Zhao
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
- Department of Hematology and Medical Oncology University Health Network Toronto Ontario Canada
| | - Entsar Eladl
- Department of Hematology and Medical Oncology University Health Network Toronto Ontario Canada
- Department of Pathology, Faculty of Medicine Mansoura University Mansoura Egypt
| | - Mojgan Zarif
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
- Department of Hematology and Medical Oncology University Health Network Toronto Ontario Canada
| | - José‐Mario Capo‐Chichi
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
- Department of Hematology and Medical Oncology University Health Network Toronto Ontario Canada
| | - Andre Schuh
- Department of Hematology and Medical Oncology University Health Network Toronto Ontario Canada
| | - Eshetu Atenafu
- Department of Biostatistics University Health Network Toronto Ontario Canada
| | - Mark Minden
- Department of Hematology and Medical Oncology University Health Network Toronto Ontario Canada
| | - Hong Chang
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
- Department of Hematology and Medical Oncology University Health Network Toronto Ontario Canada
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6
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Shanmuganathan N, Wadham C, Thomson D, Shahrin NH, Vignaud C, Obourn V, Chaturvedi S, Yang F, Feng J, Saunders V, Kok CH, Yeung D, King RM, Kenyon RR, Lin M, Wang P, Scott H, Hughes T, Schreiber AW, Branford S. RNA-Based Targeted Gene Sequencing Improves the Diagnostic Yield of Mutant Detection in Chronic Myeloid Leukemia. J Mol Diagn 2022; 24:803-822. [PMID: 35550185 DOI: 10.1016/j.jmoldx.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 11/28/2022] Open
Abstract
Mutation detection is increasingly used for the management of hematological malignancies. Prior whole transcriptome and whole exome sequencing studies using total RNA and DNA identified diverse mutation types in cancer-related genes associated with treatment failure in patients with chronic myeloid leukemia. Variants included single-nucleotide variants and small insertions/deletions, plus fusion transcripts and partial or whole gene deletions. The hypothesis that all of these mutation types could be detected by a single cost-effective hybridization capture next-generation sequencing method using total RNA was assessed. A method was developed that targeted 130 genes relevant for myeloid and lymphoid leukemia. Retrospective samples with 121 precharacterized variants were tested using total RNA and/or DNA. Concordance of detection of precharacterized variants using RNA or DNA was 96%, whereas the enhanced sensitivity identified additional variants. Comparison between 24 matched DNA and RNA samples demonstrated 95.3% of 170 variants detectable using DNA were detected using RNA, including all but one variant predicted to activate nonsense-mediated decay. RNA identified an additional 10 variants, including fusion transcripts. Furthermore, the true effect of splice variants on RNA splicing was only evident using RNA. In conclusion, capture sequencing using total RNA alone is suitable for detecting a range of variants relevant in chronic myeloid leukemia and may be more broadly applied to other hematological malignancies where diverse variant types define risk groups.
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Affiliation(s)
- Naranie Shanmuganathan
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia; Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
| | - Carol Wadham
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Daniel Thomson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Nur H Shahrin
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | | | - Vanessa Obourn
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Feng Yang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Jinghua Feng
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Verity Saunders
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Chung H Kok
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - David Yeung
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Rob M King
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Rosalie R Kenyon
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Ming Lin
- Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Paul Wang
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Timothy Hughes
- Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Andreas W Schreiber
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
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7
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Zhao D, Zarif M, Eladl E, Capo-Chichi JM, CSmith A, Atenafu E, Tierens A, Minden M, Schuh A, Chang H. NPM1-mutated AML-MRC diagnosed on the basis of history of MDS or MDS/MPN frequently harbours secondary-type mutations and confers inferior outcome compared to AML with mutated NPM1. Leuk Res 2022; 118:106869. [DOI: 10.1016/j.leukres.2022.106869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
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8
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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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9
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Ferrone CK, Wong H, Semenuk L, Werunga B, Snetsinger B, Zhang X, Zhang G, Lui J, Richard-Carpentier G, Crocker S, Good D, Hay AE, Quest G, Carson N, Feilotter HE, Rauh MJ. Validation, Implementation, and Clinical Impact of the Oncomine Myeloid Targeted-Amplicon DNA and RNA Ion Semiconductor Sequencing Assay. J Mol Diagn 2021; 23:1292-1305. [PMID: 34365012 DOI: 10.1016/j.jmoldx.2021.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/04/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022] Open
Abstract
The identification of clinically significant genes recurrently mutated in myeloid malignancies necessitates expanding diagnostic testing with higher throughput, such as targeted next-generation sequencing. We present validation of the Thermo Fisher Oncomine Myeloid Next-Generation Sequencing Panel (OMP), targeting 40 genes and 29 fusion drivers recurrently mutated in myeloid malignancies. The study includes data from a sample exchange between two Canadian hospitals demonstrating high concordance for detection of DNA and RNA aberrations. Clinical validation demonstrates high accuracy, sensitivity, and specificity of the OMP, with a lower limit of detection of 5% for single-nucleotide variants and 10% for insertions/deletions. Prospective sequencing was performed for 187 samples from 168 unique patients presenting with suspected or confirmed myeloid malignancy and other hematological conditions to assess clinical impact of identifying variants. Of detected variants, 48% facilitated or clarified diagnoses, 29% affected prognoses, and 25% had the potential to influence clinical management. Of note, OMP was essential to identifying patients with premalignant clonal states likely contributing to cytopenias. We also found that the detection of even a single variant by the OMP assay, versus 0 variants, was predictive of overall survival, independent of age, sex, or diagnosis (P = 0.03). This study demonstrates that molecular profiling of myeloid malignancies with the OMP represents a promising strategy to advance molecular diagnostics.
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Affiliation(s)
- Christina K Ferrone
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Henry Wong
- Molecular Genetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Laura Semenuk
- Molecular Genetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Barnaba Werunga
- Division of Genetics, Department of Lab Medicine and Pathology, Saint John Regional Hospital, Saint John, New Brunswick, Canada
| | - Brooke Snetsinger
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Xiao Zhang
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Grace Zhang
- Division of Hematology, Department of Medicine, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Janet Lui
- Division of Hematology, Department of Medicine, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | | | - Susan Crocker
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada; Cytogenetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - David Good
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Annette E Hay
- Division of Hematology, Department of Medicine, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Graeme Quest
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Nancy Carson
- Division of Genetics, Department of Lab Medicine and Pathology, Saint John Regional Hospital, Saint John, New Brunswick, Canada
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada; Molecular Genetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.
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10
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Sahajpal NS, Mondal AK, Ananth S, Njau A, Ahluwalia P, Jones K, Ahluwalia M, Okechukwu N, Savage NM, Kota V, Rojiani AM, Kolhe R. Clinical performance and utility of a comprehensive next-generation sequencing DNA panel for the simultaneous analysis of variants, TMB and MSI for myeloid neoplasms. PLoS One 2020; 15:e0240976. [PMID: 33075099 PMCID: PMC7571681 DOI: 10.1371/journal.pone.0240976] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 10/06/2020] [Indexed: 01/10/2023] Open
Abstract
The extensively employed limited-gene coverage NGS panels lead to clinically inadequate molecular profiling of myeloid neoplasms. The aim of the present investigation was to assess performance and clinical utility of a comprehensive DNA panel for myeloid neoplasms. Sixty-one previously well characterized samples were sequenced using TSO500 library preparation kit on NextSeq550 platform. Variants with a VAF ≥ 5% and a total read depth of >50X were filtered for analysis. The following results were recorded-for clinical samples: clinical sensitivity (97%), specificity (100%), precision (100%) and accuracy (99%) whereas reference control results were 100% for analytical sensitivity, specificity, precision and accuracy, with high intra- and inter-run reproducibility. The panel identified 880 variants across 292 genes, of which, 749 variants were in genes not covered in the 54 gene panel. The investigation revealed 14 variants in ten genes, and at least one was present in 96.2% patient samples that were pathogenic/ likely pathogenic in myeloid neoplasms. Also, 15 variants in five genes were found to be pathogenic/ likely pathogenic in other tumor types. Further, the TMB and MSI scores ranged from 0–7 and 0–9, respectively. The high analytical performance and clinical utility of this comprehensive NGS panel makes it practical and clinically relevant for adoption in clinical laboratories for routine molecular profiling of myeloid neoplasms.
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Affiliation(s)
- Nikhil Shri Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Allan Njau
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Kimya Jones
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Meenakshi Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Nwogbo Okechukwu
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Natasha M. Savage
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Amyn M. Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, United States of America
- * E-mail:
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11
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Jiang G, Capo-Chichi JM, Liu A, Atenafu EG, Guo R, Tierens A, Minden MD, Chang H. Acute myeloid leukemia with myelodysplasia-related changes diagnosed with multilineage dysplasia alone demonstrates a superior clinical outcome. Hum Pathol 2020; 104:117-126. [PMID: 32798550 DOI: 10.1016/j.humpath.2020.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) generally confers poor prognosis; however, the clinical outcome remains heterogeneous. We sought to further stratify this subentity of AML by performing a retrospective analysis of 179 adult patients with AML-MRC diagnosed at our institution. Based on 2016 World Health Organization diagnostic criteria, 44 (25%) patients had multilineage dysplasia alone (AML-MRC-M), 74 (41%) had history of myelodysplastic syndrome (MDS) or myelodysplastic/myeloproliferative disease (AML-MRC-H), and 61 (34%) had MDS-related cytogenetics (AML-MRC-C). AML-MRC-M and hematopoietic stem cell transplantation (HSCT) were associated with prolonged event-free survival (EFS) (P = 0.0051 and P < 0.0001, respectively) and overall survival (OS) (P = 0.0015 and P < 0.0001, respectively), whereas AML-MRC-C and age ≥60 years were associated with shorter EFS (P = 0.028 and P = 0.015, respectively) and OS (P = 0.021 and P = 0.013, respectively). Of note, NPM1mut did not affect the patient's outcome. Multivariable analysis confirmed HSCT and AML-MRC-C as independent predictors for EFS (P < 0.0001 and P = 0.0342, respectively) and OS (P < 0.0001 and P = 0.0295, respectively). AML-MRC-M was an independent predictor for OS (P = 0.0449). When compared with a control group of 105 patients with normal karyotype AML not otherwise specified (NK-AML-NOS), patients with AML-MRC-M had similar EFS and OS (P = 0.99 and P = 0.91, respectively). However, AML-MRC-H and AML-MRC-C were associated with shorter EFS and OS (P = 0.0002 and P < 0.0001, respectively) than the same control group. In a subset of patients, next-generation sequencing analysis showed AML-MRC-M was associated with ASXL1 mutation compared with NK-AML (56% vs 6%). In conclusion, AML-MRC-M demonstrates a superior clinical outcome compared with the rest of the AML-MRC group. They have comparable outcomes to NK-AML-NOS, and these data suggest AML-MRC-M may be considered not to be classified in the same group as patients with other AML-MRC.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Cell Lineage
- Female
- Genetic Predisposition to Disease
- Hematopoietic Stem Cell Transplantation/adverse effects
- Hematopoietic Stem Cell Transplantation/mortality
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/surgery
- Male
- Middle Aged
- Mutation
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Myelodysplastic Syndromes/pathology
- Myelodysplastic Syndromes/surgery
- Nuclear Proteins/genetics
- Nucleophosmin
- Progression-Free Survival
- Repressor Proteins/genetics
- Retrospective Studies
- Risk Assessment
- Risk Factors
- Time Factors
- Young Adult
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Affiliation(s)
- Gina Jiang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Jose-Mario Capo-Chichi
- Department of Clinical Laboratory Genetics, Genome Diagnostics, University Health Network, Canada
| | - Aijun Liu
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, China
| | | | - Robert Guo
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Ann Tierens
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada
| | - Mark D Minden
- Department of Hematology and Medical Oncology, University Health Network, University of Toronto, Toronto, Canada
| | - Hong Chang
- Department of Laboratory Hematology, University Health Network, University of Toronto, Toronto, Canada.
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12
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Northrup V, Maybank A, Carson N, Rahmeh T. The Value of Next-Generation Sequencing in the Screening and Evaluation of Hematologic Neoplasms in Clinical Practice. Am J Clin Pathol 2020; 153:639-645. [PMID: 31875888 DOI: 10.1093/ajcp/aqz203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES The implementation of next-generation sequencing (NGS) in routine clinical hematology practice remains limited. We evaluate the clinical value of NGS in the screening, diagnosis, and follow-up in hematologic neoplasms. METHODS A targeted NGS panel was used to assess a total of 178 patients for questionable or previously diagnosed myeloid neoplasms. RESULTS Gene variants were identified in 53% of patients. Novel variants were identified in 29% of patients and variants of unknown significance in 34%. Bone marrow samples yielded a higher number of variants than in peripheral blood. NGS is a more sensitive test than conventional cytogenetics. In several cases, NGS played a key role in the screening, diagnostics, prognostic stratification, and the clinical follow-up of a wide variety of myeloid neoplasms. CONCLUSIONS NGS is an effective tool in the evaluation of suspected and confirmed hematologic neoplasms and could become part of the routine workup of patients.
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Affiliation(s)
- Victoria Northrup
- Dalhousie Medicine New Brunswick, Saint John, Canada
- Departments of Laboratory Medicine, Saint John Regional Hospital, Saint John, Canada
- Research Services, Saint John Regional Hospital, Saint John, Canada
| | | | - Nancy Carson
- Departments of Laboratory Medicine, Saint John Regional Hospital, Saint John, Canada
| | - Tarek Rahmeh
- Dalhousie Medicine New Brunswick, Saint John, Canada
- Departments of Laboratory Medicine, Saint John Regional Hospital, Saint John, Canada
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13
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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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14
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Aguilera-Diaz A, Vazquez I, Ariceta B, Mañú A, Blasco-Iturri Z, Palomino-Echeverría S, Larrayoz MJ, García-Sanz R, Prieto-Conde MI, del Carmen Chillón M, Alfonso-Pierola A, Prosper F, Fernandez-Mercado M, Calasanz MJ. Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design. PLoS One 2020; 15:e0227986. [PMID: 31978184 PMCID: PMC6980571 DOI: 10.1371/journal.pone.0227986] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/04/2020] [Indexed: 12/17/2022] Open
Abstract
The diagnosis of myeloid neoplasms (MN) has significantly evolved through the last few decades. Next Generation Sequencing (NGS) is gradually becoming an essential tool to help clinicians with disease management. To this end, most specialized genetic laboratories have implemented NGS panels targeting a number of different genes relevant to MN. The aim of the present study is to evaluate the performance of four different targeted NGS gene panels based on their technical features and clinical utility. A total of 32 patient bone marrow samples were accrued and sequenced with 3 commercially available panels and 1 custom panel. Variants were classified by two geneticists based on their clinical relevance in MN. There was a difference in panel’s depth of coverage. We found 11 discordant clinically relevant variants between panels, with a trend to miss long insertions. Our data show that there is a high risk of finding different mutations depending on the panel of choice, due both to the panel design and the data analysis method. Of note, CEBPA, CALR and FLT3 genes, remains challenging the use of NGS for diagnosis of MN in compliance with current guidelines. Therefore, conventional molecular testing might need to be kept in place for the correct diagnosis of MN for now.
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Affiliation(s)
- Almudena Aguilera-Diaz
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Iria Vazquez
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Beñat Ariceta
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Amagoia Mañú
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Zuriñe Blasco-Iturri
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | | | - María José Larrayoz
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca, IBSAL and CIBERONC, Salamanca, Spain
| | | | | | - Ana Alfonso-Pierola
- Hematology Department, Clinica Universidad de Navarra (CUN), Pamplona, Spain
| | - Felipe Prosper
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematology Department, Clinica Universidad de Navarra (CUN), Pamplona, Spain
| | - Marta Fernandez-Mercado
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
- Biomedical Engineering Department, School of Engineering, University of Navarra, San Sebastian, Spain
- * E-mail: ,
| | - María José Calasanz
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
- Scientific Co-Director of CIMA LAB Diagnostics, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
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15
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Standardization of Somatic Variant Classifications in Solid and Haematological Tumours by a Two-Level Approach of Biological and Clinical Classes: An Initiative of the Belgian ComPerMed Expert Panel. Cancers (Basel) 2019; 11:cancers11122030. [PMID: 31888289 PMCID: PMC6966529 DOI: 10.3390/cancers11122030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
In most diagnostic laboratories, targeted next-generation sequencing (NGS) is currently the default assay for the detection of somatic variants in solid as well as haematological tumours. Independent of the method, the final outcome is a list of variants that differ from the human genome reference sequence of which some may relate to the establishment of the tumour in the patient. A critical point towards a uniform patient management is the assignment of the biological contribution of each variant to the malignancy and its subsequent clinical impact in a specific malignancy. These so-called biological and clinical classifications of somatic variants are currently not standardized and are vastly dependent on the subjective analysis of each laboratory. This subjectivity can thus result in a different classification and subsequent clinical interpretation of the same variant. Therefore, the ComPerMed panel of Belgian experts in cancer diagnostics set up a working group with the goal to harmonize the biological classification and clinical interpretation of somatic variants detected by NGS. This effort resulted in the establishment of a uniform, two-level classification workflow system that should enable high consistency in diagnosis, prognosis, treatment and follow-up of cancer patients. Variants are first classified into a tumour-independent biological five class system and subsequently in a four tier ACMG clinical classification. Here, we describe the ComPerMed workflow in detail including examples for each step of the pipeline. Moreover, this workflow can be implemented in variant classification software tools enabling automatic reporting of NGS data, independent of panel, method or analysis software.
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16
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Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia. Genes (Basel) 2019; 10:genes10121026. [PMID: 31835432 PMCID: PMC6947272 DOI: 10.3390/genes10121026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but these methods remain expensive and time consuming. In this context, we present a nanopore-based assay for rapid (24 h) sequencing of six genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2) that are recurrently mutated in AML. The study included 22 AML patients at diagnosis; all data were compared with the results of S5 sequencing, and discordant variants were validated by Sanger sequencing. Nanopore approach showed substantial advantages in terms of speed and low cost. Furthermore, the ability to generate long reads allows a more accurate detection of longer FLT3 internal tandem duplications and phasing double CEBPA mutations. In conclusion, we propose a cheap, rapid workflow that can potentially enable all basic molecular biology laboratories to perform detailed targeted gene sequencing analysis in AML patients, in order to define their prognosis and the appropriate treatment.
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17
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The mutational landscape of accelerated- and blast-phase myeloproliferative neoplasms impacts patient outcomes. Blood Adv 2019; 2:2658-2671. [PMID: 30327374 DOI: 10.1182/bloodadvances.2018021469] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/23/2018] [Indexed: 12/11/2022] Open
Abstract
There is a paucity of data regarding the impact of mutations on outcomes in accelerated-phase (AP) and blast-phase (BP) myeloproliferative neoplasms (MPNs). Moreover, it is unknown whether mutational status affects survival, as seen in chronic-phase MPNs. Therefore, we performed a retrospective analysis of all patients treated at our institution with AP/BP MPNs (N = 122; AP = 14; BP = 108) to comprehensively describe the mutational profile and correlate with clinical outcomes. Targeted sequencing with a 54-gene panel was performed. Forty-four patients were treated with intensive therapy, 27 with nonintensive therapy, and 51 with best supportive care (BSC). The most common mutation was JAK2V617F, occurring in 55% of subjects; CALR was found in 13% of patients and MPL in 6%. Thirty-two (26%) patients were triple negative. Other frequently mutated genes were ASXL1 (30%), TET2 (25%), SRSF2 (22%), RUNX1 (20%), and TP53 (17%). Mutations in 1, 2, 3, and ≥4 genes were seen in 15%, 13%, 25%, and 46% of patients, respectively. There was no difference in survival between patients treated with intensive vs nonintensive therapy, and the benefit of intensive therapy was limited to patients who were able to undergo transplantation. TP53 was the only individual mutation to correlate with shorter overall survival (hazard ratio, 1.89; P = .03). In the multivariate analysis, mutated TP53, ≥4 mutations, low albumin, increased peripheral blood blasts, ≥3 cytogenetic abnormalities, and BSC were associated with shorter survival. In conclusion, mutational data enhance the understanding of patients with AP/BP MPN who are likely to benefit from current therapeutic options.
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18
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Asavei T, Bobeica M, Nastasa V, Manda G, Naftanaila F, Bratu O, Mischianu D, Cernaianu MO, Ghenuche P, Savu D, Stutman D, Tanaka KA, Radu M, Doria D, Vasos PR. Laser-driven radiation: Biomarkers for molecular imaging of high dose-rate effects. Med Phys 2019; 46:e726-e734. [PMID: 31357243 PMCID: PMC6899889 DOI: 10.1002/mp.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/11/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022] Open
Abstract
Recently developed short‐pulsed laser sources garner high dose‐rate beams such as energetic ions and electrons, x rays, and gamma rays. The biological effects of laser‐generated ion beams observed in recent studies are different from those triggered by radiation generated using classical accelerators or sources, and this difference can be used to develop new strategies for cancer radiotherapy. High‐power lasers can now deliver particles in doses of up to several Gy within nanoseconds. The fast interaction of laser‐generated particles with cells alters cell viability via distinct molecular pathways compared to traditional, prolonged radiation exposure. The emerging consensus of recent literature is that the differences are due to the timescales on which reactive molecules are generated and persist, in various forms. Suitable molecular markers have to be adopted to monitor radiation effects, addressing relevant endogenous molecules that are accessible for investigation by noninvasive procedures and enable translation to clinical imaging. High sensitivity has to be attained for imaging molecular biomarkers in cells and in vivo to follow radiation‐induced functional changes. Signal‐enhanced MRI biomarkers enriched with stable magnetic nuclear isotopes can be used to monitor radiation effects, as demonstrated recently by the use of dynamic nuclear polarization (DNP) for biomolecular observations in vivo. In this context, nanoparticles can also be used as radiation enhancers or biomarker carriers. The radiobiology‐relevant features of high dose‐rate secondary radiation generated using high‐power lasers and the importance of noninvasive biomarkers for real‐time monitoring the biological effects of radiation early on during radiation pulse sequences are discussed.
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Affiliation(s)
- Theodor Asavei
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Mariana Bobeica
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Viorel Nastasa
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Street, RO-077125, Bucharest-Magurele, Romania
| | - Gina Manda
- Cellular and Molecular Medicine Department, "Victor Babes" National Institute of Pathology, 99-101 Splaiul Independentei, Bucharest, 050096, Romania
| | - Florin Naftanaila
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania.,Amethyst Radiotherapy Clinic, Dr Odaii 42, Otopeni, Romania
| | - Ovidiu Bratu
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania
| | - Dan Mischianu
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania
| | - Mihail O Cernaianu
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Petru Ghenuche
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Diana Savu
- Department of Life and Environmental Physics, Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Dan Stutman
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Street, RO-077125, Bucharest-Magurele, Romania.,Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland, 21218, USA
| | - Kazuo A Tanaka
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Mihai Radu
- Department of Life and Environmental Physics, Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Domenico Doria
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,Centre for Plasma Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast, BT7 1NN, United Kingdom
| | - Paul R Vasos
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,Research Institute of the University of Bucharest (ICUB), 36-46 B-dul M. Kogalniceanu, RO-050107, Bucharest, Romania
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19
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Levy MA, Santos S, Kerkhof J, Stuart A, Aref‐Eshghi E, Guo F, Hedley B, Wong H, Rauh M, Feilotter H, Berardi P, Semenuk L, Yang P, Knoll J, Ainsworth P, McLachlin CM, Chin‐Yee I, Kovacs M, Deotare U, Lazo‐Langner A, Hsia C, Keeney M, Xenocostas A, Howlett C, Lin H, Sadikovic B. Implementation of an NGS‐based sequencing and gene fusion panel for clinical screening of patients with suspected hematologic malignancies. Eur J Haematol 2019; 103:178-189. [DOI: 10.1111/ejh.13272] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Michael A. Levy
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Erfan Aref‐Eshghi
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Fen Guo
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Ben Hedley
- Pathology and Laboratory Medicine London Health Sciences Centre London Ontario Canada
| | - Henry Wong
- Clinical Laboratories Kingston Health Sciences Centre Kingston Ontario Canada
| | - Michael Rauh
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine Queen's University Kingston Ontario Canada
- Molecular Diagnostics Kingston Health Sciences Centre Kingston Ontario Canada
| | - Philip Berardi
- University of Ottawa Ottawa Ontario Canada
- Eastern Ontario Regional Laboratory Association (EORLA) The Ottawa Hospital Ottawa Ontario Canada
| | - Laura Semenuk
- DNA Diagnostics & Cytogenetics Laboratory Kingston Health Sciences Centre Kingston Ontario Canada
| | - Ping Yang
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Cytogenetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Joan Knoll
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
- Department of Biochemistry Western University London Ontario Canada
| | | | - Ian Chin‐Yee
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Michael Kovacs
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Uday Deotare
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
- Departments of Medicine and Oncology London Health Sciences Centre London Ontario Canada
| | - Alejandro Lazo‐Langner
- Hematology Division London Health Sciences Centre London Ontario Canada
- Department of Epidemiology and Biostatistics Western University London Ontario Canada
| | - Cyrus Hsia
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Mike Keeney
- Hematology Division London Health Sciences Centre London Ontario Canada
| | - Anargyros Xenocostas
- Hematology Division London Health Sciences Centre London Ontario Canada
- Schulich School of Medicine and Dentistry Western University London Ontario Canada
| | - Christopher Howlett
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Hanxin Lin
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division London Health Sciences Centre London Ontario Canada
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20
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Diagnosis and Treatment of Chronic Myelomonocytic Leukemias in Adults: Recommendations From the European Hematology Association and the European LeukemiaNet. Hemasphere 2018; 2:e150. [PMID: 31723789 PMCID: PMC6745959 DOI: 10.1097/hs9.0000000000000150] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/11/2018] [Indexed: 02/07/2023] Open
Abstract
Chronic myelomonocytic leukemia (CMML) is a disease of the elderly, and by far the most frequent overlap myelodysplastic/myeloproliferative neoplasm in adults. Aside from the chronic monocytosis that remains the cornerstone of its diagnosis, the clinical presentation of CMML includes dysplastic features, cytopenias, excess of blasts, or myeloproliferative features including high white blood cell count or splenomegaly. Prognosis is variable, with several prognostic scoring systems reported in recent years, and treatment is poorly defined, with options ranging from watchful waiting to allogeneic stem cell transplantation, which remains the only curative therapy for CMML. Here, we present on behalf of the European Hematology Association and the European LeukemiaNet, evidence- and consensus-based guidelines, established by an international group of experts, from Europe and the United States, for standardized diagnostic and prognostic procedures and for an appropriate choice of therapeutic interventions in adult patients with CMML.
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21
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Clinical Utility of Next-generation Sequencing in the Management of Myeloproliferative Neoplasms: A Single-Center Experience. Hemasphere 2018; 2:e44. [PMID: 31723772 PMCID: PMC6745993 DOI: 10.1097/hs9.0000000000000044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 01/09/2023] Open
Abstract
Supplemental Digital Content is available in the text Although next-generation sequencing (NGS) has helped characterize the complex genomic landscape of myeloid malignancies, its clinical utility remains undefined. This has resulted in variable funding for NGS testing, limiting its accessibility. At our center, targeted sequencing (TAR-SEQ) using a 54-gene NGS myeloid panel is offered to all new patients referred for myeloid malignancies, as part of a prospective observational study. Here, we evaluated the diagnostic, prognostic, and potential therapeutic utility of clinical grade TAR-SEQ in the routine workflow of 179 patients with myeloproliferative neoplasms (MPN). Of 13 patients with triple negative (TN) MPN, who lacked driver mutations in JAK2, CALR, and MPL, TAR-SEQ confirmed clonal hematopoiesis in 8 patients. In patients with intermediate-risk myelofibrosis (MF), TAR-SEQ helped optimize clinical decisions in hematopoietic cell transplant (HCT)-eligible patients through identifying a high molecular risk (HMR) mutation profile. The presence of an HMR profile favored HCT in 9 patients with intermediate-1 risk MF. Absence of an HMR profile resulted in a delayed HCT strategy in 10 patients with intermediate-2 risk MF, 7 of which were stable at the last follow-up. Finally, TAR-SEQ identified patients with various targetable mutations in IDH1/2 (4%), spliceosome genes (28%), and EZH2 (7%). Some of these patients can be potential candidates for future targeted therapy trials. In conclusion, we have demonstrated that TAR-SEQ improves the characterization of TN MPN, can be integrated in clinical practice as an additional tool to refine decision making in HCT, and has the potential to identify candidates for future targeted therapy trials.
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22
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Münz M, Mahamdallie S, Yost S, Rimmer A, Poyastro-Pearson E, Strydom A, Seal S, Ruark E, Rahman N. CoverView: a sequence quality evaluation tool for next generation sequencing data. Wellcome Open Res 2018; 3:36. [PMID: 29881786 PMCID: PMC5964631 DOI: 10.12688/wellcomeopenres.14306.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 01/05/2023] Open
Abstract
Quality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review. It also provides an interactive graphical user interface (GUI) that can be opened in a web browser and allows intuitive exploration of results. We have integrated CoverView into our accredited clinical cancer predisposition gene testing laboratory that uses the TruSight Cancer Panel (TSCP). CoverView has been invaluable for optimisation and quality control of our testing pipeline, providing transparent, consistent quality metric information and automatic flagging of regions that fall below quality thresholds. We demonstrate this utility with TSCP data from the Genome in a Bottle reference sample, which CoverView analysed in 13 seconds. CoverView uses data routinely generated by NGS pipelines, reads standard input formats, and rapidly creates easy-to-parse output text (.txt) files that are customised by a simple configuration file. CoverView can therefore be easily integrated into any NGS pipeline. CoverView and detailed documentation for its use are freely available at
github.com/RahmanTeamDevelopment/CoverView/releases and
www.icr.ac.uk/CoverView
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Affiliation(s)
- Márton Münz
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Andrew Rimmer
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Poyastro-Pearson
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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23
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Frawley T, O'Brien CP, Conneally E, Vandenberghe E, Percy M, Langabeer SE, Haslam K. Development of a Targeted Next-Generation Sequencing Assay to Detect Diagnostically Relevant Mutations of JAK2, CALR, and MPL in Myeloproliferative Neoplasms. Genet Test Mol Biomarkers 2018; 22:98-103. [PMID: 29323541 DOI: 10.1089/gtmb.2017.0203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), consisting of polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are a heterogeneous group of neoplasms that harbor driver mutations in the JAK2, CALR, and MPL genes. The detection of mutations in these genes has been incorporated into the recent World Health Organization (WHO) diagnostic criteria for MPN. Given a pressing clinical need to screen for mutations in these genes in a routine diagnostic setting, a targeted next-generation sequencing (NGS) assay for the detection of MPN-associated mutations located in JAK2 exon 14, JAK2 exon 12, CALR exon 9, and MPL exon 10 was developed to provide a single platform alternative to reflexive, stepwise diagnostic algorithms. METHODS Polymerase chain reaction (PCR) primers were designed to target mutation hotspots in JAK2 exon 14, JAK2 exon 12, MPL exon 10, and CALR exon 9. Multiplexed PCR conditions were optimized by using qualitative PCR followed by NGS. Diagnostic genomic DNA from 35 MPN patients, known to harbor driver mutations in one of the target genes, was used to validate the assay. RESULTS One hundred percent concordance was observed between the previously-identified mutations and those detected by NGS, with no false positives, nor any known mutations missed (specificity = 100%, CI = 0.96, sensitivity = 100%, CI = 0.89). Improved resolution of mutation sequences was also revealed by NGS analysis. CONCLUSION Detection of diagnostically relevant driver mutations of MPN is enhanced by employing a targeted multiplex NGS approach. This assay presents a robust solution to classical MPN mutation screening, providing an alternative to time-consuming sequential analyses.
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Affiliation(s)
- Thomas Frawley
- 1 Cancer Molecular Diagnostics, St. James's Hospital , Dublin, Ireland
| | - Cathal P O'Brien
- 1 Cancer Molecular Diagnostics, St. James's Hospital , Dublin, Ireland
| | | | | | - Melanie Percy
- 3 Department of Haematology, Belfast City Hospital , Belfast, United Kingdom
| | | | - Karl Haslam
- 1 Cancer Molecular Diagnostics, St. James's Hospital , Dublin, Ireland
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24
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Yannakou CK, Jones K, McBean M, Thompson ER, Ryland GL, Doig K, Markham J, Westerman D, Blombery P. ASXL1 c.1934dup;p.Gly646Trpfs*12-a true somatic alteration requiring a new approach. Blood Cancer J 2017; 7:656. [PMID: 29242575 PMCID: PMC5802455 DOI: 10.1038/s41408-017-0025-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 10/11/2017] [Indexed: 12/31/2022] Open
Affiliation(s)
- Costas K Yannakou
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia. .,University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Kate Jones
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Michelle McBean
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Ella R Thompson
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Ken Doig
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - John Markham
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,University of Melbourne, Parkville, VIC, 3010, Australia
| | - David Westerman
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,University of Melbourne, Parkville, VIC, 3010, Australia
| | - Piers Blombery
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,University of Melbourne, Parkville, VIC, 3010, Australia
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25
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Ng CWS, Kosmo B, Lee PL, Lee CK, Guo J, Chen Z, Chiu L, Lee HK, Ho S, Zhou J, Lin M, Tan KML, Ban KHK, Tan TW, Chng WJ, Yan B. CEBPA mutational analysis in acute myeloid leukaemia by a laboratory-developed next-generation sequencing assay. J Clin Pathol 2017; 71:522-531. [PMID: 29180507 DOI: 10.1136/jclinpath-2017-204825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 11/03/2022]
Abstract
AIM The presence of biallelic CEBPA mutations is a favourable prognostic feature in acute myeloid leukaemia (AML). CEBPA mutations are currently identified through conventional capillary sequencing (CCS). With the increasing adoption of next-generation sequencing (NGS) platforms, challenges with regard to amplification efficiency of CEBPA due to the high GC content may be encountered, potentially resulting in suboptimal coverage. Here, the performance of an amplicon-based NGS method using a laboratory-developed CEBPA-specific Nextera XT (CEBNX) was evaluated. METHODS Mutational analyses of the CEBPA gene of 137 AML bone marrow or peripheral blood retrospective specimens were performed by the amplification of the CEBPA gene using the Expand Long Range dNTPack and the amplicons processed by CCS and NGS. CEBPA-specific libraries were then constructed using the Nextera XT V.2 kit. All FASTQ files were then processed with the MiSeq Reporter V.2.6.2.3 using the PCR Amplicon workflow via the customised CEBPA-specific manifest file. The variant calling format files were analysed using the Illumina Variant Studio V.2.2. RESULTS A coverage per base of 3631X to 28184X was achieved. 22 samples (16.1%) were found to contain CEBPA mutations, with variant allele frequencies (VAF) ranging from 3.8% to 58.2%. Taking CCS as the 'gold standard', sensitivity and specificity of 97% and 97% was achieved. For the transactivation domain 2 polymorphism (c.584_589dupACCCGC/p.His195_Pro196dup), the CEBNX achieved 100% sensitivity and 100% specificity relative to CCS. CONCLUSIONS Our laboratory-developed CEBNX workflow shows high coverage and thus overcomes the challenges associated with amplification efficiency and low coverage of CEBPA. Therefore, our assay is suitable for deployment in the clinical laboratory.
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Affiliation(s)
- Christopher Wai Siong Ng
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Bustamin Kosmo
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Peak-Ling Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Jingxue Guo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhaojin Chen
- Investigational Medicine Unit, National University Health System, Singapore, Singapore
| | - Lily Chiu
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Hong Kai Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Sherry Ho
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Mingxuan Lin
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Karen M L Tan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Kenneth H K Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tin Wee Tan
- National Supercomputing Centre Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore.,Translational Centre for Development and Research, National University Health System, Singapore, Singapore
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