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Leung B, Aung H, Nandini A, Abdulrasool G, Lau C, Seymour L. Analytical Validation of a 37-Gene Next-Generation Sequencing Panel for Myeloid Malignancies and Review of Initial Findings Incorporating Updated 2022 Diagnostic and Prognostic Guidelines. J Mol Diagn 2024; 26:399-412. [PMID: 38367765 DOI: 10.1016/j.jmoldx.2024.01.010] [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: 02/14/2023] [Revised: 10/23/2023] [Accepted: 01/16/2024] [Indexed: 02/19/2024] Open
Abstract
Myeloid neoplasms are clonal disorders that arise via acquisition of genetic mutations leading to excessive proliferation and defective differentiation. Mutational profiling is vital as it has implications for diagnosis, prognosis, and therapeutic decision-making. Next-generation sequencing (NGS) has become a mainstay in the evaluation of myeloid malignancies, as it enables efficient characterization of multiple genetic changes. Herein, the analytical validation of the 37-gene Archer VariantPlex Core Myeloid panel is reported, using 58 DNA specimens with 87 single-nucleotide variants and 23 insertions/deletions. The panel achieved good depth of coverage, 100% analytical sensitivity and specificity for single-nucleotide variants and insertions/deletions ≤21 bp, and 100% reproducibility, with a reportable limit of detection determined as 5%. The Archer NGS panel can accurately and reproducibly detect variants of clinical significance in myeloid neoplasms. A retrospective analysis of 535 clinical specimens tested with the Archer NGS panel showed a frequency and pattern of mutations across myeloid malignancies that were similar to other published studies. A review of the diagnostic classification of patients with acute myeloid leukemia and myelodysplastic syndrome using the World Health Organization 2017/2022 and International Consensus Classification 2022 guidelines, in addition to European LeukemiaNet 2017/2022 risk stratification of patients with acute myeloid leukemia, was also performed to assess the utility of the molecular information provided by the Archer NGS panel.
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Affiliation(s)
- Becky Leung
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, Griffith University, Gold Coast, Queensland, Australia.
| | - Hnin Aung
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Adayapalam Nandini
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Ghusoon Abdulrasool
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Chiyan Lau
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Louise Seymour
- Department of Haematology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; School of Medicine, University of Queensland, Brisbane, Queensland, Australia
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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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Nann D, Rau A, Mahmutovic L, Steinhilber J, Meca V, Federmann B, Vogel W, Bonzheim I, Quintanilla-Martinez L, Fend F. Targeted NGS on sequential bone marrow biopsies aids in the evaluation of cytopenias and monocytosis and documents clonal evolution-a proof of principle study. Virchows Arch 2023; 483:835-845. [PMID: 37610626 DOI: 10.1007/s00428-023-03627-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/01/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
Differential diagnosis of clonal versus reactive cytopenia and monocytosis, respectively, frequently presents a diagnostic challenge. With the two recent classifications of myeloid disorders, mutational analysis has gained importance as a diagnostic tool. However, reports on its utility on trephine bone marrow biopsies (BMB) are sparse. The aim of our proof of principle study was to determine the suitability of targeted sequencing for the longitudinal evaluation of cytopenia and monocytosis and demonstration of clonal evolution on sequential BMB. Seventy-seven EDTA-decalcified BMB of 33 patients with peripheral cytopenia and/or monocytosis, including at least one follow-up biopsy/patient, were included. Initial morphological diagnoses were idiopathic cytopenia of undetermined significance (ICUS, 8 cases), MDS (without blast increase, 7 cases), MDS with increased blasts/excess blasts (MDS-IB/EB) (11 cases), and CMML (7 cases). Thirty-one genes relevant for myeloid disorders were examined using two custom AmpliSeq NGS panels. Mutations were found in the initial BMB of 5/8 cases of ICUS, thus changing the diagnosis to clonal cytopenia of unknown significance (CCUS), 5/7 MDS, 10/11 MDS-IB/EB, and 7/7 CMML. Clonal evolution was observed in 14/33 (42%) cases, mostly associated with disease progression. None of the wild-type patients acquired mutations during follow-up. NGS-based mutation profiling is a robust diagnostic tool for BMB and provides valuable additional information, especially for cases with no/minimal dysplasia, and for better risk stratification of MDS. Tracking variant allele frequency and appearance of mutations over time allows for observing clonal evolution or relapse.
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Affiliation(s)
- Dominik Nann
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Achim Rau
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Lejla Mahmutovic
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Julia Steinhilber
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Vanessa Meca
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Birgit Federmann
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
- Department of Peptide-Based Immunotherapy and Clinical Collaboration Unit Translational Immunology, Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tuebingen, Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tuebingen, Germany
| | - Wichard Vogel
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Tuebingen, Germany
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tuebingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tuebingen and Comprehensive Cancer Center, Tuebingen, Germany.
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Ibrar W, Zhang W, Cox JL, Cushman-Vokoun A, Fu K, Greiner TC, Yuan J. The utility of a myeloid mutation panel for the diagnosis of myelodysplastic syndrome and myelodysplastic/myeloproliferative neoplasm. Int J Lab Hematol 2021; 43:1501-1509. [PMID: 34270867 DOI: 10.1111/ijlh.13659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The diagnosis of myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) is based on morphology and cytogenetics/FISH findings per 2017 WHO classification. With rare exceptions, somatic mutations have not been incorporated as the diagnostic criteria. METHODS We analyzed the utility of mutational analysis with a targeted 54-gene or 40-gene next-generation sequencing (NGS) panel in the diagnosis of MDS and MDS/MPN. RESULTS We retrospectively collected 92 patients who presented with unexplained cytopenia with or without cytosis, including 32 low-grade MDS (MDS-L), 18 high-grade MDS (MDS-H), 5 therapy-related MDS (MDS-TR), 19 MDS/MPN, and 18 negative cases. Of 92 patients, 197 somatic mutations involving 38 genes were detected and had variant allele frequency (VAF) ranging from 3% to 99%. The most common mutated genes were TET2, ASXL1, RUNX1, TP53, SRSF2, and SF3B1. MDS-L, MDS-H, MDS-TR, and MDS/MPN showed an average number of somatic mutations with a mean VAF of 1.9/33%, 2.6/30%, 2/36%, and 4/41%, respectively. SF3B1 mutations were exclusively observed in MDS-L and MDS/MPN. TP53 gene mutations were more frequently seen in MDS-H and MDS-TR. Among 34 patients with a diagnosis of MDS or MDS/MPN with normal cytogenetics, 31 patients (91%) had at least 1 mutation and 24 patients (71%) had ≥2 mutations with ≥10% VAF. CONCLUSION A myeloid mutational panel provides additional evidence of clonality besides cytogenetics/FISH studies in the diagnosis of cytopenia with or without cytosis. Two or more mutations with ≥10% VAF highly predicts MDS and MDS/MPN with a positive predictive value of 100%.
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Affiliation(s)
- Warda Ibrar
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Weiwei Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jesse Lee Cox
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Allison Cushman-Vokoun
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kai Fu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ji Yuan
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
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Radner M, van Luttikhuizen JL, Bartels S, Bublitz J, Grote I, Rieger L, Christgen H, Stark H, Werlein C, Lafos M, Steinemann D, Lehmann U, Christgen M, Kreipe H. Chromosome 2q gain and epigenetic silencing of GATA3 in microglandular adenosis of the breast. J Pathol Clin Res 2021; 7:220-232. [PMID: 33382535 PMCID: PMC8073017 DOI: 10.1002/cjp2.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/06/2020] [Accepted: 11/20/2020] [Indexed: 01/30/2023]
Abstract
Microglandular adenosis (MGA) represents a rare neoplasm of the mammary gland, which in a subset of cases may be associated with triple-negative breast cancer (BC). The biology of MGA is poorly understood. In this study, eight MGA cases (n = 4 with and n = 4 without associated BC) were subjected to a comprehensive characterization using immunohistochemistry, genome-wide DNA copy number (CN) profiling, fluorescence in situ hybridization (FISH), next-generation sequencing (NGS), and DNA methylation profiling using 850 K arrays and bisulfite pyrosequencing. Median patient age was 61 years (range 57-76 years). MGA lesions were estrogen receptor (ER)-negative, progesterone receptor-negative, HER2-negative, and S100-positive. DNA CN alterations (CNAs) were complex or limited to few gains and losses. CN gain on chromosome 2q was the most common CNA and was validated by FISH in five of eight cases. NGS demonstrated an average of two mutations per case (range 0-5) affecting 10 different genes (ARID1A, ATM, CTNNB1, FBXW7, FGFR2, MET, PIK3CA, PMS2, PTEN, and TP53). CNAs and mutations were similar in MGA and adjacent BC, indicating clonal relatedness. DNA methylation profiling identified aberrant hypermethylation of CpG sites within GATA3, a key transcription factor required for luminal differentiation. Immunohistochemistry showed regular GATA3 protein expression in the normal mammary epithelium and in ER-positive BC. Conversely, GATA3 was reduced or lost in all MGA cases tested (8/8). In conclusion, MGA is characterized by common CN gain on chromosome 2q and loss of GATA3. Epigenetic inactivation of GATA3 may provide a new clue to the peculiar biology of this rare neoplasia.
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Affiliation(s)
- Martin Radner
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Stephan Bartels
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | - Janin Bublitz
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Isabel Grote
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | - Luisa Rieger
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Helge Stark
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Marcel Lafos
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | - Doris Steinemann
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Ulrich Lehmann
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Hans Kreipe
- Institute of PathologyHannover Medical SchoolHannoverGermany
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Jiang L, Pallavajjala A, Huang J, Haley L, Morsberger L, Stinnett V, Hardy M, Park R, Ament C, Finch A, Shane A, Parish R, Nozari A, Long P, Adams E, Smith K, Parimi V, Dougaparsad S, Long L, Gocke CD, Zou YS. Clinical Utility of Targeted Next-Generation Sequencing Assay to Detect Copy Number Variants Associated with Myelodysplastic Syndrome in Myeloid Malignancies. J Mol Diagn 2021; 23:467-483. [PMID: 33577993 DOI: 10.1016/j.jmoldx.2021.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/17/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Copy number variants (CNVs) and gene mutations are important for diagnosis and treatment of myeloid malignancies. In a routine clinical setting, somatic gene mutations are detected by targeted next-generation sequencing (NGS) assay, but CNVs are commonly detected by conventional chromosome analysis and fluorescence in situ hybridization (FISH). The aim of this proof-of-principle study was to investigate the feasibility of using targeted NGS to simultaneously detect both somatic mutations and CNVs. Herein, we sequenced 406 consecutive patients with myeloid malignancies by targeted NGS and performed a head-to-head comparison with the results from a myelodysplastic syndrome (MDS) FISH and conventional chromosome analysis to detect CNVs. Among 91 patients with abnormal MDS FISH results, the targeted NGS revealed all 120 CNVs detected by MDS FISH (including -5/5q-, -7/7q-, +8, and 20q-) and 193 extra CNVs detected by conventional chromosome analysis. The targeted NGS achieved 100% concordance with the MDS FISH. The lower limit of detection of MDS CNVs by the targeted NGS was generally 5% variant allele fraction for DNA, based on the lowest percentages of abnormal cells detected by MDS FISH in this study. This proof-of-principle study demonstrated that the targeted NGS assay can simultaneously detect both MDS CNVs and somatic mutations, which can provide a more comprehensive genetic profiling for patients with myeloid malignancies using a single assay in a clinical setting.
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Affiliation(s)
- Liqun Jiang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jialing Huang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania; BioDiscovery Inc., El Segundo, California
| | - Lisa Haley
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Laura Morsberger
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victoria Stinnett
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Melanie Hardy
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rebecca Park
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Candice Ament
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexandra Finch
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alison Shane
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rebecca Parish
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Azin Nozari
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Patty Long
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily Adams
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kirstin Smith
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vamsi Parimi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Lori Long
- MacroGenics Inc., Rockville, Maryland
| | - Christopher D Gocke
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ying S Zou
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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NPM1-Mutated Myeloid Neoplasms with <20% Blasts: A Really Distinct Clinico-Pathologic Entity? Int J Mol Sci 2020; 21:ijms21238975. [PMID: 33255988 PMCID: PMC7730332 DOI: 10.3390/ijms21238975] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleophosmin (NPM1) gene mutations rarely occur in non-acute myeloid neoplasms (MNs) with <20% blasts. Among nearly 10,000 patients investigated so far, molecular analyses documented NPM1 mutations in around 2% of myelodysplastic syndrome (MDS) cases, mainly belonging to MDS with excess of blasts, and 3% of myelodysplastic/myeloproliferative neoplasm (MDS/MPN) cases, prevalently classified as chronic myelomonocytic leukemia. These uncommon malignancies are associated with an aggressive clinical course, relatively rapid progression to overt acute myeloid leukemia (AML) and poor survival outcomes, raising controversies on their classification as distinct clinico-pathologic entities. Furthermore, fit patients with NPM1-mutated MNs with <20% blasts could benefit most from upfront intensive chemotherapy for AML rather than from moderate intensity MDS-directed therapies, although no firm conclusion can currently be drawn on best therapeutic approaches, due to the limited available data, obtained from small and mainly retrospective series. Caution is also suggested in definitely diagnosing NPM1-mutated MNs with blast count <20%, since NPM1-mutated AML cases frequently present dysplastic features and multilineage bone marrow cells showing abnormal cytoplasmic NPM1 protein delocalization by immunohistochemical staining, therefore belonging to NPM1-mutated clone regardless of blast morphology. Further prospective studies are warranted to definitely assess whether NPM1 mutations may become sufficient to diagnose AML, irrespective of blast percentage.
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Chase A, Score J, Lin F, Bryant C, Waghorn K, Yapp S, Carreno-Tarragona G, Aranaz P, Villasante A, Ernst T, Cross NCP. Mutational mechanisms of EZH2 inactivation in myeloid neoplasms. Leukemia 2020; 34:3206-3214. [PMID: 32322039 PMCID: PMC7610374 DOI: 10.1038/s41375-020-0816-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/20/2020] [Accepted: 03/26/2020] [Indexed: 12/18/2022]
Abstract
EZH2, a component of the polycomb repressive complex 2, catalyses the trimethylation of histone H3 lysine 27, a chromatin mark associated with transcriptional repression. EZH2 loss-of-function mutations are seen in myeloid neoplasms and are associated with an adverse prognosis. Missense mutations in the SET/CXC domain abrogate catalytic activity as assessed by in vitro histone methylation assays, but missense mutations clustering in the conserved DI and DII regions retain activity. To understand the role of DI and DII mutations, we initially developed a cell-based histone methylation assay to test activity in a cellular context. Murine induced pluripotent stem cells lacking EZH2 were transiently transfected with wild type or mutant EZH2 (n=15) and any resulting histone methylation was measured by flow cytometry. All DI mutations (n=5) resulted in complete or partial loss of methylation activity whilst 5/6 DII mutations retained activity. Next, we assessed the possibility of splicing abnormalities induced by exon 8 mutations (encoding DII) using RT-PCR from primary patient samples and mini-gene assays. Exon 8 mutations resulted in skipping of exon 8 and an out-of-frame transcript. We have therefore shown that mutations within regions encoding EZH2 domains DI and DII are pathogenic by loss of function and exon skipping, respectively.
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Affiliation(s)
- Andrew Chase
- Faculty of Medicine, University of Southampton, Southampton, UK. .,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.
| | - Joannah Score
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Feng Lin
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Catherine Bryant
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Katherine Waghorn
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Sarah Yapp
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | | | - Paula Aranaz
- Centre for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Aranzazu Villasante
- Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain.,Department of Electronics and Biomedical Engineering, University of Barcelona, Barcelona, Spain
| | - Thomas Ernst
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
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9
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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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10
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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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11
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Liang S, Zhou X, Pan H, Yang Y, Shi L, Wang L. Prognostic value of DNMT3A mutations in myelodysplastic syndromes: a meta-analysis. ACTA ACUST UNITED AC 2020; 24:613-622. [PMID: 31482762 DOI: 10.1080/16078454.2019.1657613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Objectives: Although DNA (cytosine-5)-methyltransferase 3 alpha (DNMT3A) gene mutations have been widely reported in myelodysplastic syndromes (MDS), the prognostic significance of DNMT3A mutations is still controversial. In this study, we conducted a meta-analysis to determine the prognostic effect of DNMT3A mutations in patients with MDS. Methods: Eligible studies from PubMed, Embase, Web of Science, Clinical Trials and the Cochrane Library were searched. Hazard ratios (HRs) and their 95% confidence intervals (CIs) for overall survival (OS) and leukemia-free survival (LFS) were pooled to assess the effect of DNMT3A mutations on the prognosis in MDS patients. Results: A total of 12 studies with 2236 patients were included in this meta-analysis. The pooled HRs for OS and LFS revealed that MDS patients with DNMT3A mutations had a significantly poor prognosis as compared with those without mutations (OS: HR = 1.654, 95% CI = 1.387-1.973, p < 0.001; LFS: HR = 4.624, 95% CI = 3.121-6.851, p < 0.001). Discussion and Conclusion: This meta-analysis showed an adverse prognostic effect of DNMT3A mutations in patients with MDS, which will contribute to risk stratification and prognostic assessment in the disease.
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Affiliation(s)
- Simin Liang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Xiaojia Zhou
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Hui Pan
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Yichun Yang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Lin Shi
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
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12
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Chammas P, Mocavini I, Di Croce L. Engaging chromatin: PRC2 structure meets function. Br J Cancer 2019; 122:315-328. [PMID: 31708574 PMCID: PMC7000746 DOI: 10.1038/s41416-019-0615-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/24/2019] [Indexed: 01/01/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a key epigenetic multiprotein complex involved in the regulation of gene expression in metazoans. PRC2 is formed by a tetrameric core that endows the complex with histone methyltransferase activity, allowing it to mono-, di- and tri-methylate histone H3 on lysine 27 (H3K27me1/2/3); H3K27me3 is a hallmark of facultative heterochromatin. The core complex of PRC2 is bound by several associated factors that are responsible for modulating its targeting specificity and enzymatic activity. Depletion and/or mutation of the subunits of this complex can result in severe developmental defects, or even lethality. Furthermore, mutations of these proteins in somatic cells can be drivers of tumorigenesis, by altering the transcriptional regulation of key tumour suppressors or oncogenes. In this review, we present the latest results from structural studies that have characterised PRC2 composition and function. We compare this information with data and literature for both gain-of function and loss-of-function missense mutations in cancers to provide an overview of the impact of these mutations on PRC2 activity.
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Affiliation(s)
- Paul Chammas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Ivano Mocavini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,ICREA, Pg Lluis Companys 23, Barcelona, 08010, Spain.
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13
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Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms. Cancers (Basel) 2019; 11:cancers11091364. [PMID: 31540291 PMCID: PMC6770229 DOI: 10.3390/cancers11091364] [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: 08/21/2019] [Revised: 09/04/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
Molecular diagnosis of myeloid neoplasms (MN) is based on the detection of multiple genetic alterations using various techniques. Next-generation sequencing (NGS) has been proved as a useful method for analyzing many genes simultaneously. In this context, we analyzed diagnostic samples from 121 patients affected by MN and ten relapse samples from a subset of acute myeloid leukemia patients using two enrichment-capture NGS gene panels. Pathogenicity classification of variants was enhanced by the development and application of a custom onco-hematology score. A total of 278 pathogenic variants were detected in 84% of patients. For structural alterations, 82% of those identified by cytogenetics were detected by NGS, 25 of 31 copy number variants and three out of three translocations. The detection of variants using NGS changed the diagnosis of seven patients and the prognosis of 15 patients and enabled us to identify 44 suitable candidates for clinical trials. Regarding AML, six of the ten relapsed patients lost or gained variants, comparing with diagnostic samples. In conclusion, the use of NGS panels in MN improves genetic characterization of the disease compared with conventional methods, thus demonstrating its potential clinical utility in routine clinical testing. This approach leads to better-adjusted treatments for each patient.
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14
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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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15
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Zakrzewski F, Gieldon L, Rump A, Seifert M, Grützmann K, Krüger A, Loos S, Zeugner S, Hackmann K, Porrmann J, Wagner J, Kast K, Wimberger P, Baretton G, Schröck E, Aust D, Klink B. Targeted capture-based NGS is superior to multiplex PCR-based NGS for hereditary BRCA1 and BRCA2 gene analysis in FFPE tumor samples. BMC Cancer 2019; 19:396. [PMID: 31029168 PMCID: PMC6487025 DOI: 10.1186/s12885-019-5584-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/05/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND With the introduction of Olaparib treatment for BRCA-deficient recurrent ovarian cancer, testing for somatic and/or germline mutations in BRCA1/2 genes in tumor tissues became essential for treatment decisions. In most cases only formalin-fixed paraffin-embedded (FFPE) samples, containing fragmented and chemically modified DNA of minor quality, are available. Thus, multiplex PCR-based sequencing is most commonly applied in routine molecular testing, which is predominantly focused on the identification of known hot spot mutations in oncogenes. METHODS We compared the overall performance of an adjusted targeted capture-based enrichment protocol and a multiplex PCR-based approach for calling of pathogenic SNVs and InDels using DNA extracted from 13 FFPE tissue samples. We further applied both strategies to seven blood samples and five matched FFPE tumor tissues of patients with known germline exon-spanning deletions and gene-wide duplications in BRCA1/2 to evaluate CNV detection based solely on panel NGS data. Finally, we analyzed DNA from FFPE tissues of 11 index patients from families suspected of having hereditary breast and ovarian cancer, of whom no blood samples were available for testing, in order to identify underlying pathogenic germline BRCA1/2 mutations. RESULTS The multiplex PCR-based protocol produced inhomogeneous coverage among targets of each sample and between samples as well as sporadic amplicon drop out, leading to insufficiently or non-covered nucleotides, which subsequently hindered variant detection. This protocol further led to detection of PCR-artifacts that could easily have been misinterpreted as pathogenic mutations. No such limitations were observed by application of an adjusted targeted capture-based protocol, which allowed for CNV calling with 86% sensitivity and 100% specificity. All pathogenic CNVs were confirmed in the five matched FFPE tumor samples from patients carrying known pathogenic germline mutations and we additionally identified somatic loss of the second allele in BRCA1/2. Furthermore we detected pathogenic BRCA1/2 variants in four the eleven FFPE samples from patients of whom no blood was available for analysis. CONCLUSIONS We demonstrate that an adjusted targeted capture-based enrichment protocol is superior to commonly applied multiplex PCR-based protocols for reliable BRCA1/2 variant detection, including CNV-detection, using FFPE tumor samples.
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Affiliation(s)
- Falk Zakrzewski
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
| | - Laura Gieldon
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
- Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Andreas Rump
- Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Konrad Grützmann
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
| | - Alexander Krüger
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
| | - Sina Loos
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Silke Zeugner
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Joseph Porrmann
- Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Johannes Wagner
- Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karin Kast
- National Center for Tumor Diseases (NCT), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden, Germany
| | - Pauline Wimberger
- National Center for Tumor Diseases (NCT), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden, Germany
| | - Gustavo Baretton
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Tumor- and Normal Tissue Bank of the University Cancer Center (UCC), University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany
| | - Evelin Schröck
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
- Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Daniela Aust
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Tumor- and Normal Tissue Bank of the University Cancer Center (UCC), University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany
| | - Barbara Klink
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), Schubertstraße 15, 01307 Dresden, Germany
- Institute for Clinical Genetics, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
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16
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Palumbo GA, Stella S, Pennisi MS, Pirosa C, Fermo E, Fabris S, Cattaneo D, Iurlo A. The Role of New Technologies in Myeloproliferative Neoplasms. Front Oncol 2019; 9:321. [PMID: 31106152 PMCID: PMC6498877 DOI: 10.3389/fonc.2019.00321] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/09/2019] [Indexed: 12/17/2022] Open
Abstract
The hallmark of BCR-ABL1-negative myeloproliferative neoplasms (MPNs) is the presence of a driver mutation in JAK2, CALR, or MPL gene. These genetic alterations represent a key feature, useful for diagnostic, prognostic and therapeutical approaches. Molecular biology tests are now widely available with different specificity and sensitivity. Recently, the allele burden quantification of driver mutations has become a useful tool, both for prognostication and efficacy evaluation of therapies. Moreover, other sub-clonal mutations have been reported in MPN patients, which are associated with poorer prognosis. ASXL1 mutation appears to be the worst amongst them. Both driver and sub-clonal mutations are now taken into consideration in new prognostic scoring systems and may be better investigated using next generation sequence (NGS) technology. In this review we summarize the value of NGS and its contribution in providing a comprehensive picture of mutational landscape to guide treatment decisions. Finally, discussing the role that NGS has in defining the potential risk of disease development, we forecast NGS as the standard molecular biology technique for evaluating these patients.
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Affiliation(s)
- Giuseppe A Palumbo
- Department of Scienze Mediche, Chirurgiche e Tecnologie Avanzate "G.F. Ingrassia," University of Catania, Catania, Italy
| | - Stefania Stella
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, Catania, Italy.,Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Maria Stella Pennisi
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, Catania, Italy.,Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Cristina Pirosa
- Postgraduate School of Hematology, University of Catania, Catania, Italy
| | - Elisa Fermo
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Fabris
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Cattaneo
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Iurlo
- Hematology Division, Myeloproliferative Syndromes Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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17
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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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18
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Faisal M, Stark H, Büsche G, Schlue J, Teiken K, Kreipe HH, Lehmann U, Bartels S. Comprehensive mutation profiling and mRNA expression analysis in atypical chronic myeloid leukemia in comparison with chronic myelomonocytic leukemia. Cancer Med 2019; 8:742-750. [PMID: 30635983 PMCID: PMC6382710 DOI: 10.1002/cam4.1946] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/30/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
Atypical chronic myeloid leukemia (aCML) and chronic myelomonocytic leukemia (CMML) represent two histologically and clinically overlapping myelodysplastic/myeloproliferative neoplasms. Also the mutational landscapes of both entities show congruencies. We analyzed and compared an aCML cohort (n = 26) and a CMML cohort (n = 59) by next‐generation sequencing of 25 genes and by an nCounter approach for differential expression in 107 genes. Significant differences were found with regard to the mutation frequency of TET2, SETBP1, and CSF3R. Blast content of the bone marrow revealed an inverse correlation with the mutation status of SETBP1 in aCML and TET2 in CMML, respectively. By linear discriminant analysis, a mutation‐based machine learning algorithm was generated which placed 19/26 aCML cases (73%) and 54/59 (92%) CMML cases into the correct category. After multiple correction, differential mRNA expression could be detected between both cohorts in a subset of genes (FLT3, CSF3R, and SETBP1 showed the strongest correlation). However, due to high variances in the mRNA expression, the potential utility for the clinic is limited. We conclude that a medium‐sized NGS panel provides a valuable assistance for the correct classification of aCML and CMML.
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Affiliation(s)
- Muhammad Faisal
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Helge Stark
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Guntram Büsche
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Jerome Schlue
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Kristin Teiken
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Hans H Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Stephan Bartels
- Institute of Pathology, Hannover Medical School, Hannover, Germany
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19
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Christgen M, Bartels S, Radner M, Raap M, Rieger L, Christgen H, Gluz O, Nitz U, Harbeck N, Lehmann U, Kreipe H. ERBB2 mutation frequency in lobular breast cancer with pleomorphic histology or high-risk characteristics by molecular expression profiling. Genes Chromosomes Cancer 2019; 58:175-185. [PMID: 30520184 DOI: 10.1002/gcc.22716] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/15/2022] Open
Abstract
HER2-positive breast cancer is defined by amplification or overexpression of the HER2/ERBB2 oncogene and accounts for about 15% of breast cancer cases. Somatic mutation of ERBB2 is an alternative mechanism, by which activation of HER2 signaling can occur. ERBB2 mutation has been associated with invasive lobular breast cancer (ILBC). This study investigates the frequency and phenotype of ILBC harboring mutated ERBB2. The ERBB2 mutation status was determined by next generation sequencing and/or pyrosequencing in n = 106 ILBCs, including n = 86 primary or locally recurrent tumors and n = 20 metastases from visceral organs, soft tissue, or skin. Immunohistochemical characteristics were determined using tissue microarrays. This series was enriched for ILBCs with pleomorphic histology and/or high-risk expression profiles (Oncotype DX, recurrence score RS > 25). Nearly all specimens were E-cadherin-negative (99%), estrogen receptor (ER)-positive (92%), and lacked ERBB2 overexpression (96%). ERBB2 mutations (p.V777L, p.L755S, p.S310F) were identified in 5/106 (5%) cases. ERBB2-mutated cases included 2/86 (2%) primary tumors and 3/20 (15%) metastases (P = 0.045). ERBB2-mutated cases were associated with loss of ER (2/7, 29%, P = 0.035) and histological grade 3 (4/34, 12%, P = 0.023), but not with solid growth (3/31, 10%, P = 0.148) or pleomorphic histology (2/27, 7%, P = 0.599). No ERBB2 mutation was detected in ILBCs with RS > 25 (0/22, 0%). In 10 patients with multiple matched specimens (n = 25), the ERBB2 mutational status was always concordant. In summary, a small subset of ILBCs harbors potentially actionable ERBB2 mutations. In ERBB2-mutated ILBCs, no association with pleomorphic histology was found.
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Affiliation(s)
| | - Stephan Bartels
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Martin Radner
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Mieke Raap
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Luisa Rieger
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | | | - Oleg Gluz
- West German Study Group, Moenchengladbach, Germany.,Breast Center Niederrhein, Evangelic Bethesda Hospital, Moenchengladbach, Germany.,University Clinics Cologne, Cologne, Germany
| | - Ulrike Nitz
- West German Study Group, Moenchengladbach, Germany.,Breast Center Niederrhein, Evangelic Bethesda Hospital, Moenchengladbach, Germany
| | - Nadia Harbeck
- West German Study Group, Moenchengladbach, Germany.,Breast Center, Department of Obstetrics and Gynecology, University of Munich (LMU), Munich, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
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20
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Abstract
The introduction and advances on next-generation sequencing have led to novel ways to integrate simultaneous assessment of multiple target genes in routine laboratory analysis. Assessment of myeloid neoplasms with targeted next-generation sequencing panels shows evidence to improve diagnosis, assist therapeutic decisions, provide better information about prognosis, and better detection of minimal residual disease. Herein, we provide information for application and utilization of next-generation sequencing studies with a focus on the most important mutations in acute myeloid leukemia, myelodysplastic syndrome, myeloproliferative neoplasms, and other myelodysplastic / myeloproliferative neoplasms in order to integrate them into the daily clinical practice.
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Affiliation(s)
- Fulya Öz Puyan
- Department of Pathology, Trakya University School of Medicine, Edirne, Turkey
| | - Serhan Alkan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, California, USA
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21
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RNA-binding protein (RBFOX1) inherited polymorphism rs8051518 is not associated with splice factor mutations in myelodysplastic syndromes and myeloproliferative neoplasms. Ann Hematol 2018; 98:1297-1299. [PMID: 30159600 DOI: 10.1007/s00277-018-3478-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/13/2018] [Indexed: 10/28/2022]
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22
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Activating human epidermal growth factor receptor 2 (HER2) gene mutation in bone metastases from breast cancer. Virchows Arch 2018; 473:577-582. [PMID: 30094493 DOI: 10.1007/s00428-018-2414-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022]
Abstract
In addition to amplification, point mutations of the human epidermal growth factor receptor 2 (HER2) gene (ERBB2) have been shown to activate the corresponding signaling pathway in breast cancer. The prevalence of ERBB2/HER2 mutation in bone metastasis of breast cancer and the associated phenotype are not known. In this study, bone metastases from breast cancer patients (n = 231) were analyzed for ERBB2/HER2 mutation. In 7 patients (3%; median age 70 years, range 50-83 years), gain-of-function mutations of ERBB2/HER2 were detected. The most frequent mutation was p.L755S (71%). In 29% of mutated cases, p.V777L was found. Lobular breast cancer was present in 71% of mutated cases (n = 5) and in 49% of all samples (n = 231; p = 0.275). Mutation frequency was 4.4% in the lobular subgroup and 17.4% in the pleomorphic subtype of lobular cancer (n = 23), respectively. All but one mutated lobular cancers were of the pleomorphic subtype (p = 0.006). Mutated cancers belonged either to the luminal (n = 4) or to the triple-negative types (n = 3). With regard to protein expression and gene amplification, HER2 was negative in all mutated cases. Among the 14% of metastatic luminal cancers with estrogen receptor gene (ESR1) mutation, conveying resistance against aromatase inhibitors, no concomitant ERBB2/HER2 mutation occurred. We conclude that activating HER2 mutation is present in about 3% of bone metastases from breast cancers, with significantly higher rates in the pleomorphic subtype of lobular cancer. Since mutated cases appear to be HER2-negative by conventional testing, the opportunity for specific anti-HER2 therapy may be missed.
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Hotspot mutations in cancer genes may be missed in routine diagnostics due to neighbouring sequence variants. Exp Mol Pathol 2018; 105:37-40. [PMID: 29847769 DOI: 10.1016/j.yexmp.2018.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/26/2018] [Indexed: 11/22/2022]
Abstract
The detection of hotspot mutations in key cancer genes is now an essential part of the diagnostic work-up in molecular pathology. Nearly all assays for mutation detection involve an amplification step. A second single nucleotide variant (SNV) on the same allele adjacent to a mutational hotspot can interfere with primer binding, leading to unnoticed allele-specific amplification of the wild type allele and thereby false-negative mutation testing. We present two diagnostic cases with false negative sequence results for JAK2 and SRSF2. In both cases mutations would have escaped detection if only one strand of DNA had been analysed. Because many commercially available diagnostic kits rely on the analysis of only one DNA strand they are prone to fail in cases like these. Detailed protocols and quality control measures to prevent corresponding pitfalls are presented.
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Bräuninger A, Blau W, Kunze K, Desch AK, Brobeil A, Tur MK, Etschmann B, Günther U, Körholz D, Schliesser G, Käbisch A, Kiehl M, Rummel M, Gattenlöhner S. Targeted Next-Generation Sequencing Is a Sensitive Tool for Differential Diagnosis of Myelodysplastic Syndromes in Bone Marrow Trephines. J Mol Diagn 2018; 20:344-354. [DOI: 10.1016/j.jmoldx.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/09/2018] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
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Bartels S, Adisa A, Aladelusi T, Lemound J, Stucki-Koch A, Hussein S, Kreipe H, Hartmann C, Lehmann U, Hussein K. Molecular defects in BRAF wild-type ameloblastomas and craniopharyngiomas-differences in mutation profiles in epithelial-derived oropharyngeal neoplasms. Virchows Arch 2018; 472:1055-1059. [PMID: 29546640 DOI: 10.1007/s00428-018-2323-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/26/2018] [Accepted: 02/13/2018] [Indexed: 12/18/2022]
Abstract
The aim of this study was to evaluate the mutation profile of BRAF wild-type craniopharyngiomas and ameloblastomas. Pre-screening by immunohistochemistry and pyrosequencing for identifying BRAF wild-type tumors was performed on archived specimens of ameloblastic tumors (n = 20) and craniopharyngiomas (n = 62). Subsequently, 19 BRAF wild-type tumors (nine ameloblastic tumors and ten craniopharyngiomas) were analyzed further using next-generation sequencing (NGS) targeting hot spot mutations of 22 cancer-related genes. Thereby, we found craniopharyngiomas mainly CTNNB1 mutated (8/10), including two FGFR3/CTNNB1-double mutated tumors. Ameloblastic tumors were often FGFR2 mutated (4/9; including one FGFR2/TP53/PTEN-triple mutated case) and rarely CTNNB1/TP53-double mutated (1/9) and KRAS-mutated (1/9). In the remaining samples, no mutation could be detected in the 22 genes under investigation. In conclusion, mutation profiles of BRAF wild-type craniopharyngiomas and ameloblastomas share mutations of FGFR genes and have additional mutations with potential for targeted therapy.
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Affiliation(s)
- Stephan Bartels
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Akinyele Adisa
- Oral Pathology Department University College Hospital Ibadan, University of Ibadan, Ibadan, Nigeria
| | - Timothy Aladelusi
- Oral and Maxillofacial Surgery Department University College Hospital Ibadan, University of Ibadan, Ibadan, Nigeria
| | - Juliana Lemound
- Department of Cranio-Maxillofacial Surgery, Hannover Medical School, Hannover, Germany
| | - Angelika Stucki-Koch
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Sami Hussein
- Department of Neurosurgery, Al-Makassed-Hospital, Al-Quds School of Medicine, Jerusalem, Israel
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Christian Hartmann
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Department of Neuropathology, Hannover Medical School, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Kais Hussein
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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Estrogen receptor (ESR1) mutation in bone metastases from breast cancer. Mod Pathol 2018; 31:56-61. [PMID: 28799536 DOI: 10.1038/modpathol.2017.95] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/07/2017] [Accepted: 06/18/2017] [Indexed: 12/14/2022]
Abstract
Activating mutations of estrogen receptor α gene (ESR1) in breast cancer can cause endocrine resistance of metastatic tumor cells. The skeleton belongs to the metastatic sides frequently affected by breast cancer. The prevalence of ESR1 mutation in bone metastasis and the corresponding phenotype are not known. In this study bone metastases from breast cancer (n=231) were analyzed for ESR1 mutation. In 27 patients (12%) (median age 73 years, range: 55-82 years) activating mutations of ESR1 were detected. The most frequent mutation was p.D538G (53%), no mutations in exon 4 (K303) or 7 (S463) were found. Lobular breast cancer was present in 52% of mutated cases (n=14) and in 49% of all samples (n=231), respectively. Mutated cancers constantly displayed strong estrogen receptor expression. Progesterone receptor was positive in 78% of the mutated cases (n=21). From 194 estrogen receptor-positive samples, 14% had ESR1 mutated. Except for one mutated case, no concurrent HER2 overexpression was noted. Metastatic breast cancer with activating mutations of ESR1 had a higher Ki67 labeling index than primary luminal cancers (median 30%, ranging from 5 to 60% with 85% of cases revealing ≥20% Ki67-positive cells). From those patients from whom information on endocrine therapy was available (n=7), two had received tamoxifen only, 4 tamoxifen followed by aromatase inhibitors and one patient had been treated with aromatase inhibitors only. We conclude that ESR1 mutation is associated with estrogen receptor expression and high proliferative activity and affects about 14% of estrogen receptor-positive bone metastases from breast cancer.
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Mägel L, Bartels S, Lehmann U. Next-Generation Sequencing Analysis of Laser-Microdissected Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens. Methods Mol Biol 2018; 1723:111-118. [PMID: 29344856 DOI: 10.1007/978-1-4939-7558-7_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In recent years, next-generation sequencing (NGS) became widely used in molecular pathology. Comprehensive mutational profiling improved diagnosis and prognosis, as well as the identification of therapeutically relevant genetic alterations. However, the vast majority of studies analyzing tissue samples use DNA extracted from bulk tissue or only manually microdissected specimens. Laser-assisted microdissection offers the possibility of isolating morphologically defined small tissue compartments (like individual glands) or even of single cells for further molecular analysis. Even formalin-fixed paraffin-embedded (FFPE) tissue specimens can be used for laser-assisted microdissection. Combining these two innovative powerful methodological approaches provides invaluable insights into the genetic profile of any cell type and tissue compartment of interest, contributing to a better understanding of fundamental biological processes and disease-specific mechanisms.In this chapter, a detailed protocol is provided for microdissection of human mammary adenomyoepithelioma tissue specimens and subsequent targeted resequencing of a panel of cancer-related genes using IonTorrent/PGM technology.
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Affiliation(s)
- Lavinia Mägel
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Stephan Bartels
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany.
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Mukherjee S, Sathanoori M, Ma Z, Andreatta M, Lennon PA, Wheeler SR, Prescott JL, Coldren C, Casey T, Rietz H, Fasig K, Woodford R, Hartley T, Spence D, Donnelan W, Berdeja J, Flinn I, Kozyr N, Bouzyk M, Correll M, Ho H, Kravtsov V, Tunnel D, Chandra P. Addition of chromosomal microarray and next generation sequencing to FISH and classical cytogenetics enhances genomic profiling of myeloid malignancies. Cancer Genet 2017; 216-217:128-141. [DOI: 10.1016/j.cancergen.2017.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/28/2017] [Accepted: 07/27/2017] [Indexed: 01/31/2023]
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Fibrotic progression in Polycythemia vera is associated with early concomitant driver-mutations besides JAK2. Leukemia 2017; 32:556-558. [DOI: 10.1038/leu.2017.298] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Systematic STAT3 sequencing in patients with unexplained cytopenias identifies unsuspected large granular lymphocytic leukemia. Blood Adv 2017; 1:1786-1789. [PMID: 29296824 DOI: 10.1182/bloodadvances.2017011197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/28/2017] [Indexed: 01/09/2023] Open
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31
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Bartels S, Persing S, Hasemeier B, Schipper E, Kreipe H, Lehmann U. Molecular Analysis of Circulating Cell-Free DNA from Lung Cancer Patients in Routine Laboratory Practice. J Mol Diagn 2017; 19:722-732. [DOI: 10.1016/j.jmoldx.2017.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/18/2017] [Indexed: 01/30/2023] Open
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32
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Maes B, Willemse J, Broekmans A, Smets R, Cruys B, Put N, Madoe V, Janssen M, Soepenberg O, Bries G, Vrelust I, Achten R, Van Pelt K, Buvé K, Theunissen K, Peeters V, Froyen G. Targeted next-generation sequencing using a multigene panel in myeloid neoplasms: Implementation in clinical diagnostics. Int J Lab Hematol 2017; 39:604-612. [DOI: 10.1111/ijlh.12709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/23/2017] [Indexed: 01/22/2023]
Affiliation(s)
- B. Maes
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - J. Willemse
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
- Department of Clinical Biology; AZ Turnhout; Turnhout Belgium
| | - A. Broekmans
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - R. Smets
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - B. Cruys
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - N. Put
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - V. Madoe
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - M. Janssen
- Department of Hematology; Ziekenhuis Oost-Limburg; Genk Belgium
| | - O. Soepenberg
- Department of Hematology; Mariaziekenhuis Noord-Limburg; Overpelt Belgium
| | - G. Bries
- Department of Hematology; AZ Turnhout; Turnhout Belgium
| | - I. Vrelust
- Department of Hematology; AZ Turnhout; Turnhout Belgium
| | - R. Achten
- Department of Pathology; Jessa Ziekenhuis; Hasselt Belgium
| | - K. Van Pelt
- Department of Clinical Biology; Ziekenhuis Oost-Limburg; Genk Belgium
| | - K. Buvé
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - K. Theunissen
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - V. Peeters
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - G. Froyen
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
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Christgen M, Bartels S, van Luttikhuizen JL, Schieck M, Pertschy S, Kundu S, Lehmann U, Sander B, Pelz E, Länger F, Schlegelberger B, Steinemann D, Kreipe H. Subclonal analysis in a lobular breast cancer with classical and solid growth pattern mimicking a solid-papillary carcinoma. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2017; 3:191-202. [PMID: 28770103 PMCID: PMC5527319 DOI: 10.1002/cjp2.76] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/10/2017] [Indexed: 12/24/2022]
Abstract
Recently, a new variant of invasive lobular breast cancer (ILBC) with solid-papillary-like growth pattern has been described. We present a case of ILBC with solid-papillary-like growth pattern in the main tumour mass and classical invasive lobular growth pattern in adjacent satellite foci. The two tumour components were subjected to comprehensive molecular analyses. Both components were ER/PR-positive, HER2-negative, and showed a complete loss of E-cadherin and beta-catenin protein expression, as determined by immunohistochemistry. Gene expression profiling classified the main tumour and a satellite focus as luminal-B and luminal-A subtypes, respectively. Whole-genome copy number profiles were highly similar in both tumour components. Shared copy number alterations (CNAs) included gains of chromosome 1q21.1-q43 and losses of chromosome 16q11.2-q24.3, the locus of the CDH1/E-cadherin tumour suppressor gene. CNAs detected only in the main tumour included a gain of chromosome 20q12-q13.33 and a loss of chromosome 1p36.33-p34.3, which has recently been associated with the solid variant of ILBC. Next generation sequencing revealed an identical, truncating CDH1 mutation (p.G169fs*5) in both tumour components confirming a common clonal ancestry. In conclusion, we confirm the recently described variant of ILBC with solid-papillary-like growth pattern and provide evidence that it evolves from classical ILBC by subclonal evolution.
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Affiliation(s)
| | - Stephan Bartels
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | | | | | - Stefanie Pertschy
- Department of Diagnostic RadiologyHannover Medical SchoolHannoverGermany
| | - Sudip Kundu
- Department of Obstetrics and GynecologyHannover Medical SchoolHannoverGermany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | - Bjoern Sander
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | - Enrico Pelz
- Institute of Pathology ViersenViersenGermany
| | - Florian Länger
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | | | - Doris Steinemann
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
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Guglielmelli P, Pietra D, Pane F, Pancrazzi A, Cazzola M, Vannucchi AM, Tura S, Barosi G. Recommendations for molecular testing in classical Ph1-neg myeloproliferative disorders-A consensus project of the Italian Society of Hematology. Leuk Res 2017; 58:63-72. [PMID: 28460339 DOI: 10.1016/j.leukres.2017.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/26/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Abstract
The discovery that Philadelphia-negative classical myeloproliferative neoplasms (MPNs) present with several molecular abnormalities, including the mostly represented JAK2V617F mutation, opened new horizons in the diagnosis, prognosis, and monitoring of these disorders. However, the great strides in the knowledge on molecular genetics need parallel progresses on the best approach to methods for detecting and reporting disease-associated mutations, and to shape the most effective and rationale testing pathway in the diagnosis, prognosis and monitoring of MPNs. The MPN taskforce of the Italian Society of Hematology (SIE) assessed the scientific literature and composed a framework of the best, possibly evidence-based, recommendations for optimal molecular methods as well as insights about the applicability and interpretation of those tests in the clinical practice, and clinical decision for testing MPNs patients. The issues dealt with: source of samples and nucleic acid template, the most appropriate molecular abnormalities and related detection methods required for diagnosis, prognosis, and monitoring of MPNs, how to report a diagnostic molecular test, calibration and quality control. For each of these issues, practice recommendations were provided.
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Affiliation(s)
- Paola Guglielmelli
- CRIMM-Centro Ricerca e Innovazione delle Malattie Mieloproliferative, Azienda Ospedaliera-Universitaria Careggi, Florence, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Daniela Pietra
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Alessandro Pancrazzi
- CRIMM-Centro Ricerca e Innovazione delle Malattie Mieloproliferative, Azienda Ospedaliera-Universitaria Careggi, Florence, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Department of Haematology Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia, Italy
| | - Alessandro M Vannucchi
- CRIMM-Centro Ricerca e Innovazione delle Malattie Mieloproliferative, Azienda Ospedaliera-Universitaria Careggi, Florence, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Giovanni Barosi
- Center for the Study of Myelofibrosis, Biotechnology Research Area, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico S. Matteo, Pavia, Italy.
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Thomas M, Sukhai MA, Zhang T, Dolatshahi R, Harbi D, Garg S, Misyura M, Pugh T, Stockley TL, Kamel-Reid S. Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies. Arch Pathol Lab Med 2017; 141:759-775. [PMID: 28557600 DOI: 10.5858/arpa.2016-0547-ra] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes. OBJECTIVE - To apply a systematic approach to evaluate and validate a commercially available next-generation sequencing panel (TruSight Myeloid Sequencing Panel, Illumina, San Diego, California) targeting 54 genes. In this manuscript, we focused on the parameters that were used to evaluate assay performance characteristics. DATA SOURCES - Analytical validation was performed using samples containing known variants that had been identified previously. Cases were selected from different disease types, with variants in a range of genes. Panel performance characteristics were assessed and genomic regions requiring additional analysis or wet-bench approaches identified. CONCLUSIONS - We validated the performance characteristics of a myeloid next-generation sequencing panel for detection of variants. The TruSight Myeloid Sequencing Panel covers more than 95% of target regions with depth greater than 500×. However, because of unique variant types such as large insertions or deletions or genomic regions of high GC content, variants in CEBPA, FLT3, and CALR required supplementation with non-next-generation sequencing assays or with informatics approaches to address deficiencies in performance. The use of multiple bioinformatics approaches (2 variant callers and informatics scripts) allows for maximizing calling of true positives, while identifying limitations in using either method alone.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Suzanne Kamel-Reid
- From the Laboratory Medicine Program, Advanced Molecular Diagnostics Laboratory, Departments of Pathology and Genetics (Drs Thomas, Sukhai, Garg, Misyura, Stockley, and Kamel-Reid), the Princess Margaret Cancer Centre (Drs Thomas, Sukhai, Garg, Misyura, Pugh, Stockley, and Kamel-Reid and Ms Zhang), and High Performance Computing and Bioinformatics Services, Princess Margaret Genomics Centre (Dr Harbi and Mr Dolatshahi), University Health Network, Toronto, Ontario, Canada; and the Departments of Medical Biophysics (Drs Pugh and Kamel-Reid) and Laboratory Medicine and Pathobiology (Drs Stockley and Kamel-Reid), The University of Toronto, Toronto, Ontario, Canada
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Evolution of chronic myelomonocytic leukemia to myeloproliferative neoplasm. Ann Hematol 2016; 95:1377-80. [PMID: 27220638 DOI: 10.1007/s00277-016-2699-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/14/2016] [Indexed: 10/21/2022]
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