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Huang K, Zhang Q, Wu S, Zhou L, Liang W, Hu X, Ye S, Zhou W. Case report: A successful clinical experience of transplantation of liver and kidney from a donor with myelodysplastic syndromes. Front Immunol 2024; 15:1360955. [PMID: 38633259 PMCID: PMC11021682 DOI: 10.3389/fimmu.2024.1360955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
With a shortage of organs for transplant, the use of marginal donors can be an effective measure to meet the shortfall. Myelodysplastic syndromes (MDS) are considered an absolute contraindication for organ donation because of the high invasive potential. Currently, organ transplantation from donors with a past history of MDS has not been reported. In this paper, we report the successful clinical experience of one liver transplantation and two kidney transplantations, with organs donated by a 39-year-old patient diagnosed with a past history of MDS following intracranial hemorrhage. Four and a half years after transplantation, the three recipients are all doing well. However, it is still not clear to what extent organs donated by patients with a past history of MDS can be safely transplanted. This report provides support for the careful use of marginal donors. With effective treatment and full peer assessment, livers and kidneys from donors with a past history of MDS may be safely transplanted.
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Affiliation(s)
- Kang Huang
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, Hubei, China
| | - Qiuyan Zhang
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Sanyun Wu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lihua Zhou
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, Hubei, China
| | - Wenjin Liang
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, Hubei, China
| | - Xiaoyan Hu
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, Hubei, China
| | - Shaojun Ye
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, Hubei, China
| | - Wei Zhou
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, National Quality Control Center for Donated Organ Procurement, Hubei Key Laboratory of Medical Technology on Transplantation, Hubei Clinical Research Center for Natural Polymer Biological Liver, Hubei Engineering Center of Natural Polymer-based Medical Materials, Wuhan, Hubei, China
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Measurable Residual Disease and Clonal Evolution in Acute Myeloid Leukemia from Diagnosis to Post-Transplant Follow-Up: The Role of Next-Generation Sequencing. Biomedicines 2023; 11:biomedicines11020359. [PMID: 36830896 PMCID: PMC9953407 DOI: 10.3390/biomedicines11020359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
It has now been ascertained that acute myeloid leukemias-as in most type of cancers-are mixtures of various subclones, evolving by acquiring additional somatic mutations over the course of the disease. The complexity of leukemia clone architecture and the phenotypic and/or genotypic drifts that can occur during treatment explain why more than 50% of patients-in hematological remission-could relapse. Moreover, the complexity and heterogeneity of clone architecture represent a hindrance for monitoring measurable residual disease, as not all minimal residual disease monitoring methods are able to detect genetic mutations arising during treatment. Unlike with chemotherapy, which imparts a relatively short duration of selective pressure on acute myeloid leukemia clonal architecture, the immunological effect related to allogeneic hematopoietic stem cell transplant is prolonged over time and must be overcome for relapse to occur. This means that not all molecular abnormalities detected after transplant always imply inevitable relapse. Therefore, transplant represents a critical setting where a measurable residual disease-based strategy, performed during post-transplant follow-up by highly sensitive methods such as next-generation sequencing, could optimize and improve treatment outcome. The purpose of our review is to provide an overview of the role of next-generation sequencing in monitoring both measurable residual disease and clonal evolution in acute myeloid leukemia patients during the entire course of the disease, with special focus on the transplant phase.
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Tichkule S, Myung Y, Naung MT, Ansell BRE, Guy AJ, Srivastava N, Mehra S, Cacciò SM, Mueller I, Barry AE, van Oosterhout C, Pope B, Ascher DB, Jex AR. VIVID: a web application for variant interpretation and visualisation in multidimensional analyses. Mol Biol Evol 2022; 39:6697981. [PMID: 36103257 PMCID: PMC9514033 DOI: 10.1093/molbev/msac196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an individual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of diversity and selection, and 3D visualization of genotypic information encoded in Variant Call Format on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritizing targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum, revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.
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Affiliation(s)
- Swapnil Tichkule
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research , Melbourne , Australia
- Department of Medical Biology, University of Melbourne , Melbourne , Australia
| | - Yoochan Myung
- Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne , Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes , Melbourne , Australia
| | - Myo T Naung
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research , Melbourne , Australia
- Department of Medical Biology, University of Melbourne , Melbourne , Australia
| | - Brendan R E Ansell
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research , Melbourne , Australia
| | - Andrew J Guy
- School of Science, RMIT University , Melbourne , Australia
| | - Namrata Srivastava
- Department of Data Science and AI, Monash University , Melbourne , Australia
| | - Somya Mehra
- Life Sciences Discipline, Burnet Institute , Melbourne , Australia
| | - Simone M Cacciò
- Department of Infectious Disease, Istituto Superiore di Sanità , Rome , Italy
| | - Ivo Mueller
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research , Melbourne , Australia
| | - Alyssa E Barry
- Life Sciences Discipline, Burnet Institute , Melbourne , Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University , Geelong , Australia
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park , Norwich , UK
| | - Bernard Pope
- Melbourne Bioinformatics, University of Melbourne , Melbourne , Australia
- Australian BioCommons , Sydney , Australia
- Department of Clinical Pathology, University of Melbourne , Melbourne , Australia
- Department of Surgery (Royal Melbourne Hospital), University of Melbourne , Melbourne , Australia
| | - David B Ascher
- Systems and Computational Biology, Bio21 Institute, University of Melbourne , Melbourne , Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes , Melbourne , Australia
| | - Aaron R Jex
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research , Melbourne , Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne , Melbourne , Australia
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4
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Reverse Electrochemical Sensing of FLT3-ITD Mutations in Acute Myeloid Leukemia Using Gold Sputtered ZnO-Nanorod Configured DNA Biosensors. BIOSENSORS 2022; 12:bios12030170. [PMID: 35323440 PMCID: PMC8946250 DOI: 10.3390/bios12030170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
Detection of genetic mutations leading to hematological malignancies is a key factor in the early diagnosis of acute myeloid leukemia (AML). FLT3-ITD mutations are an alarming gene defect found commonly in AML patients associated with high cases of leukemia and low survival rates. Available diagnostic assessments for FLT3-ITD are incapable of combining cost-effective detection platforms with high analytical performances. To circumvent this, we developed an efficient DNA biosensor for the recognition of AML caused by FLT3-ITD mutation utilizing electrochemical impedance characterization. The system was designed by adhering gold-sputtered zinc oxide (ZnO) nanorods onto interdigitated electrode (IDE) sensor chips. The sensing surface was biointerfaced with capture probes designed to hybridize with unmutated FLT3 sequences instead of the mutated FLT3-ITD gene, establishing a reverse manner of target detection. The developed biosensor demonstrated specific detection of mutated FLT3 genes, with high levels of sensitivity in response to analyte concentrations as low as 1 nM. The sensor also exhibited a stable functional life span of more than five weeks with good reproducibility and high discriminatory properties against FLT3 gene targets. Hence, the developed sensor is a promising tool for rapid and low-cost diagnostic applications relevant to the clinical prognosis of AML stemming from FLT3-ITD mutations.
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Radhachandran A, Garikipati A, Iqbal Z, Siefkas A, Barnes G, Hoffman J, Mao Q, Das R. A machine learning approach to predicting risk of myelodysplastic syndrome. Leuk Res 2021; 109:106639. [PMID: 34171604 DOI: 10.1016/j.leukres.2021.106639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/18/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Early myelodysplastic syndrome (MDS) diagnosis can allow physicians to provide early treatment, which may delay advancement of MDS and improve quality of life. However, MDS often goes unrecognized and is difficult to distinguish from other disorders. We developed a machine learning algorithm for the prediction of MDS one year prior to clinical diagnosis of the disease. METHODS Retrospective analysis was performed on 790,470 patients over the age of 45 seen in the United States between 2007 and 2020. A gradient boosted decision tree model (XGB) was built to predict MDS diagnosis using vital signs, lab results, and demographics from the prior two years of patient data. The XGB model was compared to logistic regression (LR) and artificial neural network (ANN) models. The models did not use blast percentage and cytogenetics information as inputs. Predictions were made one year prior to MDS diagnosis as determined by International Classification of Diseases (ICD) codes, 9th and 10th revisions. Performance was assessed with regard to area under the receiver operating characteristic curve (AUROC). RESULTS On a hold-out test set, the XGB model achieved an AUROC value of 0.87 for prediction of MDS one year prior to diagnosis, with a sensitivity of 0.79 and specificity of 0.80. The XGB model was compared against LR and ANN models, which achieved an AUROC of 0.838 and 0.832, respectively. CONCLUSIONS Machine learning may allow for early MDS diagnosis MDS and more appropriate treatment administration.
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Rosenthal SH, Gerasimova A, Ma C, Li HR, Grupe A, Chong H, Acab A, Smolgovsky A, Owen R, Elzinga C, Chen R, Sugganth D, Freitas T, Graham J, Champion K, Bhattacharya A, Racke F, Lacbawan F. Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms. PLoS One 2021; 16:e0243683. [PMID: 33909614 PMCID: PMC8081174 DOI: 10.1371/journal.pone.0243683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. Various NGS based in-house developed and commercial myeloid neoplasm panels have been integrated into routine clinical practice. However, some genes frequently mutated in myeloid malignancies are particularly difficult to sequence with NGS panels (e.g., CEBPA, CARL, and FLT3). We report development and validation of a 48-gene NGS panel that includes genes that are technically challenging for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies ≥5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n = 2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9-99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n = 2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms even in technically challenging genes.
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Affiliation(s)
- Sun Hee Rosenthal
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Anna Gerasimova
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Charles Ma
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hai-Rong Li
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Andrew Grupe
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hansook Chong
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Allan Acab
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Alla Smolgovsky
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Renius Owen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Christopher Elzinga
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Rebecca Chen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Daniel Sugganth
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Tracey Freitas
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Jennifer Graham
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Kristen Champion
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Anindya Bhattacharya
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Frederick Racke
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Felicitas Lacbawan
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
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Hughes CFM, Gallipoli P, Agarwal R. Design, implementation and clinical utility of next generation sequencing in myeloid malignancies: acute myeloid leukaemia and myelodysplastic syndrome. Pathology 2021; 53:328-338. [PMID: 33676768 DOI: 10.1016/j.pathol.2021.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 12/25/2022]
Abstract
Next generation sequencing (NGS) based technology has contributed enormously to our understanding of the biology of myeloid malignancies including acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Assessment of clinically important mutations by NGS is a powerful tool to define diagnosis, determine prognostic risk, monitor measurable residual disease and uncover predictive mutational markers/therapeutic targets, and is now a routine component in the workup and monitoring of haematological disorders. There are many technical challenges in the design, implementation, analysis and reporting of NGS based results, and expert interpretation is essential. It is vital to distinguish relevant somatic disease associated mutations from those that are known polymorphisms, rare germline variants and clonal haematopoiesis of indeterminate potential (CHIP) associated variants. This review highlights and addresses the technical and biological challenges that should be considered before the implementation of NGS based testing in diagnostic laboratories and seeks to outline the essential and expanding role NGS plays in myeloid malignancies. Broad aspects of NGS panel design and reporting including inherent technological, biological and economic considerations are covered, following which the utility of NGS based testing in AML and MDS are discussed. In current practice, patient care is now strongly shaped by the results of NGS assessment and is considered a vital piece of the puzzle for clinicians as they manage these complex haematological disorders.
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Affiliation(s)
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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Atli EI, Gurkan H, Atli E, Kirkizlar HO, Yalcintepe S, Demir S, Demirci U, Eker D, Mail C, Kalkan R, Demir AM. The Importance of Targeted Next-Generation Sequencing Usage in Cytogenetically Normal Myeloid Malignancies. Mediterr J Hematol Infect Dis 2021; 13:e2021013. [PMID: 33489052 PMCID: PMC7813283 DOI: 10.4084/mjhid.2021.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Advanced diagnostic methods give an advantage for the identification of abnormalities in myeloid malignancies. Various researchers have shown the potential importance of genetic tests before the disease's onset and in remission. Large testing panels prevent false-negative results in myeloid malignancies. However, the critical question is how the results of conventional cytogenetic and molecular cytogenetic techniques can be merged with NGS technologies. In this paper, we drew an algorithm for the evaluation of myeloid malignancies. To evaluate genetic abnormalities, we performed cytogenetics, molecular cytogenetics, and NGS testing in myeloid malignancies. In this study, we analyzed 100 patients admitted to the Medical Genetics Laboratory with different myeloid malignancies. We highlighted the possible diagnostic algorithm for cytogenetically normal cases. We applied NGS 141 gene panel for cytogenetically normal patients, and we detected two or more pathogenic variations in 61 out of 100 patients (61%). NGS's pathogenic variation detection rate varies in disease groups: they were present in 85% of A.M.L. and 23% of M.D.S. Here, we identified 24 novel variations out of total pathogenic variations in myeloid malignancies. A total of 18 novel variations were identified in A.M.L., and 6 novel variations were identified in M.D.S. Despite long turnaround times, conventional techniques are still a golden standard for myeloid malignancies but sometimes cryptic gene fusions or complex abnormalities cannot be easily identified by conventional techniques. In these conditions, advanced technologies like NGS are highly recommended.
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Affiliation(s)
- Emine Ikbal Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Hakan Gurkan
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Engin Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Hakki Onur Kirkizlar
- Faculty of Medicine, Department of Hematology, Trakya University, Edirne, Turkey
| | - Sinem Yalcintepe
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Selma Demir
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Ufuk Demirci
- Faculty of Medicine, Department of Hematology, Trakya University, Edirne, Turkey
| | - Damla Eker
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Cisem Mail
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Rasime Kalkan
- Faculty of Medicine, Department of Medical Genetics, Near East University, Nicosia, Cyprus
| | - Ahmet Muzaffer Demir
- Faculty of Medicine, Department of Hematology, Trakya University, Edirne, Turkey
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Wang RQ, Chen CJ, Jing Y, Qin JY, Li Y, Chen GF, Zhou W, Li YH, Wang J, Li DW, Zhao HM, Wang BH, Wang LL, Wang H, Wang MZ, Gao XN, Yu L. Characteristics and prognostic significance of genetic mutations in acute myeloid leukemia based on a targeted next-generation sequencing technique. Cancer Med 2020; 9:8457-8467. [PMID: 32970934 PMCID: PMC7666719 DOI: 10.1002/cam4.3467] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 08/22/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022] Open
Abstract
To explore the characteristics and prognostic significance of genetic mutations in acute myeloid leukemia (AML), we screened the gene mutation profile of 171 previously untreated AML patients using a next‐generation sequencing technique targeting 127 genes with potential prognostic significance. A total of 390 genetic alterations were identified in 149 patients with a frequency of 87.1%. Younger age and high sensitivity to induction chemotherapy were associated with a lower number of mutations. NPM1 mutation was closely related to DNMT3A and FLT3‐internal tandem duplication (FLT3‐ITD) mutations, but mutually exclusive with ASXL1 mutation and CEBPAdouble mutation. In univariate analysis, ASXL1 or TET2 mutation predicted shorter overall survival (OS) or relapse‐free survival (RFS), DNMT3A, FLT3‐ITD, or RUNX1 mutation predicted a higher likelihood of remission‐induction failure, whereas NRAS mutation or CEBPAdouble mutation predicted longer OS. Concurrent DNMT3A, FLT3‐ITD, and NPM1 mutations predicted shorter OS. Hypomethylation agents could improve the OS in patients with DNA methylation‐related mutations. According to multivariate analysis, TET2 mutation was recognized as an independent prognostic factors for RFS. In summary, our study provided a detailed pattern of gene mutations and their prognostic relevance in Chinese AML patients based on targeted next‐generation sequencing screening.
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Affiliation(s)
- Rui-Qi Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Medicine School, Nankai University, Tianjin, China
| | - Chong-Jian Chen
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Yu Jing
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Jia-Yue Qin
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Yan Li
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Guo-Feng Chen
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Wei Zhou
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Yong-Hui Li
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Juan Wang
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Da-Wei Li
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Hong-Mei Zhao
- Annoroad Gene Technology Co, Beijing Economic-Technological Development Area, Beijing, China
| | - Bian-Hong Wang
- Beijing Tsinghua Changgung Hospital, Changping District, Beijing, China
| | - Li-Li Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Hong Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Meng-Zhen Wang
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Xiao-Ning Gao
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China.,Department of Hematology-Oncology, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China
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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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11
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He R, Devine DJ, Tu ZJ, Mai M, Chen D, Nguyen PL, Oliveira JL, Hoyer JD, Reichard KK, Ollila PL, Al-Kali A, Tefferi A, Begna KH, Patnaik MM, Alkhateeb H, Viswanatha DS. Hybridization capture-based next generation sequencing reliably detects FLT3 mutations and classifies FLT3-internal tandem duplication allelic ratio in acute myeloid leukemia: a comparative study to standard fragment analysis. Mod Pathol 2020; 33:334-343. [PMID: 31471587 PMCID: PMC7051912 DOI: 10.1038/s41379-019-0359-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 01/12/2023]
Abstract
FLT3-internal tandem duplication occurs in 20-30% of acute myeloid leukemia and confers an adverse prognosis with its allelic ratio being a key risk stratifier. The US Food and Drug Administration recently approved FLT3 inhibitors midostaurin and gilteritinib in FLT3 mutation-positive acute myeloid leukemia. Historically, FLT3 was tested by fragment analysis, which has become the standard method endorsed by international guidelines. However, next generation sequencing is increasingly used at acute myeloid leukemia diagnosis given its ability to simultaneously evaluate multiple clinically informative markers. As FLT3-internal tandem duplication detection was known to be challenging by next generation sequencing and the results carry profound prognostic and therapeutic implications, it is important to thoroughly examine its performance in FLT3-internal tandem duplication detection and allelic ratio classification. In a comparative study with fragment analysis, we retrospectively reviewed our experience using a custom-designed, hybridization capture-based, targeted next generation sequencing panel. Among 7902 cases, FLT3-internal tandem duplication was detected in 335 with variable sizes (3-231 bp) and insertion sites. Fragment analysis was also performed in 402 cases, demonstrating 100% concordance in FLT3-internal tandem duplication detection. In 136 dual-tested, positive cases, 128/136 (94%) exhibited concordant high/low allelic ratio classifications. The remaining 6% showed borderline low allelic ratio by next generation sequencing. The two methods were concordant in FLT3-tyrosine kinase domain mutation detection at the hotspot D835/I836 targeted by fragment analysis. Furthermore, seven mutations which may benefit from FLT3 inhibitor therapy were detected by next generation sequencing, in regions not covered by fragment analysis. Our study demonstrates that using a hybridization capture-based chemistry and optimized bioinformatics pipeline, next generation sequencing can reliably detect FLT3-internal tandem duplication and classify its allelic ratio for acute myeloid leukemia risk stratification. Next generation sequencing also exhibits superior comprehensiveness in FLT3 mutation detection and may further improve personalized, targeted therapy in acute myeloid leukemia.
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Affiliation(s)
- Rong He
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA.
| | - Daniel J Devine
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Zheng Jin Tu
- Biomedical statistics and informatics, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Ming Mai
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Dong Chen
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Phuong L Nguyen
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jennifer L Oliveira
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - James D Hoyer
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kaaren K Reichard
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Paul L Ollila
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Aref Al-Kali
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Ayalew Tefferi
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kebede H Begna
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mrinal M Patnaik
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Hassan Alkhateeb
- Division of Hematology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - David S Viswanatha
- Division of Hematopathology, Mayo Clinic College of Medicine, Rochester, MN, USA
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12
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AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting. BMC Med Genomics 2020; 13:17. [PMID: 32019565 PMCID: PMC7001226 DOI: 10.1186/s12920-020-0668-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-Generation Sequencing (NGS) enables large-scale and cost-effective sequencing of genetic samples in order to detect genetic variants. After successful use in research-oriented projects, NGS is now entering clinical practice. Consequently, variant analysis is increasingly important to facilitate a better understanding of disease entities and prognoses. Furthermore, variant calling allows to adapt and optimize specific treatments of individual patients, and thus is an integral part of personalized medicine.However, the analysis of NGS data typically requires a number of complex bioinformatics processing steps. A flexible and reliable software that combines the variant analysis process with a simple, user-friendly interface is therefore highly desirable, but still lacking. RESULTS With AMLVaran (AML Variant Analyzer), we present a web-based software, that covers the complete variant analysis workflow of targeted NGS samples. The software provides a generic pipeline that allows free choice of variant calling tools and a flexible language (SSDL) for filtering variant lists. AMLVaran's interactive website presents comprehensive annotation data and includes curated information on relevant hotspot regions and driver mutations. A concise clinical report with rule-based diagnostic recommendations is generated.An AMLVaran configuration with eight variant calling tools and a complex scoring scheme, based on the somatic variant calling pipeline appreci8, was used to analyze three datasets from AML and MDS studies with 402 samples in total. Maximum sensitivity and positive predictive values were 1.0 and 0.96, respectively. The tool's usability was found to be satisfactory by medical professionals. CONCLUSION Coverage analysis, reproducible variant filtering and software usability are important for clinical assessment of variants. AMLVaran performs reliable NGS variant analyses and generates reports fulfilling the requirements of a clinical setting. Due to its generic design, the software can easily be adapted for use with different targeted panels for other tumor entities, or even for whole-exome data. AMLVaran has been deployed to a public web server and is distributed with Docker scripts for local use.
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13
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Yu G, Yin C, Wu F, Jiang L, Zheng Z, Xu D, Zhou J, Jiang X, Liu Q, Meng F. Gene mutation profile and risk stratification in AML1‑ETO‑positive acute myeloid leukemia based on next‑generation sequencing. Oncol Rep 2019; 42:2333-2344. [PMID: 31638252 PMCID: PMC6826310 DOI: 10.3892/or.2019.7375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/09/2019] [Indexed: 12/31/2022] Open
Abstract
Gene mutations play an important role in the development and progression of AML1-ETO-positive acute myeloid leukemia (AE-AML). Nevertheless, the gene mutation profile in this subtype of leukemia remains unclear. In addition, the clinical and prognostic effects of different mutant genes may be underestimated. In the present study, gene sequencing was conducted at diagnosis and relapse with next-generation sequencing (NGS) in 64 patients with newly diagnosed AE-AML, and 44/64 (68.8%) patients were found to present with a median of 2 (1–10) recurrent mutations at diagnosis and 6/11 (54.5%) cases were found to present with genetic alterations at relapse. c-KIT mutation was the most common in this cohort, with an incidence of 27/64 (42.2%) at diagnosis, followed by ASXL1 (n=10, 15.6%), MET (n=8, 12.5%), MLH1 (n=6, 9.4%), TET2 (n=5, 7.8%), and FBXW7, TP53 and DNMT3A (n=5, 7.8%). Survival analysis showed that c-KIT (exon 8, 17) but not exon 10 adversely affected survival. In addition, ASXL1 and TP53 were poor impact factors for recurrence-free survival (RFS) (P<0.05), and ASXL1, MET, FBXW7 and TP53 had a negative impact on overall survival (OS) (P<0.05). Multivariate analysis showed that c-KIT (exon 8, 17) [RFS: hazard ratio (HR) 3.36, 95% confidence interval (CI) 1.54–7.34, P=0.002; OS: HR 2.84, 95% CI 1.20–6.71, P=0.018] and ASXL1 mutations (RFS: HR 3.13, 95% CI 1.34–7.32, P=0.009; OS: HR 3.94, 95% CI 1.62–9.61, P=0.003) were independent adverse factors for survival. Further, co-mutation of these two genes showed even worse effect on disease outcome. Collectively, additional gene mutations play critical role in AE-AML. C-KIT and ASXL1 mutations are the two most common mutations in this subtype of leukemia. C-KIT (exon 8, 17) but not exon 10, and also the ASXL1 mutation poorly affect the disease outcome of this disease.
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Affiliation(s)
- Guopan Yu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Changxin Yin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fuqun Wu
- Hematopathy Diagnosis and Therapy Center, Kanghua Hospital, Dongguan, Guangdong 523000, P.R. China
| | - Ling Jiang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhongxin Zheng
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Dan Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Jiaheng Zhou
- Department of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xuejie Jiang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fanyi Meng
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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14
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Spaulding TP, Stockton SS, Savona MR. The evolving role of next generation sequencing in myelodysplastic syndromes. Br J Haematol 2019; 188:224-239. [PMID: 31571207 DOI: 10.1111/bjh.16212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 12/11/2022]
Abstract
Myelodysplastic syndromes (MDS) are clonal haematological disorders characterized by haematopoietic cell dysplasia, peripheral blood cytopenias, and a predisposition for developing acute myeloid leukaemia (AML). Cytogenetics have historically been important in diagnosis and prognosis in MDS, but the growing accessibility of next generation sequencing (NGS) has led to growing research in the roles of molecular genetic variation on clinical decision-making in these disorders. Multiple genes have been previously studied and found to be associated with specific outcomes or disease types within MDS and knowledge of mutations in these genes provides insight into previously defined MDS subtypes. Knowledge of these mutations also informs development of novel therapies in the treatment of MDS. The precise role of NGS in the diagnosis, prognosis and monitoring of MDS remains unclear but the improvements in NGS technology and accessibility affords clinicians an additional practice tool to provide the best care for patients.
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Affiliation(s)
- Travis P Spaulding
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shannon S Stockton
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.,Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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15
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Next-generation sequencing-based minimal residual disease monitoring in patients receiving allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia or myelodysplastic syndrome. Curr Opin Hematol 2019; 25:425-432. [PMID: 30281033 DOI: 10.1097/moh.0000000000000464] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW The monitoring of minimal residual disease (MRD) has important clinical implications in both the pre and postallogeneic stem cell transplant (SCT) setting in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Next-generation sequencing (NGS) is a rapidly improving technology whose application to the monitoring of MRD is an active area of research. We aim to describe existing methods of MRD in AML and MDS, with a focus on the utility of NGS in patients undergoing SCT. RECENT FINDINGS Flow cytometry and quantitative PCR have been recommended by the European Leukemia Net as the preferred methods of MRD in AML and MDS, but these methods have limitations in cases without a disease-defining phenotype and genotype. Clinical trials are currently ongoing to assess the use of NGS in the setting of SCT for MDS and AML. Few studies have so far assessed the optimal method of MRD monitoring in the posttransplant setting. SUMMARY The optimal method for the monitoring of MRD in AML and MDS both pre and post transplant may require more than one technology. NGS holds great promise for the monitoring of MRD, with prospective trials currently ongoing to evaluate its efficacy in this regard.
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16
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Shumilov E, Flach J, Joncourt R, Porret N, Wiedemann G, Angelillo‐Scherrer A, Trümper L, Fiedler M, Jeker B, Amstutz U, Pabst T, Bacher U. Critical evaluation of current molecular MRD strategies including NGS for the management of AML patients with multiple mutations. Hematol Oncol 2019; 37:319-322. [DOI: 10.1002/hon.2603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/11/2019] [Accepted: 03/01/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Evgenii Shumilov
- Department of Hematology and Medical OncologyUniversity Medicine Göttingen (UMG) Göttingen Germany
| | - Johanna Flach
- Department of Hematology and OncologyMedical Faculty Mannheim of the Heidelberg University Mannheim Germany
| | - Raphael Joncourt
- University Department of Hematology and Central Hematology LaboratoryInselspital, Bern University Hospital Bern Switzerland
| | - Naomi Porret
- University Department of Hematology and Central Hematology LaboratoryInselspital, Bern University Hospital Bern Switzerland
| | - Gertrud Wiedemann
- University Department of Hematology and Central Hematology LaboratoryInselspital, Bern University Hospital Bern Switzerland
| | - Anne Angelillo‐Scherrer
- University Department of Hematology and Central Hematology LaboratoryInselspital, Bern University Hospital Bern Switzerland
| | - Lorenz Trümper
- Department of Hematology and Medical OncologyUniversity Medicine Göttingen (UMG) Göttingen Germany
| | - Martin Fiedler
- Center of Laboratory Medicine (ZLM)/University Institute of Clinical ChemistryInselspital, Bern University Hospital Bern Switzerland
| | - Barbara Jeker
- Department of Medical OncologyInselspital, Bern University Hospital Bern Switzerland
| | - Ursula Amstutz
- Center of Laboratory Medicine (ZLM)/University Institute of Clinical ChemistryInselspital, Bern University Hospital Bern Switzerland
| | - Thomas Pabst
- Department of Medical OncologyInselspital, Bern University Hospital Bern Switzerland
| | - Ulrike Bacher
- University Department of Hematology and Central Hematology LaboratoryInselspital, Bern University Hospital Bern Switzerland
- Center of Laboratory Medicine (ZLM)/University Institute of Clinical ChemistryInselspital, Bern University Hospital Bern Switzerland
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17
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Abstract
Clonal hematopoiesis is a common, age-related process in which a somatically mutated hematopoietic precursor gives rise to a genetically distinct subpopulation in the blood. This phenomenon has been observed in populations across the globe and, while virtually non-existent in children is estimated to affect >10% of the 70-and-older age group. The mutations are thought to occur in stem cells, which makes them pre-cancerous, and precursors to cancer stem cells. Many of the genes most commonly mutated in clonal hematopoiesis are also recurrently mutated in leukemia, genes such as DNMT3A, TET2, ASXL1, JAK2, and TP53. However, between 40% and 60% of cases arise from the accumulation of what appear to be random mutations outside of known driver genes. Clonal hematopoiesis is frequently present in otherwise healthy individuals and may persist for many years. Though largely asymptomatic, carrying these somatic mutations confers a small but significantly increased risk of leukemic transformation, affecting 0.5-1% carriers per year; although most genes confer an increased risk of transformation, mutations in TP53 and U2AF1 appear to carry a particularly high risk for transformation. Additionally, a patient's history of prior treatment with cytotoxic chemotherapy and/or radiation are correlated with the development of clonal hematopoiesis; in the setting of chemotherapy treatment of solid tumors, hematopoietic mutations in TP53 and PPM1D appear to contribute to outgrowth of clones that may lead to subsequent malignancy. The presence of a clone also imparts a significantly increased risk of cardiovascular disease, which in some cases appears to be due to increased inflammation and atherosclerosis. Clonal hematopoiesis is correlated with several other diseases as well, including diabetes, chronic pulmonary disease, and aplastic anemia, with other associations probably yet to be uncovered.
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Affiliation(s)
- Alexander J Silver
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University, Stanford, CA, United States.
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18
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Bacher U, Shumilov E, Flach J, Porret N, Joncourt R, Wiedemann G, Fiedler M, Novak U, Amstutz U, Pabst T. Challenges in the introduction of next-generation sequencing (NGS) for diagnostics of myeloid malignancies into clinical routine use. Blood Cancer J 2018; 8:113. [PMID: 30420667 PMCID: PMC6232163 DOI: 10.1038/s41408-018-0148-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/17/2018] [Accepted: 10/15/2018] [Indexed: 12/20/2022] Open
Abstract
Given the vast phenotypic and genetic heterogeneity of acute and chronic myeloid malignancies, hematologists have eagerly awaited the introduction of next-generation sequencing (NGS) into the routine diagnostic armamentarium to enable a more differentiated disease classification, risk stratification, and improved therapeutic decisions. At present, an increasing number of hematologic laboratories are in the process of integrating NGS procedures into the diagnostic algorithms of patients with acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myeloproliferative neoplasms (MPNs). Inevitably accompanying such developments, physicians and molecular biologists are facing unexpected challenges regarding the interpretation and implementation of molecular genetic results derived from NGS in myeloid malignancies. This article summarizes typical challenges that may arise in the context of NGS-based analyses at diagnosis and during follow-up of myeloid malignancies.
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Affiliation(s)
- Ulrike Bacher
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Center for Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
| | - Evgenii Shumilov
- Department of Hematology and Medical Oncology, University Medicine Göttingen (UMG), Göttingen, Germany
| | - Johanna Flach
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Naomi Porret
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Raphael Joncourt
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gertrud Wiedemann
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Martin Fiedler
- Center for Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Urban Novak
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ursula Amstutz
- Center for Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Pabst
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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19
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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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20
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Buccisano F, Hourigan CS, Walter RB. The Prognostic Significance of Measurable ("Minimal") Residual Disease in Acute Myeloid Leukemia. Curr Hematol Malig Rep 2018; 12:547-556. [PMID: 29027628 DOI: 10.1007/s11899-017-0420-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review was to evaluate recent literature on detection methodologies for, and prognostic significance of, measurable ("minimal") residual disease (MRD) in acute myeloid leukemia (AML). RECENT FINDINGS There is no "one-fits-all" approach to MRD testing in AML. Most exploited to date are methods relying on immunophenotypic aberrancies (identified via multiparameter flow cytometry) or genetic abnormalities (identified via PCR-based assays). Current methods have important shortcomings, including the lack of assay platform standardization/harmonization across laboratories. In parallel to refinements of existing technologies and data analysis/interpretation, new methodologies (e.g., next-generation sequencing-based assays) are emerging that eventually may complement or replace existing ones. This dynamic evolution of MRD testing has complicated comparisons between individual studies. Nonetheless, an ever-growing body of data demonstrates that a positive MRD test at various time points throughout chemotherapy and hematopoietic cell transplantation identifies patients at particularly high risks of disease recurrence and short survival even after adjustment for other risk factors.
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Affiliation(s)
- Francesco Buccisano
- Department of Biomedicine and Prevention, Hematology, University Tor Vergata, Via Montpellier 1, 00133, Rome, Italy.
| | - Christopher S Hourigan
- Myeloid Malignancies Section, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Roland B Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA
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21
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Abstract
PURPOSE OF REVIEW Assessment of measurable residual disease (MRD) after treatment can identify patients with acute myeloid leukemia (AML) that are at high risk of poor outcomes. However, there is no consensus yet regarding a standardized approach to measuring MRD that is most clinically meaningful. We review multiparameter flow cytometry (MFC) and reverse transcriptase polymerase chain reaction (RT-PCR), and discuss a framework for assessing remission MRD using next-generation sequencing (NGS). RECENT FINDINGS MFC and RT-PCR may not fully capitalize on the major advances that have been made in characterizing the genetic landscape of AML, which has offered insight into the biological and clinical implications of clonal genetic architecture. NGS has increasingly been shown to provide a qualitative and quantitative assessment of MRD with significant prognostic implications. The assessment of clonal architecture by NGS may complement or extend existing approaches for MRD monitoring. Long-term serial monitoring of diagnostic, remission, and relapse samples with clinical correlation will need to be performed in order to determine the impact of various MRD patterns using this technique.
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22
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Shumilov E, Flach J, Kohlmann A, Banz Y, Bonadies N, Fiedler M, Pabst T, Bacher U. Current status and trends in the diagnostics of AML and MDS. Blood Rev 2018; 32:508-519. [PMID: 29728319 DOI: 10.1016/j.blre.2018.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 01/01/2023]
Abstract
Diagnostics of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) have recently been experiencing extensive modifications regarding the incorporation of next-generation sequencing (NGS) strategies into established diagnostic algorithms, classification and risk stratification systems, and minimal residual disease (MRD) detection. Considering the increasing arsenal of targeted therapies (e.g. FLT3 or IDH1/IDH2 inhibitors) for AML, timely and comprehensive molecular mutation screening has arrived in daily practice. Next-generation flow strategies allow for immunophenotypic minimal residual disease (MRD) monitoring with very high sensitivity. At the same time, standard diagnostic tools such as cytomorphology or conventional cytogenetics remain cornerstones for the diagnostic workup of myeloid malignancies. Herein, we summarize the most recent advances and new trends for the diagnostics of AML and MDS, discuss the difficulties, which accompany the integration of these new methods and their results into daily routine, and aim to define the role hemato-oncologists may play in this new diagnostic era.
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Affiliation(s)
- Evgenii Shumilov
- Department of Hematology and Medical Oncology, University Medicine Göttingen (UMG), Göttingen, Germany
| | - Johanna Flach
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany
| | - Alexander Kohlmann
- Precision Medicine and Genomics, Innovative Medicines and Early Development, AstraZeneca, Cambridge, UK
| | - Yara Banz
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Nicolas Bonadies
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland; Department for BioMedical Research, Inselspital, Bern, Bern University Hospital, University of Bern, Switzerland
| | - Martin Fiedler
- Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Thomas Pabst
- Department of Medical Oncology, Inselspital, Bern University Hospital, Bern, Switzerland.
| | - Ulrike Bacher
- University Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, Bern, Switzerland; Center of Laboratory Medicine (ZLM)/University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland.
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23
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Tran AN, Taylan F, Zachariadis V, Ivanov Öfverholm I, Lindstrand A, Vezzi F, Lötstedt B, Nordenskjöld M, Nordgren A, Nilsson D, Barbany G. High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing. PLoS One 2018. [PMID: 29529047 PMCID: PMC5846771 DOI: 10.1371/journal.pone.0193928] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The detection of recurrent somatic chromosomal rearrangements is standard of care for most leukemia types. Even though karyotype analysis-a low-resolution genome-wide chromosome analysis-is still the gold standard, it often needs to be complemented with other methods to increase resolution. To evaluate the feasibility and applicability of mate pair whole genome sequencing (MP-WGS) to detect structural chromosomal rearrangements in the diagnostic setting, we sequenced ten bone marrow samples from leukemia patients with recurrent rearrangements. Samples were selected based on cytogenetic and FISH results at leukemia diagnosis to include common rearrangements of prognostic relevance. Using MP-WGS and in-house bioinformatic analysis all sought rearrangements were successfully detected. In addition, unexpected complexity or additional, previously undetected rearrangements was unraveled in three samples. Finally, the MP-WGS analysis pinpointed the location of chromosome junctions at high resolution and we were able to identify the exact exons involved in the resulting fusion genes in all samples and the specific junction at the nucleotide level in half of the samples. The results show that our approach combines the screening character from karyotype analysis with the specificity and resolution of cytogenetic and molecular methods. As a result of the straightforward analysis and high-resolution detection of clinically relevant rearrangements, we conclude that MP-WGS is a feasible method for routine leukemia diagnostics of structural chromosomal rearrangements.
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Affiliation(s)
- Anh Nhi Tran
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ingegerd Ivanov Öfverholm
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Francesco Vezzi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Britta Lötstedt
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
- * E-mail:
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25
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Rasighaemi P, Ward AC. ETV6 and ETV7: Siblings in hematopoiesis and its disruption in disease. Crit Rev Oncol Hematol 2017; 116:106-115. [PMID: 28693791 DOI: 10.1016/j.critrevonc.2017.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/05/2017] [Accepted: 05/28/2017] [Indexed: 01/07/2023] Open
Abstract
ETV6 (TEL1) and ETV7 (TEL2) are closely-related members of the ETS family of transcriptional regulators. Both ETV6 and ETV7 have been demonstrated to play key roles in hematopoiesis, particularly with regard to maintenance of hematopoietic stem cells and control of lineage-specific differentiation, with evidence of functional interactions between both proteins. ETV6 has been strongly implicated in the molecular etiology of a number of hematopoietic diseases, including as a tumor suppressor, an oncogenic fusion partner, and an important regulator of thrombopoiesis, but recent evidence has also identified ETV7 as a potential oncogene in certain malignancies. This review provides an overview of ETV6 and ETV7 and their contribution to both normal and disrupted hematopoiesis. It also highlights the key clinical implications of the growing knowledge base regarding ETV6 abnormalities with respect to prognosis and treatment.
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Affiliation(s)
- Parisa Rasighaemi
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, 3216, Australia.
| | - Alister C Ward
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria, 3216, Australia.
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26
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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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27
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Ng IK, Ng C, Low JJ, Chiu L, Seah E, Ng CH, Chng WJ, Yan B, Ban KHK. Identifying large indels in targeted next generation sequencing assays for myeloid neoplasms: a cautionary tale of the ZRSR1 pseudogene. J Clin Pathol 2017; 70:1069-1073. [PMID: 28676493 DOI: 10.1136/jclinpath-2017-204440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 11/04/2022]
Abstract
Targeted next generation sequencing platforms have been increasingly utilised for identification of novel mutations in myeloid neoplasms, such as acute myeloid leukaemia (AML), and hold great promise for use in routine clinical diagnostics. In this study, we evaluated the utility of an open source variant caller in detecting large indels in a targeted sequencing of AML samples. While we found that this bioinformatics pipeline has the potential to accurately capture large indels (>20 bp) in patient samples, we highlighted the pitfall of a confounding ZRSR1 pseudogene that led to an erroneous ZRSR2 variant call. We further discuss possible clinical implications of the ZRSR1 pseudogene in myeloid neoplasms based on its molecular features. Knowledge of the confounding ZRSR1 pseudogene in ZRSR2 sequencing assays could be particularly important in AML diagnostics because the detection of ZRSR2 in AML patients is highly specific for an s-AML diagnosis.
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Affiliation(s)
- Isaac Ks Ng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christopher Ng
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Jia Jin Low
- Department of Statistics, National University of Singapore, Singapore
| | - Lily Chiu
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Elaine Seah
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Chin Hin Ng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Wee-Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore.,Cancer Science Institute, National University of Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Kenneth H K Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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28
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Valent P, Orazi A, Steensma DP, Ebert BL, Haase D, Malcovati L, van de Loosdrecht AA, Haferlach T, Westers TM, Wells DA, Giagounidis A, Loken M, Orfao A, Lübbert M, Ganser A, Hofmann WK, Ogata K, Schanz J, Béné MC, Hoermann G, Sperr WR, Sotlar K, Bettelheim P, Stauder R, Pfeilstöcker M, Horny HP, Germing U, Greenberg P, Bennett JM. Proposed minimal diagnostic criteria for myelodysplastic syndromes (MDS) and potential pre-MDS conditions. Oncotarget 2017; 8:73483-73500. [PMID: 29088721 PMCID: PMC5650276 DOI: 10.18632/oncotarget.19008] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Myelodysplastic syndromes (MDS) comprise a heterogeneous group of myeloid neoplasms characterized by peripheral cytopenia, dysplasia, and a variable clinical course with about 30% risk to transform to secondary acute myeloid leukemia (AML). In the past 15 years, diagnostic evaluations, prognostication, and treatment of MDS have improved substantially. However, with the discovery of molecular markers and advent of novel targeted therapies, new challenges have emerged in the complex field of MDS. For example, MDS-related molecular lesions may be detectable in healthy individuals and increase in prevalence with age. Other patients exhibit persistent cytopenia of unknown etiology without dysplasia. Although these conditions are potential pre-phases of MDS they may also transform into other bone marrow neoplasms. Recently identified molecular, cytogenetic, and flow-based parameters may add in the delineation and prognostication of these conditions. However, no generally accepted integrated classification and no related criteria are as yet available. In an attempt to address this challenge, an international consensus group discussed these issues in a working conference in July 2016. The outcomes of this conference are summarized in the present article which includes criteria and a proposal for the classification of pre-MDS conditions as well as updated minimal diagnostic criteria of MDS. Moreover, we propose diagnostic standards to delineate between ´normal´, pre-MDS, and MDS. These standards and criteria should facilitate diagnostic and prognostic evaluations in clinical studies as well as in clinical practice.
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Affiliation(s)
- Peter Valent
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria.,Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria
| | - Attilio Orazi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David P Steensma
- Division of Hematological Malignancies, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Benjamin L Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Detlef Haase
- Clinic of Hematology and Medical Oncology, Universitymedicine Göttingen, Göttingen, Germany
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Arjan A van de Loosdrecht
- Department of Hematology Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Theresia M Westers
- Department of Hematology Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | - Alberto Orfao
- Servicio Central de Citometría, Centro de Investigación del Cáncer (IBMCC, CSIC-USAL) and IBSAL, Universidad de Salamanca, Salamanca, Spain
| | - Michael Lübbert
- Department of Medicine I, Medical Center-University of Freiburg, Freiburg, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Kiyoyuki Ogata
- Metropolitan Research and Treatment Center for Blood Disorders (MRTC Japan), Tokyo, Japan
| | - Julie Schanz
- Clinic of Hematology and Medical Oncology, Universitymedicine Göttingen, Göttingen, Germany
| | - Marie C Béné
- Laboratoire d'Hématologie CHU de Nantes, Nantes, France
| | - Gregor Hoermann
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Wolfgang R Sperr
- Department of Internal Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria.,Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria
| | - Karl Sotlar
- Institute of Pathology, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Reinhard Stauder
- Department of Internal Medicine V (Haematology and Oncology) Innsbruck Medical University, Innsbruck, Austria
| | | | - Hans-Peter Horny
- Institute of Pathology, Ludwig-Maximilians University, Munich, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology, and Clinical Immunology, Heinrich-Heine-University, Düsseldorf, Germany
| | | | - John M Bennett
- Department of Pathology, Hematopathology Unit and James P Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
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29
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The relative utilities of genome-wide, gene panel, and individual gene sequencing in clinical practice. Blood 2017; 130:433-439. [PMID: 28600338 DOI: 10.1182/blood-2017-03-734533] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/09/2017] [Indexed: 12/12/2022] Open
Abstract
Advances in technology that have transpired over the past 2 decades have enabled the analysis of cancer samples for genomic alterations to understand their biologic function and to translate that knowledge into clinical practice. With the power to analyze entire genomes in a clinically relevant time frame and with manageable costs comes the question of whether we ought to and when. This review focuses on the relative merits of 3 approaches to molecular diagnostics in hematologic malignancies: indication-specific single gene assays, gene panel assays that test for genes selected for their roles in cancer, and genome-wide assays that broadly analyze the tumor exomes or genomes. After addressing these in general terms, we review specific use cases in myeloid and lymphoid malignancies to highlight the utility of single gene testing and/or larger panels.
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30
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Waalkes A, Penewit K, Wood BL, Wu D, Salipante SJ. Ultrasensitive detection of acute myeloid leukemia minimal residual disease using single molecule molecular inversion probes. Haematologica 2017; 102:1549-1557. [PMID: 28572161 PMCID: PMC5685235 DOI: 10.3324/haematol.2017.169136] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/31/2017] [Indexed: 12/11/2022] Open
Abstract
The identification of minimal residual disease is the primary diagnostic finding which predicts relapse in patients treated for acute myeloid leukemia. Ultrasensitive detection of minimal residual disease would enable better patient risk stratification and could open opportunities for early therapeutic intervention. Herein we apply single molecule molecular inversion probe capture, a technology combining multiplexed targeted sequencing with error correction schemes based on molecular barcoding, in order to detect mutations identifying minimal residual disease with ultrasensitive and quantitative precision. We designed a single molecule molecular inversion probe capture panel spanning >50 kb and targeting 32 factors relevant to acute myeloid leukemia pathogenesis. We demonstrate linearity and quantitative precision over 100-fold relative abundance of mutant cells (1 in 100 to 1 in 1,500), with estimated error rates approaching 1 in 1,200 base pairs sequenced and maximum theoretical limits of detection exceeding 1 in 60,000 mutant alleles. In 3 of 4 longitudinally collected specimens from patients with acute myeloid leukemia, we find that single molecule molecular inversion probe capture detects somatic mutations identifying minimal residual disease at substantially earlier time points and with greater sensitivity than clinical diagnostic approaches used as current standard of care (flow cytometry and conventional molecular diagnosis), and identifies persisting neoplastic cells during clinical remission. In 2 patients, single molecule molecular inversion probe capture detected heterogeneous, subclonal acute myeloid leukemia populations carrying distinct mutational signatures. Single molecule molecular inversion probe technology uniquely couples scalable target enrichment with sequence read error correction, providing an integrated, ultrasensitive approach for detecting minimal residual disease identifying mutations.
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Affiliation(s)
- Adam Waalkes
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Brent L Wood
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
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31
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Song Q, Peng M, Chu Y, Huang S. Techniques for detecting chromosomal aberrations in myelodysplastic syndromes. Oncotarget 2017; 8:62716-62729. [PMID: 28977983 PMCID: PMC5617543 DOI: 10.18632/oncotarget.17698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/19/2017] [Indexed: 11/25/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic diseases. Chromosomal aberrations are important for the initiation, development, and progression of MDS. Detection of chromosomal abnormalities in MDS is important for categorization, risk stratification, therapeutic selection, and prognosis evaluation of the disease. Recent progress of multiple techniques has brought powerful molecular cytogenetic information to reveal copy number variation, uniparental disomy, and complex chromosomal aberrations in MDS. In this review, we will introduce some common chromosomal aberrations in MDS and their clinical significance. Then we will explain the application, advantages, and limitations of different techniques for detecting chromosomal abnormalities in MDS. The information in this review may be helpful for clinicians to select appropriate methods in patient-related decision making.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar Global, Wuhan, China
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32
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Hourigan CS, Gale RP, Gormley NJ, Ossenkoppele GJ, Walter RB. Measurable residual disease testing in acute myeloid leukaemia. Leukemia 2017; 31:1482-1490. [PMID: 28386105 DOI: 10.1038/leu.2017.113] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 12/24/2022]
Abstract
There is considerable interest in developing techniques to detect and/or quantify remaining leukaemia cells termed measurable or, less precisely, minimal residual disease (MRD) in persons with acute myeloid leukaemia (AML) in complete remission defined by cytomorphological criteria. An important reason for AML MRD-testing is the possibility of estimating the likelihood (and timing) of leukaemia relapse. A perfect MRD-test would precisely quantify leukaemia cells biologically able and likely to cause leukaemia relapse within a defined interval. AML is genetically diverse and there is currently no uniform approach to detecting such cells. Several technologies focused on immune phenotype or cytogenetic and/or molecular abnormalities have been developed, each with advantages and disadvantages. Many studies report a positive MRD-test at diverse time points during AML therapy identifies persons with a higher risk of leukaemia relapse compared with those with a negative MRD-test even after adjusting for other prognostic and predictive variables. No MRD-test in AML has perfect sensitivity and specificity for relapse prediction at the cohort- or subject levels and there are substantial rates of false-positive and -negative tests. Despite these limitations, correlations between MRD-test results and relapse risk have generated interest in MRD-test result-directed therapy interventions. However, convincing proof that a specific intervention will reduce relapse risk in persons with a positive MRD-test is lacking and needs testing in randomized trials. Routine clinical use of MRD-testing requires further refinements and standardization/harmonization of assay platforms and results reporting. Such data are needed to determine whether results of MRD-testing can be used as a surrogate end point in AML therapy trials. This could make drug-testing more efficient and accelerate regulatory approvals. Although MRD-testing in AML has advanced substantially, much remains to be done.
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Affiliation(s)
- C S Hourigan
- Myeloid Malignancies Section, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - R P Gale
- Haematology Research Centre, Division of Experimental Medicine, Department of Medicine, Imperial College London, London, UK
| | - N J Gormley
- Division of Hematology Products, Office of Hematology and Oncology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - G J Ossenkoppele
- Division of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - R B Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA
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33
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Stahl M, Zeidan AM. Management of lower-risk myelodysplastic syndromes without del5q: current approach and future trends. Expert Rev Hematol 2017; 10:345-364. [PMID: 28277851 DOI: 10.1080/17474086.2017.1297704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Myelodysplastic syndromes (MDS) are characterized by progressive bone marrow failure manifesting as blood cytopenia and a variable risk of progression into acute myeloid leukemia. MDS is heterogeneous in biology and clinical behavior. MDS are generally divided into lower-risk (LR) and higher-risk (HR) MDS. Goals of care in HR-MDS focus on changing the natural history of the disease, whereas in LR-MDS symptom control and quality of life are the main goals. Areas covered: We review the epidemiology, tools of risk assessment, and the available therapeutic modalities for LR-MDS. We discuss the use of erythropoiesis stimulating agents (ESAs), immunosuppressive therapy (IST), lenalidomide and the hypomethylating agents (HMAs). We also discuss the predictors of response, combination treatment modalities, and management of iron overload. Lastly, we overview the most promising investigational agents for LR-MDS. Expert commentary: It remains unclear how to best incorporate a wealth of new genetic and epigenetic prognostic markers into risk assessment tools especially for LR-MDS patients. Only a subset of patients respond to current treatment modalities and most responders eventually lose their response. Once standard therapeutic options fail, management becomes more challenging. Combination-based approaches have been largely unsuccessful. Among the most promising investigational are the TPO agonists, TGF- β pathway inhibitors, telomerase inhibitors, and the splicing modifiers.
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Affiliation(s)
- Maximilian Stahl
- a Section of Hematology, Department of Internal Medicine, Section of Hematology, Yale University and the Yale Comprehensive Cancer Center , Yale University School of Medicine , New Haven , CT , USA
| | - Amer M Zeidan
- a Section of Hematology, Department of Internal Medicine, Section of Hematology, Yale University and the Yale Comprehensive Cancer Center , Yale University School of Medicine , New Haven , CT , USA
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34
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Abstract
Application of next-generation sequencing (NGS) on myeloid neoplasms has expanded our knowledge of genomic alterations in this group of diseases. Genomic alterations in myeloid neoplasms are complex, heterogeneous, and not specific to a disease entity. NGS-based panel testing of myeloid neoplasms can complement existing diagnostic modalities and is gaining acceptance in the clinics and diagnostic laboratories. Prospective, randomized trials to evaluate the prognostic significance of genomic markers in myeloid neoplasms are under way in academic medical centers.
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Affiliation(s)
- Frank C Kuo
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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35
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Pettit K, Stock W, Walter RB. Incorporating measurable ('minimal') residual disease-directed treatment strategies to optimize outcomes in adults with acute myeloid leukemia. Leuk Lymphoma 2016; 57:1527-33. [PMID: 27269126 DOI: 10.3109/10428194.2016.1160085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Curative-intent therapy leads to complete remissions in many adults with acute myeloid leukemia (AML), but relapse remains common. Numerous studies have unequivocally demonstrated that the persistence of measurable ('minimal') residual disease (MRD) at the submicroscopic level during morphologic remission identifies patients at high risk of disease recurrence and short survival. This association has provided the impetus to customize anti-leukemia therapy based on MRD data, a strategy that is now routinely pursued in acute promyelocytic leukemia (APL). While it is currently uncertain whether this approach will improve outcomes in AML other than APL, randomized studies have validated MRD-based risk-stratified treatment algorithms in acute lymphoblastic leukemia. Here, we review the available studies examining MRD-directed therapy in AML, appraise their strengths and limitations, and discuss avenues for future investigation.
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Affiliation(s)
- Kristen Pettit
- a Section of Hematology/Oncology and University of Chicago Comprehensive Cancer Center , University of Chicago , Chicago , IL , USA
| | - Wendy Stock
- a Section of Hematology/Oncology and University of Chicago Comprehensive Cancer Center , University of Chicago , Chicago , IL , USA
| | - Roland B Walter
- b Clinical Research Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA ;,c Department of Medicine, Division of Hematology , University of Washington , Seattle , WA , USA ;,d Department of Epidemiology , University of Washington , Seattle , WA , USA
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36
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Abstract
Acute myeloid leukaemia (AML) is a heterogeneous disease that is, in general, associated with a very poor prognosis. Multiple cytogenetic and molecular abnormalities that characterize different forms of AML have been used to better prognosticate patients and inform treatment decisions. Indeed, risk status in patients with this disease has classically been based on cytogenetic findings; however, additional molecular characteristics have been shown to inform risk assessment, including FLT3, NPM1, KIT, and CEBPA mutation status. Advances in sequencing technology have led to the discovery of novel somatic mutations in tissue samples from patients with AML, providing deeper insight into the mutational landscape of the disease. The majority of patients with AML (>97%) are found to have a clonal somatic abnormality on mutational profiling. Nevertheless, our understanding of the utility of mutation profiling in clinical practice remains incomplete and is continually evolving, and evidence-based approaches to application of these data are needed. In this Review, we discuss the evidence-base for integrating mutational data into treatment decisions for patients with AML, and propose novel therapeutic algorithms in the era of molecular medicine.
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Affiliation(s)
- Catherine C Coombs
- Leukemia Service, Department of Medicine, Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Martin S Tallman
- Leukemia Service, Department of Medicine, Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
- Weill Cornell Medical Center, 1300 York Avenue, New York, New York 10065, USA
| | - Ross L Levine
- Leukemia Service, Department of Medicine, Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
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37
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Grünmüller L, Thierauf J, Weissinger SE, Bergmann C, Bankfalvi A, Veit J, Hoffmann TK, Möller P, Lennerz JK. Biopanel identifies expression status of targetable proteins in sinonasal melanoma. Per Med 2016; 13:291-301. [PMID: 29749817 DOI: 10.2217/pme-2016-0023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Advanced stage at presentation, lack of BRAF mutations and overall rarity pose unique challenges to the therapy and trial design in sinonasal melanoma. METHODS Here, we assessed the expression status of 12 proteins in two independent cohorts of sinonasal melanoma (n = 20). RESULTS Each case showed expression of at least one protein (KIT, TP53, MYC, HER2, EGFR, MET, VEGFR, BRAF V600E and/or MDM2), whereas lack of ALK, FLI1 and PDGFRα expression underscores differences to cutaneous melanoma. Comparison of marker frequencies to a metareview of the literature indicates that MYC, HER2, EGFR and MET had not been previously assessed. CONCLUSION Expression of at least one potentially targetable protein per case illustrates proteome pathway profiling as one starting point for marker stratified trial design.
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Affiliation(s)
| | - Julia Thierauf
- Department of Otorhinolaryngology, Head & Neck Surgery, University Medical Center Ulm, Ulm, Germany
| | | | | | - Agnes Bankfalvi
- Department of Pathology, University Hospital Essen, Essen, Germany
| | - Johannes Veit
- Department of Otorhinolaryngology, Head & Neck Surgery, University Medical Center Ulm, Ulm, Germany
| | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head & Neck Surgery, University Medical Center Ulm, Ulm, Germany
| | - Peter Möller
- Institute of Pathology, Ulm University, Ulm, Germany
| | - Jochen K Lennerz
- Institute of Pathology, Ulm University, Ulm, Germany.,Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
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Berenstein R. Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis. Biomark Insights 2015; 10:1-14. [PMID: 26309392 PMCID: PMC4527365 DOI: 10.4137/bmi.s22433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)-based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.
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Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Berlin, Germany
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