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Yuan D, He X, Han X, Yang C, Liu F, Zhang S, Luan H, Li R, He J, Duan X, Wang D, Zhou Q, Gao S, Niu B. Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. Brief Bioinform 2021; 22:6225087. [PMID: 33851200 DOI: 10.1093/bib/bbab099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/15/2021] [Accepted: 03/06/2021] [Indexed: 12/25/2022] Open
Abstract
Internal tandem duplication (ITD) of FMS-like tyrosine kinase 3 (FLT3-ITD) constitutes an independent indicator of poor prognosis in acute myeloid leukaemia (AML). AML with FLT3-ITD usually presents with poor treatment outcomes, high recurrence rate and short overall survival. Currently, polymerase chain reaction and capillary electrophoresis are widely adopted for the clinical detection of FLT3-ITD, whereas the length and mutation frequency of ITD are evaluated using fragment analysis. With the development of sequencing technology and the high incidence of FLT3-ITD mutations, a multitude of bioinformatics tools and pipelines have been developed to detect FLT3-ITD using next-generation sequencing data. However, systematic comparison and evaluation of the methods or software have not been performed. In this study, we provided a comprehensive review of the principles, functionality and limitations of the existing methods for detecting FLT3-ITD. We further compared the qualitative and quantitative detection capabilities of six representative tools using simulated and biological data. Our results will provide practical guidance for researchers and clinicians to select the appropriate FLT3-ITD detection tools and highlight the direction of future developments in this field. Availability: A Docker image with several programs pre-installed is available at https://github.com/niu-lab/docker-flt3-itd to facilitate the application of FLT3-ITD detection tools.
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Affiliation(s)
- Danyang Yuan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in leukaemia-related bioinformatics and cancer genomics research. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in research related to the cancer genome and construction of the Chinese Cancer Genome Database. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences. He is mainly engaged in cancer genomics research focusing on the precise detection of tumour immunotherapy biomarkers. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Chunyan Yang
- Vice Director of the Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in research regarding solid tumours and haematologic malignancy using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Fei Liu
- bioinformatics analysis engineer of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the collection of biological information and analysis of genomic and cancer data or other biological information. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Shuying Zhang
- Computer Network Information Center, Chinese Academy of Sciences. Her research mainly focuses on the cancer genome and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Haijing Luan
- Computer Network Information Center, Chinese Academy of Sciences. She is mainly engaged in researching cancers of unknown primary sites (CUP) based on deep learning. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China
| | - Ruilin Li
- Computer Network Information Center, Chinese Academy of Sciences. Her research interests include high-performance computing and bioinformatics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiayin He
- George Washington University. She is currently researching at the Computer Network Information Center, Chinese Academy of Sciences. Her research interests include biostatistics and computational statistics. Her affiliation is with Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaohong Duan
- Laboratory of ChosenMed Technology (Beijing) Co., Ltd. She is mainly engaged in the research of solid tumours and haematologic malignancies using multiple approaches, including next-generation sequencing. Her affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Dongliang Wang
- Harbin Medical University. He is now the Chief Medical Officer of ChosenMed Technology (Beijing). His research mainly focuses on the mining and verification of molecular markers for tumour therapy. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Qiming Zhou
- CTO of ChosenMed Technology (Beijing) Co., Ltd. He is mainly engaged in the development of new molecular diagnostics technologies in genetic testing. His affiliation is with ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Sujun Gao
- Department of Haematology, The First Hospital of Jilin University. Her research mainly focuses on the experimental and clinical research of malignant haematological disorders and haematopoietic stem cell transplantation. Her affiliation is with Department of Haematology, The First Hospital of Jilin University, Changchun 130021, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences. His research interests include cancer genomics, metagenomics, and the development of computational tools for working with data from next-generation sequencing technologies. His affiliation is with Computer Network Information Center, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Beijing 100190, China, ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China
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Singh N, Huang L, Wang DB, Shao N, Zhang XE. Simultaneous Detection of a Cluster of Differentiation Markers on Leukemia-Derived Exosomes by Multiplex Immuno-Polymerase Chain Reaction via Capillary Electrophoresis Analysis. Anal Chem 2020; 92:10569-10577. [DOI: 10.1021/acs.analchem.0c01464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Netrapal Singh
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China
- CAS Center for Biological Macromolecules, National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Lin Huang
- CAS Center for Biological Macromolecules, National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Dian-Bing Wang
- CAS Center for Biological Macromolecules, National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Nan Shao
- CAS Center for Biological Macromolecules, National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Xian-En Zhang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China
- CAS Center for Biological Macromolecules, National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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