1
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AIM in Haematology. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Walter W, Haferlach C, Nadarajah N, Schmidts I, Kühn C, Kern W, Haferlach T. How artificial intelligence might disrupt diagnostics in hematology in the near future. Oncogene 2021; 40:4271-4280. [PMID: 34103684 PMCID: PMC8225509 DOI: 10.1038/s41388-021-01861-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/11/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Artificial intelligence (AI) is about to make itself indispensable in the health care sector. Examples of successful applications or promising approaches range from the application of pattern recognition software to pre-process and analyze digital medical images, to deep learning algorithms for subtype or disease classification, and digital twin technology and in silico clinical trials. Moreover, machine-learning techniques are used to identify patterns and anomalies in electronic health records and to perform ad-hoc evaluations of gathered data from wearable health tracking devices for deep longitudinal phenotyping. In the last years, substantial progress has been made in automated image classification, reaching even superhuman level in some instances. Despite the increasing awareness of the importance of the genetic context, the diagnosis in hematology is still mainly based on the evaluation of the phenotype. Either by the analysis of microscopic images of cells in cytomorphology or by the analysis of cell populations in bidimensional plots obtained by flow cytometry. Here, AI algorithms not only spot details that might escape the human eye, but might also identify entirely new ways of interpreting these images. With the introduction of high-throughput next-generation sequencing in molecular genetics, the amount of available information is increasing exponentially, priming the field for the application of machine learning approaches. The goal of all the approaches is to allow personalized and informed interventions, to enhance treatment success, to improve the timeliness and accuracy of diagnoses, and to minimize technically induced misclassifications. The potential of AI-based applications is virtually endless but where do we stand in hematology and how far can we go?
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3
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Machine learning and augmented human intelligence use in histomorphology for haematolymphoid disorders. Pathology 2021; 53:400-407. [PMID: 33642096 DOI: 10.1016/j.pathol.2020.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]
Abstract
Advances in digital pathology have allowed a number of opportunities such as decision support using artificial intelligence (AI). The application of AI to digital pathology data shows promise as an aid for pathologists in the diagnosis of haematological disorders. AI-based applications have embraced benign haematology, diagnosing leukaemia and lymphoma, as well as ancillary testing modalities including flow cytometry. In this review, we highlight the progress made to date in machine learning applications in haematopathology, summarise important studies in this field, and highlight key limitations. We further present our outlook on the future direction and trends for AI to support diagnostic decisions in haematopathology.
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4
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Davids J, Ashrafian H. AIM in Haematology. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_182-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Computational analysis of flow cytometry data in hematological malignancies: future clinical practice? Curr Opin Oncol 2020; 32:162-169. [PMID: 31876546 DOI: 10.1097/cco.0000000000000607] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE OF REVIEW This review outlines the advancements that have been made in computational analysis for clinical flow cytometry data in hematological malignancies. RECENT FINDINGS In recent years, computational analysis methods have been applied to clinical flow cytometry data of hematological malignancies with promising results. Most studies combined dimension reduction (principle component analysis) or clustering methods (FlowSOM, generalized mixture models) with machine learning classifiers (support vector machines, random forest). For diagnosis and classification of hematological malignancies, many studies have reported results concordant with manual expert analysis, including B-cell chronic lymphoid leukemia detection and acute leukemia classification. Other studies, e.g. concerning diagnosis of myelodysplastic syndromes and classification of lymphoma, have shown to be able to increase diagnostic accuracy. With respect to treatment response monitoring, studies have focused on, for example, computational minimal residual disease detection in multiple myeloma and posttreatment classification of healthy or diseased in acute myeloid leukemia. The results of these studies are encouraging, although accurate relapse prediction remains challenging. To facilitate clinical implementation, collaboration and (prospective) validation in multicenter setting are necessary. SUMMARY Computational analysis methods for clinical flow cytometry data hold the potential to increase ease of use, objectivity and accuracy in the clinical work-up of hematological malignancies.
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Gaidano V, Tenace V, Santoro N, Varvello S, Cignetti A, Prato G, Saglio G, De Rosa G, Geuna M. A Clinically Applicable Approach to the Classification of B-Cell Non-Hodgkin Lymphomas with Flow Cytometry and Machine Learning. Cancers (Basel) 2020; 12:cancers12061684. [PMID: 32599959 PMCID: PMC7352227 DOI: 10.3390/cancers12061684] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/15/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
The immunophenotype is a key element to classify B-cell Non-Hodgkin Lymphomas (B-NHL); while it is routinely obtained through immunohistochemistry, the use of flow cytometry (FC) could bear several advantages. However, few FC laboratories can rely on a long-standing practical experience, and the literature in support is still limited; as a result, the use of FC is generally restricted to the analysis of lymphomas with bone marrow or peripheral blood involvement. In this work, we applied machine learning to our database of 1465 B-NHL samples from different sources, building four artificial predictive systems which could classify B-NHL in up to nine of the most common clinico-pathological entities. Our best model shows an overall accuracy of 92.68%, a mean sensitivity of 88.54% and a mean specificity of 98.77%. Beyond the clinical applicability, our models demonstrate (i) the strong discriminatory power of MIB1 and Bcl2, whose integration in the predictive model significantly increased the performance of the algorithm; (ii) the potential usefulness of some non-canonical markers in categorizing B-NHL; and (iii) that FC markers should not be described as strictly positive or negative according to fixed thresholds, but they rather correlate with different B-NHL depending on their level of expression.
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Affiliation(s)
- Valentina Gaidano
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (V.G.); (G.S.)
- Division of Hematology, A.O. SS Antonio e Biagio e Cesare Arrigo, 15121 Alessandria, Italy
| | - Valerio Tenace
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112, USA
- Correspondence: (V.T.); (M.G.)
| | - Nathalie Santoro
- Laboratory of Immunopathology, Division of Pathology, A.O. Ordine Mauriziano, 10128 Turin, Italy; (N.S.); (G.D.R.)
| | - Silvia Varvello
- University Division of Hematology and Cell Therapy, A.O. Ordine Mauriziano, 10128 Turin, Italy; (S.V.); (A.C.)
| | - Alessandro Cignetti
- University Division of Hematology and Cell Therapy, A.O. Ordine Mauriziano, 10128 Turin, Italy; (S.V.); (A.C.)
| | - Giuseppina Prato
- Division of Pathology, San Lazzaro Hospital, ASL CN2, 12051 Alba, Italy;
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (V.G.); (G.S.)
- University Division of Hematology and Cell Therapy, A.O. Ordine Mauriziano, 10128 Turin, Italy; (S.V.); (A.C.)
| | - Giovanni De Rosa
- Laboratory of Immunopathology, Division of Pathology, A.O. Ordine Mauriziano, 10128 Turin, Italy; (N.S.); (G.D.R.)
| | - Massimo Geuna
- Laboratory of Immunopathology, Division of Pathology, A.O. Ordine Mauriziano, 10128 Turin, Italy; (N.S.); (G.D.R.)
- Correspondence: (V.T.); (M.G.)
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7
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Lucchesi S, Furini S, Medaglini D, Ciabattini A. From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies. Vaccines (Basel) 2020; 8:vaccines8010138. [PMID: 32244919 PMCID: PMC7157606 DOI: 10.3390/vaccines8010138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/15/2022] Open
Abstract
Flow and mass cytometry are used to quantify the expression of multiple extracellular or intracellular molecules on single cells, allowing the phenotypic and functional characterization of complex cell populations. Multiparametric flow cytometry is particularly suitable for deep analysis of immune responses after vaccination, as it allows to measure the frequency, the phenotype, and the functional features of antigen-specific cells. When many parameters are investigated simultaneously, it is not feasible to analyze all the possible bi-dimensional combinations of marker expression with classical manual analysis and the adoption of advanced automated tools to process and analyze high-dimensional data sets becomes necessary. In recent years, the development of many tools for the automated analysis of multiparametric cytometry data has been reported, with an increasing record of publications starting from 2014. However, the use of these tools has been preferentially restricted to bioinformaticians, while few of them are routinely employed by the biomedical community. Filling the gap between algorithms developers and final users is fundamental for exploiting the advantages of computational tools in the analysis of cytometry data. The potentialities of automated analyses range from the improvement of the data quality in the pre-processing steps up to the unbiased, data-driven examination of complex datasets using a variety of algorithms based on different approaches. In this review, an overview of the automated analysis pipeline is provided, spanning from the pre-processing phase to the automated population analysis. Analysis based on computational tools might overcame both the subjectivity of manual gating and the operator-biased exploration of expected populations. Examples of applications of automated tools that have successfully improved the characterization of different cell populations in vaccination studies are also presented.
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Affiliation(s)
- Simone Lucchesi
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
- Correspondence:
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8
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Ji D, Putzel P, Qian Y, Chang I, Mandava A, Scheuermann RH, Bui JD, Wang H, Smyth P. Machine Learning of Discriminative Gate Locations for Clinical Diagnosis. Cytometry A 2020; 97:296-307. [PMID: 31691488 PMCID: PMC7079150 DOI: 10.1002/cyto.a.23906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 08/22/2019] [Accepted: 09/18/2019] [Indexed: 01/03/2023]
Abstract
High-throughput single-cell cytometry technologies have significantly improved our understanding of cellular phenotypes to support translational research and the clinical diagnosis of hematological and immunological diseases. However, subjective and ad hoc manual gating analysis does not adequately handle the increasing volume and heterogeneity of cytometry data for optimal diagnosis. Prior work has shown that machine learning can be applied to classify cytometry samples effectively. However, many of the machine learning classification results are either difficult to interpret without using characteristics of cell populations to make the classification, or suboptimal due to the use of inaccurate cell population characteristics derived from gating boundaries. To date, little has been done to optimize both the gating boundaries and the diagnostic accuracy simultaneously. In this work, we describe a fully discriminative machine learning approach that can simultaneously learn feature representations (e.g., combinations of coordinates of gating boundaries) and classifier parameters for optimizing clinical diagnosis from cytometry measurements. The approach starts from an initial gating position and then refines the position of the gating boundaries by gradient descent until a set of globally-optimized gates across different samples are achieved. The learning procedure is constrained by regularization terms encoding domain knowledge that encourage the algorithm to seek interpretable results. We evaluate the proposed approach using both simulated and real data, producing classification results on par with those generated via human expertise, in terms of both the positions of the gating boundaries and the diagnostic accuracy. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Disi Ji
- Department of Computer ScienceUniversity of CaliforniaIrvineCalifornia
| | - Preston Putzel
- Department of Computer ScienceUniversity of CaliforniaIrvineCalifornia
| | - Yu Qian
- InformaticsJ. Craig Venter InstituteLa JollaCalifornia
| | - Ivan Chang
- InformaticsJ. Craig Venter InstituteLa JollaCalifornia
| | | | - Richard H. Scheuermann
- InformaticsJ. Craig Venter InstituteLa JollaCalifornia
- Department of PathologyUniversity of CaliforniaSan Diego, La JollaCalifornia
| | - Jack D. Bui
- Department of PathologyUniversity of CaliforniaSan Diego, La JollaCalifornia
| | - Huan‐You Wang
- Department of PathologyUniversity of CaliforniaSan Diego, La JollaCalifornia
| | - Padhraic Smyth
- Department of Computer ScienceUniversity of CaliforniaIrvineCalifornia
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Pedreira CE, Costa ESD, Lecrevise Q, Grigore G, Fluxa R, Verde J, Hernandez J, van Dongen JJM, Orfao A. From big flow cytometry datasets to smart diagnostic strategies: The EuroFlow approach. J Immunol Methods 2019; 475:112631. [PMID: 31306640 DOI: 10.1016/j.jim.2019.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/01/2019] [Accepted: 07/10/2019] [Indexed: 01/07/2023]
Abstract
The rise in the analytical speed of mutiparameter flow cytometers made possible by the introduction of digital instruments, has brought up the possibility to manage progressively higher number of parameters simultaneously on significantly greater numbers of individual cells. This has led to an exponential increase in the complexity and volume of flow cytometry data generated about cells present in individual samples evaluated in a single measurement. This increase demands for new developments in flow cytometry data analysis, graphical representation, and visualization and interpretation tools to address the new big data challenges, i.e. processing data files of ≥10-25 parameters per cell in samples with >5-10 million cells (= up to 250 million data points per cell sample) obtained in a few minutes. Here, we present a comprehensive review of some of the tools developed by the EuroFlow consortium for processing flow cytometric big data files in diagnostic laboratories, particularly focused on automated EuroFlow approaches for: i) identification of all cell populations coexisting in a sample (automated gating); ii) smart classification of aberrant cell populations in routine diagnostics; iii) automated reporting; together with iv) new tools developed to visualize n-dimensional data in 2-dimensional plots to support expert-guided automated data analysis. The concept of using reference data bases implemented into software programs, in combination with multivariate statistical analysis pioneered by EuroFlow, provides an innovative, highly efficient and fast approach for diagnostic screening, classification and monitoring of patients with distinct hematological and immune disorders, as well as other diseases.
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Affiliation(s)
- C E Pedreira
- Systems and Computing Department (PESC), COPPE, Federal University of Rio de Janeiro (UFRJ), Brazil
| | - E Sobral da Costa
- School of Medicine, Federal University of Rio de Janeiro (UFRJ), Brazil
| | - Q Lecrevise
- Cancer Research Centre (IBMCC, USAL-CSIC), Department of Medicine and Cytometry Service (NUCLEUS), IBSAL and CIBERONC, University of Salamanca, Spain
| | | | - R Fluxa
- Cytognos SL, Salamanca, Spain
| | - J Verde
- Cytognos SL, Salamanca, Spain
| | | | - J J M van Dongen
- Dept. of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center (LUMC), Leiden, the Netherlands.
| | - A Orfao
- Cancer Research Centre (IBMCC, USAL-CSIC), Department of Medicine and Cytometry Service (NUCLEUS), IBSAL and CIBERONC, University of Salamanca, Spain.
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10
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Park D, Chang J, Kahng J, Park H, Jo I, Kim Y, Han K. Development of a Novel Flow Cytometry-Based System for White Blood Cell Differential Counts: 10-color LeukoDiff. Ann Lab Med 2019; 39:141-149. [PMID: 30430776 PMCID: PMC6240530 DOI: 10.3343/alm.2019.39.2.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/04/2018] [Accepted: 08/28/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Flow cytometry (FCM) is commonly used to identify many cell populations. We developed a white blood cell (WBC) differential counting system for detecting abnormal cells using FCM incorporating 10 colors and 11 antibodies in a single tube, called "10-color LeukoDiff," and evaluated its performance. METHODS Ninety-one EDTA-anti-coagulated peripheral blood samples from 76 patients were analyzed using 10-color LeukoDiff. We compared 10 color LeukoDiff results with the results of manual differential count (manual diff). WBCs were classified into 17 cell populations: neutrophils, total lymphocytes, T lymphocytes, B lymphocytes, CD5 and CD19 co-expressing lymphocytes, natural killer cells, total monocytes, 16+ monocytes, eosinophils, immature granulocytes, basophils, myeloblasts, B-blasts, T-blasts, myeloid antigen-positive B-blasts, CD19- plasma cells, and 19+ plasma cells. RESULTS The correlations between the 10-color LeukoDiff and manual diff results were strong (r>0.9) for mature neutrophils, lymphocytes, eosinophils, immature granulocytes, and blasts and moderate for monocytes and basophils (r=0.86 and 0.74, respectively). There was no discrepancy in blast detection between 10-color LeukoDiff and manual diff results. Furthermore, 10-color LeukoDiff could differentiate the lineage of the blasts and separately count chronic lymphocytic leukemic cells and multiple myeloma cells. CONCLUSIONS The 10-color LeukoDiff provided an accurate and comprehensive WBC differential count. The most important ability of 10-color LeukoDiff is to detect blasts accurately. This system is clinically useful, especially for patients with hematologic diseases, such as acute leukemia, chronic lymphocytic leukemia, and multiple myeloma. Application of this system will improve the development of FCM gating strategy designs.
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Affiliation(s)
- Dongjin Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyoung Chang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jimin Kahng
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hunhee Park
- Department of Clinical Laboratory Science, Ansan University, Ansan, Korea
| | - Irene Jo
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyungja Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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11
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Duetz C, Westers TM, van de Loosdrecht AA. Clinical Implication of Multi-Parameter Flow Cytometry in Myelodysplastic Syndromes. Pathobiology 2018; 86:14-23. [PMID: 30227408 DOI: 10.1159/000490727] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/08/2018] [Indexed: 12/16/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a challenging group of diseases for clinicians and researchers, as both disease course and pathobiology are highly heterogeneous. In (suspected) MDS patients, multi-parameter flow cytometry can aid in establishing diagnosis, risk stratification and choice of therapy. This review addresses the developments and future directions of multi-parameter flow cytometry scores in MDS. Additionally, we propose an integrated diagnostic algorithm for suspected MDS.
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12
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Agrahari R, Foroushani A, Docking TR, Chang L, Duns G, Hudoba M, Karsan A, Zare H. Applications of Bayesian network models in predicting types of hematological malignancies. Sci Rep 2018; 8:6951. [PMID: 29725024 PMCID: PMC5934387 DOI: 10.1038/s41598-018-24758-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
Network analysis is the preferred approach for the detection of subtle but coordinated changes in expression of an interacting and related set of genes. We introduce a novel method based on the analyses of coexpression networks and Bayesian networks, and we use this new method to classify two types of hematological malignancies; namely, acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Our classifier has an accuracy of 93%, a precision of 98%, and a recall of 90% on the training dataset (n = 366); which outperforms the results reported by other scholars on the same dataset. Although our training dataset consists of microarray data, our model has a remarkable performance on the RNA-Seq test dataset (n = 74, accuracy = 89%, precision = 88%, recall = 98%), which confirms that eigengenes are robust with respect to expression profiling technology. These signatures are useful in classification and correctly predicting the diagnosis. They might also provide valuable information about the underlying biology of diseases. Our network analysis approach is generalizable and can be useful for classifying other diseases based on gene expression profiles. Our previously published Pigengene package is publicly available through Bioconductor, which can be used to conveniently fit a Bayesian network to gene expression data.
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Affiliation(s)
- Rupesh Agrahari
- Department of Computer Science, Texas State University, San Marcos, Texas, 78666, USA
| | - Amir Foroushani
- Department of Computer Science, Texas State University, San Marcos, Texas, 78666, USA
| | - T Roderick Docking
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Linda Chang
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Gerben Duns
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Monika Hudoba
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, V5Z 1M9, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Habil Zare
- Department of Computer Science, Texas State University, San Marcos, Texas, 78666, USA. .,Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, Texas, 78229, USA.
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13
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Scheuermann RH, Bui J, Wang HY, Qian Y. Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration. Clin Lab Med 2018; 37:931-944. [PMID: 29128077 DOI: 10.1016/j.cll.2017.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flow cytometry is used in cell-based diagnostic evaluation for blood-borne malignancies including leukemia and lymphoma. The current practice for cytometry data analysis relies on manual gating to identify cell subsets in complex mixtures, which is subjective, labor-intensive, and poorly reproducible. This article reviews recent efforts to develop, validate, and disseminate automated computational methods and pipelines for cytometry data analysis that could help overcome the limitations of manual analysis and provide for efficient and data-driven diagnostic applications. It demonstrates the performance of an optimized computational pipeline in a pilot study of chronic lymphocytic leukemia data from the authors' clinical diagnostic laboratory.
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Affiliation(s)
- Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA.
| | - Jack Bui
- Department of Pathology, University of California, San Diego, Biomedical Sciences Building Room 1028, 9500 Gilman Drive, La Jolla, CA 92093-0612, USA
| | - Huan-You Wang
- Department of Pathology, School of Medicine, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0987, USA
| | - Yu Qian
- Department of Informatics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
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14
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Rajwa B, Wallace PK, Griffiths EA, Dundar M. Automated Assessment of Disease Progression in Acute Myeloid Leukemia by Probabilistic Analysis of Flow Cytometry Data. IEEE Trans Biomed Eng 2016; 64:1089-1098. [PMID: 27416585 DOI: 10.1109/tbme.2016.2590950] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Flow cytometry (FC) is a widely acknowledged technology in diagnosis of acute myeloid leukemia (AML) and has been indispensable in determining progression of the disease. Although FC plays a key role as a posttherapy prognosticator and evaluator of therapeutic efficacy, the manual analysis of cytometry data is a barrier to optimization of reproducibility and objectivity. This study investigates the utility of our recently introduced nonparametric Bayesian framework in accurately predicting the direction of change in disease progression in AML patients using FC data. METHODS The highly flexible nonparametric Bayesian model based on the infinite mixture of infinite Gaussian mixtures is used for jointly modeling data from multiple FC samples to automatically identify functionally distinct cell populations and their local realizations. Phenotype vectors are obtained by characterizing each sample by the proportions of recovered cell populations, which are, in turn, used to predict the direction of change in disease progression for each patient. RESULTS We used 200 diseased and nondiseased immunophenotypic panels for training and tested the system with 36 additional AML cases collected at multiple time points. The proposed framework identified the change in direction of disease progression with accuracies of 90% (nine out of ten) for relapsing cases and 100% (26 out of 26) for the remaining cases. CONCLUSIONS We believe that these promising results are an important first step toward the development of automated predictive systems for disease monitoring and continuous response evaluation. SIGNIFICANCE Automated measurement and monitoring of therapeutic response is critical not only for objective evaluation of disease status prognosis but also for timely assessment of treatment strategies.
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MESH Headings
- Algorithms
- Bayes Theorem
- Biomarkers, Tumor/metabolism
- Data Interpretation, Statistical
- Disease Progression
- Flow Cytometry/methods
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/pathology
- Pattern Recognition, Automated/methods
- Recurrence
- Reproducibility of Results
- Sensitivity and Specificity
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15
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Saeys Y, Van Gassen S, Lambrecht BN. Computational flow cytometry: helping to make sense of high-dimensional immunology data. Nat Rev Immunol 2016; 16:449-62. [PMID: 27320317 DOI: 10.1038/nri.2016.56] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in flow cytometry allow scientists to measure an increasing number of parameters per cell, generating huge and high-dimensional datasets. To analyse, visualize and interpret these data, newly available computational techniques should be adopted, evaluated and improved upon by the immunological community. Computational flow cytometry is emerging as an important new field at the intersection of immunology and computational biology; it allows new biological knowledge to be extracted from high-throughput single-cell data. This Review provides non-experts with a broad and practical overview of the many recent developments in computational flow cytometry.
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Affiliation(s)
- Yvan Saeys
- VIB Inflammation Research Center, Technologiepark 927, Ghent B-9052, Belgium.,Department of Internal Medicine, Ghent University, De Pintelaan 185, Ghent B-9000, Belgium
| | - Sofie Van Gassen
- VIB Inflammation Research Center, Technologiepark 927, Ghent B-9052, Belgium.,Department of Information Technology, Technologiepark 15, Ghent B-9052, Belgium
| | - Bart N Lambrecht
- VIB Inflammation Research Center, Technologiepark 927, Ghent B-9052, Belgium.,Department of Internal Medicine, Ghent University, De Pintelaan 185, Ghent B-9000, Belgium.,Department of Pulmonary Medicine, Erasmus MC Rotterdam, Dr Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
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16
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Abstract
Multi-color flow cytometry has become a valuable and highly informative tool for diagnosis and therapeutic monitoring of patients with immune deficiencies or inflammatory disorders. However, the method complexity and error-prone conventional manual data analysis often result in a high variability between different analysts and research laboratories. Here, we provide strategies and guidelines aiming at a more standardized multi-color flow cytometric staining and unsupervised data analysis for whole blood patient samples.
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17
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Candia J, Banavar JR, Losert W. Understanding health and disease with multidimensional single-cell methods. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:073102. [PMID: 24451406 PMCID: PMC4020281 DOI: 10.1088/0953-8984/26/7/073102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in characteristic length scales, from small molecules that regulate cell function to cell ensembles that form tissues and organs working together as an organism. In order to uncover the molecular nature of the emergent properties of a cell, it is essential to measure multiple-cell components simultaneously in the same cell. In turn, cell heterogeneity requires multiple-cells to be measured in order to understand health and disease in the organism. This review summarizes current efforts towards a data-driven framework that leverages single-cell technologies to build robust signatures of healthy and diseased phenotypes. While some approaches focus on multicolor flow cytometry data and other methods are designed to analyze high-content image-based screens, we emphasize the so-called Supercell/SVM paradigm (recently developed by the authors of this review and collaborators) as a unified framework that captures mesoscopic-scale emergence to build reliable phenotypes. Beyond their specific contributions to basic and translational biomedical research, these efforts illustrate, from a larger perspective, the powerful synergy that might be achieved from bringing together methods and ideas from statistical physics, data mining, and mathematics to solve the most pressing problems currently facing the life sciences.
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Affiliation(s)
- Julián Candia
- Department of Physics, University of Maryland, College Park, MD 20742, USA. School of Medicine, University of Maryland, Baltimore, MD 21201, USA. IFLYSIB and CONICET, University of La Plata, 1900 La Plata, Argentina
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18
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Abstract
Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow cytometry data using extensive computational resources and tools. Flow cytometry bioinformatics requires extensive use of and contributes to the development of techniques from computational statistics and machine learning. Flow cytometry and related methods allow the quantification of multiple independent biomarkers on large numbers of single cells. The rapid growth in the multidimensionality and throughput of flow cytometry data, particularly in the 2000s, has led to the creation of a variety of computational analysis methods, data standards, and public databases for the sharing of results. Computational methods exist to assist in the preprocessing of flow cytometry data, identifying cell populations within it, matching those cell populations across samples, and performing diagnosis and discovery using the results of previous steps. For preprocessing, this includes compensating for spectral overlap, transforming data onto scales conducive to visualization and analysis, assessing data for quality, and normalizing data across samples and experiments. For population identification, tools are available to aid traditional manual identification of populations in two-dimensional scatter plots (gating), to use dimensionality reduction to aid gating, and to find populations automatically in higher dimensional space in a variety of ways. It is also possible to characterize data in more comprehensive ways, such as the density-guided binary space partitioning technique known as probability binning, or by combinatorial gating. Finally, diagnosis using flow cytometry data can be aided by supervised learning techniques, and discovery of new cell types of biological importance by high-throughput statistical methods, as part of pipelines incorporating all of the aforementioned methods. Open standards, data, and software are also key parts of flow cytometry bioinformatics. Data standards include the widely adopted Flow Cytometry Standard (FCS) defining how data from cytometers should be stored, but also several new standards under development by the International Society for Advancement of Cytometry (ISAC) to aid in storing more detailed information about experimental design and analytical steps. Open data is slowly growing with the opening of the CytoBank database in 2010 and FlowRepository in 2012, both of which allow users to freely distribute their data, and the latter of which has been recommended as the preferred repository for MIFlowCyt-compliant data by ISAC. Open software is most widely available in the form of a suite of Bioconductor packages, but is also available for web execution on the GenePattern platform.
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Affiliation(s)
- Kieran O'Neill
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nima Aghaeepour
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Josef Špidlen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Ryan Brinkman
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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19
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Candia J, Maunu R, Driscoll M, Biancotto A, Dagur P, McCoy JP, Sen HN, Wei L, Maritan A, Cao K, Nussenblatt RB, Banavar JR, Losert W. From cellular characteristics to disease diagnosis: uncovering phenotypes with supercells. PLoS Comput Biol 2013; 9:e1003215. [PMID: 24039568 PMCID: PMC3763994 DOI: 10.1371/journal.pcbi.1003215] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/23/2013] [Indexed: 11/25/2022] Open
Abstract
Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements, which is based on the concept of “supercell statistics”, a single-cell-based averaging procedure followed by a machine learning classification scheme. We are able to assess the optimal tradeoff between the number of single cells averaged and the number of measurements needed to capture phenotypic differences between healthy and diseased patients, as well as between different diseases that are difficult to diagnose otherwise. We apply our approach to two kinds of single-cell datasets, addressing the diagnosis of a premature aging disorder using images of cell nuclei, as well as the phenotypes of two non-infectious uveitides (the ocular manifestations of Behçet's disease and sarcoidosis) based on multicolor flow cytometry. In the former case, one nuclear shape measurement taken over a group of 30 cells is sufficient to classify samples as healthy or diseased, in agreement with usual laboratory practice. In the latter, our method is able to identify a minimal set of 5 markers that accurately predict Behçet's disease and sarcoidosis. This is the first time that a quantitative phenotypic distinction between these two diseases has been achieved. To obtain this clear phenotypic signature, about one hundred CD8+ T cells need to be measured. Although the molecular markers identified have been reported to be important players in autoimmune disorders, this is the first report pointing out that CD8+ T cells can be used to distinguish two systemic inflammatory diseases. Beyond these specific cases, the approach proposed here is applicable to datasets generated by other kinds of state-of-the-art and forthcoming single-cell technologies, such as multidimensional mass cytometry, single-cell gene expression, and single-cell full genome sequencing techniques. The behavior of organisms is based on the concerted action occurring on an astonishing range of scales from the molecular to the organismal level. Molecular properties control the function of a cell, while cell ensembles form tissues and organs, which work together as an organism. In order to understand and characterize the molecular nature of the emergent properties of a cell, it is essential that multiple components of the cell are measured simultaneously in the same cell. Similarly, multiple cells must be measured in order to understand health and disease in the organism. In this work, we develop an approach that is able to determine how many cells, how many measurements per cell, and which measurements are needed to reliably diagnose disease. We apply this method to two different problems: the diagnosis of a premature aging disorder using images of cell nuclei, and the distinction between two similar autoimmune eye diseases using stained cells from patients' blood samples. Our findings shed new light on the role of specific kinds of immune system cells in systemic inflammatory diseases and may lead to improved diagnosis and treatment.
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Affiliation(s)
- Julián Candia
- Department of Physics, University of Maryland, College Park, Maryland, United States of America ; School of Medicine, University of Maryland, Baltimore, Maryland, United States of America ; IFLYSIB and CONICET, University of La Plata, La Plata,
| | - Ryan Maunu
- Department of Physics, University of Maryland, College Park, Maryland, United States of America
| | - Meghan Driscoll
- Department of Physics, University of Maryland, College Park, Maryland, United States of America
| | - Angélique Biancotto
- Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, Maryland, United States of America, Hematology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Pradeep Dagur
- Hematology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - J Philip McCoy
- Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, Maryland, United States of America,; Hematology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - H Nida Sen
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lai Wei
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Amos Maritan
- Dipartimento di Fisica “G. Galilei,” Università di Padova, Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia and Istituto Nazionale di Fisica Nucleare, Padua, Italy
| | - Kan Cao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Robert B Nussenblatt
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jayanth R Banavar
- Department of Physics, University of Maryland, College Park, Maryland, United States of America
| | - Wolfgang Losert
- Department of Physics, University of Maryland, College Park, Maryland, United States of America
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20
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Craig FE, Brinkman RR, Ten Eyck S, Aghaeepour N. Computational analysis optimizes the flow cytometric evaluation for lymphoma. CYTOMETRY PART B-CLINICAL CYTOMETRY 2013; 86:18-24. [PMID: 24002786 DOI: 10.1002/cyto.b.21115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 05/20/2013] [Accepted: 07/01/2013] [Indexed: 11/06/2022]
Abstract
BACKGROUND Although many clinical laboratories are adopting higher color flow cytometric assays, the approach to optimizing panel design and data analysis is often traditional and subjective. In order to address the question "What is the best flow cytometric strategy to reliably distinguish germinal center B-cell lymphoma (GC-L) from germinal center hyperplasia (GC-H)?" we applied a computational tool that identifies target populations correlated with a desired outcome, in this case diagnosis. DESIGN Cases of GC-H and GC-L evaluated by flow cytometric immunophenotyping using CD45, CD20, kappa, lambda, CD19, CD5, CD10, CD38, were analyzed with flowType and RchyOptimyx to construct cellular hierarchies that best distinguished the two diagnostic groups. RESULTS The population CD5-CD19+CD10+CD38- had the highest predictive power. Manual reanalysis confirmed significantly higher CD10+/CD38-B-cells in GC-L (median 12.44%, range 0.74-63.29, n = 52) than GC-H (median 0.24%, 0.03-4.49, n = 48, P = 0.0001), but was not entirely specific. Difficulties encountered using this computational approach included the presence of CD10+ granulocytes, continuously variable B-cell expression of CD38, more variable intensity antigen staining in GC-L and inability to assess the contribution of light chain restriction. CONCLUSION Computational analysis with construction of cellular hierarchies related to diagnosis helped guide manual analysis of high dimensional flow cytometric data. This approach highlighted the diagnostic utility of CD38 expression in the evaluation of B-cells with a CD10+ GC phenotype. In contrast to computational analysis of non-neoplastic cell populations, evaluation of neoplastic cells must be able to take into consideration increased variability in antigen expression.
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Affiliation(s)
- Fiona E Craig
- Division of Hematopathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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21
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Heel K, Tabone T, Röhrig KJ, Maslen PG, Meehan K, Grimwade LF, Erber WN. Developments in the immunophenotypic analysis of haematological malignancies. Blood Rev 2013; 27:193-207. [PMID: 23845589 DOI: 10.1016/j.blre.2013.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Immunophenotyping is the method by which antibodies are used to detect cellular antigens in clinical samples. Although the major role is in the diagnosis and classification of haematological malignancies, applications have expanded over the past decade. Immunophenotyping is now used extensively for disease staging and monitoring, to detect surrogate markers of genetic aberrations, to identify potential immuno-therapeutic targets and to aid prognostic prediction. This expansion in applications has resulted from developments in antibodies, methodology, automation and data handling. In this review we describe recent advances in both the technology and applications for the analysis of haematological malignancies. We highlight the importance of the expanding repertoire of testing capability for diagnostic, prognostic and therapeutic applications. The impact and significance of immunophenotyping in the assessment of haematological neoplasms are evident.
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Affiliation(s)
- Kathy Heel
- Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA 6009, Australia.
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22
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Villanova F, Di Meglio P, Inokuma M, Aghaeepour N, Perucha E, Mollon J, Nomura L, Hernandez-Fuentes M, Cope A, Prevost AT, Heck S, Maino V, Lord G, Brinkman RR, Nestle FO. Integration of lyoplate based flow cytometry and computational analysis for standardized immunological biomarker discovery. PLoS One 2013; 8:e65485. [PMID: 23843942 PMCID: PMC3701052 DOI: 10.1371/journal.pone.0065485] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 04/23/2013] [Indexed: 12/29/2022] Open
Abstract
Discovery of novel immune biomarkers for monitoring of disease prognosis and response to therapy in immune-mediated inflammatory diseases is an important unmet clinical need. Here, we establish a novel framework for immunological biomarker discovery, comparing a conventional (liquid) flow cytometry platform (CFP) and a unique lyoplate-based flow cytometry platform (LFP) in combination with advanced computational data analysis. We demonstrate that LFP had higher sensitivity compared to CFP, with increased detection of cytokines (IFN-γ and IL-10) and activation markers (Foxp3 and CD25). Fluorescent intensity of cells stained with lyophilized antibodies was increased compared to cells stained with liquid antibodies. LFP, using a plate loader, allowed medium-throughput processing of samples with comparable intra- and inter-assay variability between platforms. Automated computational analysis identified novel immunophenotypes that were not detected with manual analysis. Our results establish a new flow cytometry platform for standardized and rapid immunological biomarker discovery with wide application to immune-mediated diseases.
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Affiliation(s)
- Federica Villanova
- St. John's Institute of Dermatology, King's College London, London, United Kingdom
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, (NIHR GSTT/KCL) London, United Kingdom
| | - Paola Di Meglio
- St. John's Institute of Dermatology, King's College London, London, United Kingdom
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, (NIHR GSTT/KCL) London, United Kingdom
- Molecular Immunology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Margaret Inokuma
- Biological Research & Development, BD Biosciences, San Jose, California, United States of America
| | - Nima Aghaeepour
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | - Esperanza Perucha
- The Medical Research Council (MRC) Centre for Transplantation, King's College London, London, United Kingdom
| | - Jennifer Mollon
- Division of Genetics and Molecular Medicine, Statistical Genetics Unit, King's College London, London, United Kingdom
| | - Laurel Nomura
- Biological Research & Development, BD Biosciences, San Jose, California, United States of America
| | - Maria Hernandez-Fuentes
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, (NIHR GSTT/KCL) London, United Kingdom
- The Medical Research Council (MRC) Centre for Transplantation, King's College London, London, United Kingdom
| | - Andrew Cope
- Academic Department of Rheumatology, King's College London, London United Kingdom
| | - A. Toby Prevost
- Department of Primary Care and Public Health Sciences, King's College London, London, United Kingdom
| | - Susanne Heck
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, (NIHR GSTT/KCL) London, United Kingdom
| | - Vernon Maino
- Biological Research & Development, BD Biosciences, San Jose, California, United States of America
| | - Graham Lord
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, (NIHR GSTT/KCL) London, United Kingdom
- The Medical Research Council (MRC) Centre for Transplantation, King's College London, London, United Kingdom
| | - Ryan R. Brinkman
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Frank O. Nestle
- St. John's Institute of Dermatology, King's College London, London, United Kingdom
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust, (NIHR GSTT/KCL) London, United Kingdom
- * E-mail:
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23
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McNeil LK, Price L, Britten CM, Jaimes M, Maecker H, Odunsi K, Matsuzaki J, Staats JS, Thorpe J, Yuan J, Janetzki S. A harmonized approach to intracellular cytokine staining gating: Results from an international multiconsortia proficiency panel conducted by the Cancer Immunotherapy Consortium (CIC/CRI). Cytometry A 2013; 83:728-38. [PMID: 23788464 DOI: 10.1002/cyto.a.22319] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/18/2013] [Accepted: 05/17/2013] [Indexed: 11/06/2022]
Abstract
Previous results from two proficiency panels of intracellular cytokine staining (ICS) from the Cancer Immunotherapy Consortium and panels from the National Institute of Allergy and Infectious Disease and the Association for Cancer Immunotherapy highlight the variability across laboratories in reported % CD8+ or % CD4+ cytokine-positive cells. One of the main causes of interassay variability in flow cytometry-based assays is due to differences in gating strategies between laboratories, which may prohibit the generation of robust results within single centers and across institutions. To study how gating strategies affect the variation in reported results, a gating panel was organized where all participants analyzed the same set of Flow Cytometry Standard (FCS) files from a four-color ICS assay using their own gating protocol (Phase I) and a gating protocol drafted by consensus from the organizers of the panel (Phase II). Focusing on analysis removed donor, assay, and instrument variation, enabling us to quantify the variability caused by gating alone. One hundred ten participating laboratories applied 110 different gating approaches. This led to high variability in the reported percentage of cytokine-positive cells and consequently in response detection in Phase I. However, variability was dramatically reduced when all laboratories used the same gating strategy (Phase II). Proximity of the cytokine gate to the negative population most impacted true-positive and false-positive response detection. Recommendations are provided for the (1) placement of the cytokine-positive gate, (2) identification of CD4+ CD8+ double-positive T cells, (3) placement of lymphocyte gate, (4) inclusion of dim cells, (5) gate uniformity, and 6) proper adjustment of the biexponential scaling.
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24
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Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods 2013; 10:228-38. [PMID: 23396282 PMCID: PMC3906045 DOI: 10.1038/nmeth.2365] [Citation(s) in RCA: 350] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 01/14/2013] [Indexed: 12/14/2022]
Abstract
In this analysis, the authors directly compared the performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information of practical utility about the performance of the algorithms as applied to different data sets and challenges. Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of these methods on two tasks: (i) mammalian cell population identification, to determine whether automated algorithms can reproduce expert manual gating and (ii) sample classification, to determine whether analysis pipelines can identify characteristics that correlate with external variables (such as clinical outcome). This analysis presents the results of the first FlowCAP challenges. Several methods performed well as compared to manual gating or external variables using statistical performance measures, which suggests that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis.
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Affiliation(s)
- Nima Aghaeepour
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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25
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Zare H, Haffari G, Gupta A, Brinkman RR. Scoring relevancy of features based on combinatorial analysis of Lasso with application to lymphoma diagnosis. BMC Genomics 2013; 14 Suppl 1:S14. [PMID: 23369194 PMCID: PMC3549810 DOI: 10.1186/1471-2164-14-s1-s14] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
One challenge in applying bioinformatic tools to clinical or biological data is high number of features that might be provided to the learning algorithm without any prior knowledge on which ones should be used. In such applications, the number of features can drastically exceed the number of training instances which is often limited by the number of available samples for the study. The Lasso is one of many regularization methods that have been developed to prevent overfitting and improve prediction performance in high-dimensional settings. In this paper, we propose a novel algorithm for feature selection based on the Lasso and our hypothesis is that defining a scoring scheme that measures the "quality" of each feature can provide a more robust feature selection method. Our approach is to generate several samples from the training data by bootstrapping, determine the best relevance-ordering of the features for each sample, and finally combine these relevance-orderings to select highly relevant features. In addition to the theoretical analysis of our feature scoring scheme, we provided empirical evaluations on six real datasets from different fields to confirm the superiority of our method in exploratory data analysis and prediction performance. For example, we applied FeaLect, our feature scoring algorithm, to a lymphoma dataset, and according to a human expert, our method led to selecting more meaningful features than those commonly used in the clinics. This case study built a basis for discovering interesting new criteria for lymphoma diagnosis. Furthermore, to facilitate the use of our algorithm in other applications, the source code that implements our algorithm was released as FeaLect, a documented R package in CRAN.
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Affiliation(s)
- Habil Zare
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
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26
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Buckle T, Kuil J, van den Berg NS, Bunschoten A, Lamb HJ, Yuan H, Josephson L, Jonkers J, Borowsky AD, van Leeuwen FWB. Use of a single hybrid imaging agent for integration of target validation with in vivo and ex vivo imaging of mouse tumor lesions resembling human DCIS. PLoS One 2013; 8:e48324. [PMID: 23326303 PMCID: PMC3543428 DOI: 10.1371/journal.pone.0048324] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/24/2012] [Indexed: 12/11/2022] Open
Abstract
Screening of biomarker expression levels in tumor biopsy samples not only provides an assessment of prognostic and predictive factors, but may also be used for selection of biomarker-specific imaging strategies. To assess the feasibility of using a biopsy specimen for a personalized selection of an imaging agent, the chemokine receptor 4 (CXCR4) was used as a reference biomarker.
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MESH Headings
- Animals
- Carcinoma, Intraductal, Noninfiltrating/diagnosis
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- Cell Line, Tumor
- Diagnosis, Differential
- Diagnostic Imaging/methods
- Feasibility Studies
- Flow Cytometry
- Fluorescent Dyes/chemistry
- Fluorescent Dyes/metabolism
- Humans
- Immunohistochemistry
- Mammary Neoplasms, Experimental/diagnosis
- Mammary Neoplasms, Experimental/metabolism
- Mice
- Molecular Structure
- Peptides/chemistry
- Peptides/metabolism
- Receptors, CXCR4/metabolism
- Reproducibility of Results
- Sensitivity and Specificity
- Tomography, Emission-Computed, Single-Photon
- Tomography, X-Ray Computed
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Affiliation(s)
- Tessa Buckle
- Department of Radiology, Interventional Molecular Imaging Laboratory, Leiden University Medical Center, Leiden, The Netherlands
- Departments of Radiology and Nuclear Medicine, Netherlands Cancer Institute- Antoni van Leeuwenhoekhuis, Amsterdam, The Netherlands
| | - Joeri Kuil
- Department of Radiology, Interventional Molecular Imaging Laboratory, Leiden University Medical Center, Leiden, The Netherlands
- Departments of Radiology and Nuclear Medicine, Netherlands Cancer Institute- Antoni van Leeuwenhoekhuis, Amsterdam, The Netherlands
| | - Nynke S. van den Berg
- Department of Radiology, Interventional Molecular Imaging Laboratory, Leiden University Medical Center, Leiden, The Netherlands
- Departments of Radiology and Nuclear Medicine, Netherlands Cancer Institute- Antoni van Leeuwenhoekhuis, Amsterdam, The Netherlands
| | - Anton Bunschoten
- Department of Radiology, Interventional Molecular Imaging Laboratory, Leiden University Medical Center, Leiden, The Netherlands
- Departments of Radiology and Nuclear Medicine, Netherlands Cancer Institute- Antoni van Leeuwenhoekhuis, Amsterdam, The Netherlands
| | - Hildo J. Lamb
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hushan Yuan
- Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States
| | - Lee Josephson
- Center for Molecular Imaging Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States
| | - Jos Jonkers
- Division of Cell Biology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Alexander D. Borowsky
- Department of Pathology and Laboratory Medicine, Center for Comparative Medicine, School of Medicine, University of California at Davis, Sacramento, California, United States of America
| | - Fijs W. B. van Leeuwen
- Department of Radiology, Interventional Molecular Imaging Laboratory, Leiden University Medical Center, Leiden, The Netherlands
- Departments of Radiology and Nuclear Medicine, Netherlands Cancer Institute- Antoni van Leeuwenhoekhuis, Amsterdam, The Netherlands
- * E-mail:
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27
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Aghaeepour N, Brinkman R. Computational analysis of high-dimensional flow cytometric data for diagnosis and discovery. Curr Top Microbiol Immunol 2013; 377:159-75. [PMID: 23975083 DOI: 10.1007/82_2013_337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent technological advancements have enabled the flow cytometric measurement of tens of parameters on millions of cells. Conventional manual data analysis and bioinformatics tools cannot provide a complete analysis of these datasets due to this complexity. In this chapter we will provide an overview of a general data analysis pipeline both for automatic identification of cell populations of known importance (e.g., diagnosis by identification of predefined cell population) and for exploratory analysis of cohorts of flow cytometry assays (e.g., discovery of new correlates of a malignancy). We provide three real-world examples of how unsupervised discovery has been used in basic and clinical research. We also discuss challenges for evaluation of the algorithms developed for (1) identification of cell populations using clustering, (2) identification of specific cell populations, and (3) supervised analysis for discriminating between patient subgroups.
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Affiliation(s)
- Nima Aghaeepour
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver BC, V5Z 1L3, Canada
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Aghaeepour N, Jalali A, O’Neill K, Chattopadhyay PK, Roederer M, Hoos HH, Brinkman RR. RchyOptimyx: cellular hierarchy optimization for flow cytometry. Cytometry A 2012; 81:1022-30. [PMID: 23044634 PMCID: PMC3726344 DOI: 10.1002/cyto.a.22209] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/07/2012] [Accepted: 09/05/2012] [Indexed: 12/19/2022]
Abstract
Analysis of high-dimensional flow cytometry datasets can reveal novel cell populations with poorly understood biology. Following discovery, characterization of these populations in terms of the critical markers involved is an important step, as this can help to both better understand the biology of these populations and aid in designing simpler marker panels to identify them on simpler instruments and with fewer reagents (i.e., in resource poor or highly regulated clinical settings). However, current tools to design panels based on the biological characteristics of the target cell populations work exclusively based on technical parameters (e.g., instrument configurations, spectral overlap, and reagent availability). To address this shortcoming, we developed RchyOptimyx (cellular hieraRCHY OPTIMization), a computational tool that constructs cellular hierarchies by combining automated gating with dynamic programming and graph theory to provide the best gating strategies to identify a target population to a desired level of purity or correlation with a clinical outcome, using the simplest possible marker panels. RchyOptimyx can assess and graphically present the trade-offs between marker choice and population specificity in high-dimensional flow or mass cytometry datasets. We present three proof-of-concept use cases for RchyOptimyx that involve 1) designing a panel of surface markers for identification of rare populations that are primarily characterized using their intracellular signature; 2) simplifying the gating strategy for identification of a target cell population; 3) identification of a non-redundant marker set to identify a target cell population.
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Affiliation(s)
- Nima Aghaeepour
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Adrin Jalali
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Kieran O’Neill
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Mario Roederer
- Vaccine Research Center, National Institute of Health, Bethesda, Massachusetts
| | - Holger H. Hoos
- Department of Computer Science, University of British Columbia, British Columbia, Canada
| | - Ryan R. Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, British Columbia, Canada
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