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Seiffert S, Weber S, Sack U, Keller T. Use of logit transformation within statistical analyses of experimental results obtained as proportions: example of method validation experiments and EQA in flow cytometry. Front Mol Biosci 2024; 11:1335174. [PMID: 39055985 PMCID: PMC11269570 DOI: 10.3389/fmolb.2024.1335174] [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: 11/08/2023] [Accepted: 06/04/2024] [Indexed: 07/28/2024] Open
Abstract
In laboratory medicine, measurement results are often expressed as proportions of concentrations or counts. These proportions have distinct mathematical properties that can lead to unexpected results when conventional parametric statistical methods are naively applied without due consideration in the analysis of method validation experiments, quality assessments, or clinical studies. In particular, data points near 0% or 100% can lead to misleading analytical conclusions. To avoid these problems, the logit transformation-defined as the natural logarithm of the proportion/(1-proportion)-is used. This transformation produces symmetric distributions centered at zero that extend infinitely in both directions without upper or lower bounds. As a result, parametric statistical methods can be used without introducing bias. Furthermore, homogeneity of variances (HoV) is given. The benefits of this technique are illustrated by two applications: (i) flow cytometry measurement results expressed as proportions and (ii) probabilities derived from multivariable models. In the first case, naive analyses within external quality assessment (EQA) evaluations that lead to inconsistent results are effectively corrected. Second, the transformation eliminates bias and variance heterogeneity, allowing for more effective precision estimation. In summary, the logit transformation ensures unbiased results in statistical analyses. Given the resulting homogeneity of variances, common parametric statistical methods can be implemented, potentially increasing the efficiency of the analysis.
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Affiliation(s)
- S. Seiffert
- Medical Faculty, Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - S. Weber
- ACOMED statistik, Leipzig, Germany
| | - U. Sack
- Medical Faculty, Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
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Sagnia B, Mbakop Ghomsi F, Moudourou S, Gutierez A, Tchadji J, Sosso SM, Ndjolo A, Colizzi V. Accurate and reproducible enumeration of CD4 T cell counts and Hemoglobin levels using a point of care system: Comparison with conventional laboratory based testing systems in a clinical reference laboratory in Cameroon. PLoS One 2024; 19:e0297790. [PMID: 38507344 PMCID: PMC10954178 DOI: 10.1371/journal.pone.0297790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/13/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Measurements of CD4 T cells and hemoglobin (Hb) are conventionally used to determine the immunological state and disease progression for HIV-infected patients. We obtained a small lightweight point-of-care device, the BD FACSPrestoTM in order to demonstrate its ability to deliver CD4 and Hb analysis in comparison with two larger clinical machines the BDFACSCantoTM analyzer and Sysmex XN 1000 haematology analyzer. The advantages of using the POC device include access to HIV patient data in remote and in resource limited settings. METHOD The analytical performance of the BD FACSPrestoTM, compared with the FACSCantoTM II flow cytometer and the Sysmex XN 1000 haematology analyzer was evaluated by testing 241 routine clinical specimens collected in EDTA tubes from patients attending the Immunology and Microbiology laboratory of Chantal BIYA International Reference Centre (Yaounde, Cameroon) between January and May 2016. RESULTS The mean in absolute counts and percentage of CD4 T cells was 606 cells/mL and 25% respectively via the FACSPrestoTM, and 574 cells/mL and 24% respectively via the BD FACSCantoTM II. The mean concentration of Hb levels was 11.90 on the Sysmex XN 1000 and 11.45 via the BD FACSPrestoTM, A high correlation (R2 = 0.95, P < 0.001) of Hb level measurements was noted between the BD FACSPrestoTM and Sysmex XN 1000 hematology analyzer. Overall, a Bland-Altman plot of the differences between the two methods showed an excellent agreement for absolute and percentage CD4 counts and hemoglobin measurements between POC and conventional methods evaluated here. Furthermore, the study demonstrated the ease of use of the BD FACSPrestoTM POC technology in remote areas. CONCLUSION The BD FACPrestoTM is a suitable tool for CD4 enumeration in resource-limited settings, specifically providing a deployable, reliable POC testing option. The BD FACSPrestoTM performed appropriately in comparison to the conventional reference standard technologies. The BD FACSPrestoTM, system provides accurate, reliable, precise CD4/%CD4/Hb results on venous blood sampling. The data showed good agreement between the BD FACSPrestoTM, BD FACSCantoTM II and Sysmex XN 1000 XN 1000 systems.
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Affiliation(s)
- Bertrand Sagnia
- Laboratory of Microbiology and Immunology of CIRCB, Yaounde, Cameroon
| | | | | | | | - Jules Tchadji
- Laboratory of Microbiology and Immunology of CIRCB, Yaounde, Cameroon
| | | | - Alexis Ndjolo
- Laboratory of Microbiology and Immunology of CIRCB, Yaounde, Cameroon
| | - Vittorio Colizzi
- Laboratory of Immunology, Faculty of Sciences, University of Rome “Tor Vergata”, Rome, Italy
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Raimo M, Zavoianu AG, Meijs W, Scholten P, Spanholtz J. Qualification of a flow cytometry-based method for the evaluation of in vitro cytotoxicity of GTA002 natural killer cell therapy. Heliyon 2024; 10:e24715. [PMID: 38304826 PMCID: PMC10830575 DOI: 10.1016/j.heliyon.2024.e24715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/03/2024] Open
Abstract
Background Natural Killer (NK) cell-based therapies represent a ground-breaking opportunity for the treatment of solid tumors and hematological malignancies. NK cell manufacturing under good manufacturing practice (GMP) is complex and requires attentive assessment the product's safety and efficacy through quality control (QC). Release testing includes monitoring of in vitro cell expansion, differentiation, purity, phenotype, and cytotoxicity. As NK cells are biologically active products, the establishment of potency methods is particularly relevant; surrogate or improper assays can lead to rejection of qualifiable batches or to release of products that falsely meet potency specifications, potentially causing low efficacy during clinical trials. As cell-based therapeutics are highly heterogeneous, no universal guidelines for product characterization are available, and developers must invest significant effort in establishing and validating robust and fit-to-purpose assays. In this study, we describe the qualification procedure of a flow cytometry-based analytical method to assess in vitro potency of GTA002 NK cells, to be applied to oNKord®/inaleucel allogeneic off-the-shelf NK cell product from Glycostem Therapeutics, undergoing a Phase I/IIa clinical trial in acute myeloid leukemia (AML) patients (NCT04632316). Methods First, we established multi-color flow cytometry panels to quantitatively determine the count of effector (E) GTA002 cells and leukemia target (T) K562 cells alone and in co-culture at different E:T ratios (10:1, 3:1, 1:1). Effector potency was then qualitatively expressed as percentage of cytotoxicity. Next, we defined protocols for method qualification to assess the pivotal features of the assays, including accuracy, precision, linearity, range, specificity, robustness, and carryover; quantitative acceptance criteria were determined for all parameters. Results of the qualification procedure are reported and discussed against pre-defined acceptance criteria. Results Overall, our methods show robust performance across all parameters, ensuring QC-compliant assessment of NK cell potency as part of the release test panel for clinical batches. Notably, we identified relevant aspects to address when progressing towards method validation to support pivotal clinical studies. Conclusions This article provides a "case-study" of how analytical method development for cell therapeutics is planned and executed from early clinical stages, anticipating the need to establish robust procedures to overcome scientific and regulatory challenges during method validation.
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Affiliation(s)
| | | | - Wilma Meijs
- Glycostem Therapeutics, Kloosterstraat 9, 5349, AB Oss, the Netherlands
| | - Pascal Scholten
- Glycostem Therapeutics, Kloosterstraat 9, 5349, AB Oss, the Netherlands
| | - Jan Spanholtz
- Glycostem Therapeutics, Kloosterstraat 9, 5349, AB Oss, the Netherlands
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Tsai DY, Wang CH, Schiro PG, Chen N, Tseng JY. Tracking B Cell Memory to SARS-CoV-2 Using Rare Cell Analysis System. Vaccines (Basel) 2023; 11:vaccines11040735. [PMID: 37112647 PMCID: PMC10145117 DOI: 10.3390/vaccines11040735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Rapid mutations within SARS-CoV-2 are driving immune escape, highlighting the need for in-depth and routine analysis of memory B cells (MBCs) to complement the important but limited information from neutralizing antibody (nAb) studies. In this study, we collected plasma samples and peripheral blood mononuclear cells (PBMCs) from 35 subjects and studied the nAb titers and the number of antigen-specific memory B cells at designated time points before and after vaccination. We developed an assay to use the MiSelect R II System with a single-use microfluidic chip to directly detect the number of spike-receptor-binding domain (RBD)-specific MBCs in PBMCs. Our results show that the number of spike-RBD-specific MBCs detected by the MiSelect R II System is highly correlated with the level of nAbs secreted by stimulated PBMCs, even 6 months after vaccination when nAbs were generally not present in plasma. We also found antigen-specific cells recognizing Omicron spike-RBD were present in PBMCs from booster vaccination of subjects, but with a high variability in the number of B cells. The MiSelect R II System provided a direct, automated, and quantitative method to isolate and analyze subsets of rare cells for tracking cellular immunity in the context of a rapidly mutating virus.
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Affiliation(s)
- Dong-Yan Tsai
- MiCareo Taiwan Co., Ltd., 5F, No. 69, Ln. 77, Xing Ai Rd., Neihu Dist., Taipei City 114, Taiwan
| | - Chun-Hung Wang
- MiCareo Taiwan Co., Ltd., 5F, No. 69, Ln. 77, Xing Ai Rd., Neihu Dist., Taipei City 114, Taiwan
| | - Perry G. Schiro
- MiCareo Taiwan Co., Ltd., 5F, No. 69, Ln. 77, Xing Ai Rd., Neihu Dist., Taipei City 114, Taiwan
| | - Nathan Chen
- Adimmune Corporation, No. 3, Sec.1, Tanxing Rd., Tanzi Dist., Taichung City 427, Taiwan
| | - Ju-Yu Tseng
- MiCareo Taiwan Co., Ltd., 5F, No. 69, Ln. 77, Xing Ai Rd., Neihu Dist., Taipei City 114, Taiwan
- Correspondence: ; Tel.: +886-2-27923976
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Shai S, Patolsky F, Drori H, Scheinman EJ, Davidovits E, Davidovits G, Tirman S, Arber N, Katz A, Adir Y. A novel, accurate, and non-invasive liquid biopsy test to measure cellular immune responses as a tool to diagnose early-stage lung cancer: a clinical trials study. Respir Res 2023; 24:52. [PMID: 36788537 PMCID: PMC9927051 DOI: 10.1186/s12931-023-02358-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023] Open
Abstract
INTRODUCTION Lung cancer remains the leading cause of death from cancer, worldwide. Developing early detection diagnostic methods, especially non-invasive methods, is a critical component to raising the overall survival rate and prognosis for lung cancer. The purpose of this study is to evaluate two protocols of a novel in vitro cellular immune response test to detect lung cancer. The test specifically quantifies the glycolysis metabolism pathway, which is a biomarker for the activation level of immune cells. It summarizes the results of two clinical trials, where each deploys a different protocol's version of this test for the detection of lung cancer. In the later clinical trial, an improved test protocol is applied. METHOD The test platform is based on changes in the metabolic pathways of the immune cells following their activation by antigenic stimuli associated with Lung cancer. Peripheral Blood Mononuclear Cells are loaded on a multiwell plate together with various lung tumor associated antigens and a fluorescent probe that exhibits a pH-dependent absorption shift. The acidification process in the extracellular fluid is monitored by a commercial fluorescence plate reader device in continuous reading for 3 h at 37 °C to document the fluorescent signal received from each well. RESULTS In the later clinical trial, an improved test protocol was applied and resulted in increased test accuracy. Specificity of the test increased to 94.0% and test sensitivity increased to 97.3% in lung cancer stage I, by using the improved protocol. CONCLUSION The improved protocol of the novel cellular immune metabolic response based test detects stage I and stage II of lung cancer with high specificity and sensitivity, with low material costs and fast results.
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Affiliation(s)
- Shafrira Shai
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, 3190501, Haifa, Israel.
| | - Fernando Patolsky
- grid.12136.370000 0004 1937 0546School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Hagai Drori
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, 3190501 Haifa, Israel
| | - Eyal J. Scheinman
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, 3190501 Haifa, Israel
| | - Eyal Davidovits
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, 3190501 Haifa, Israel
| | - Giora Davidovits
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, 3190501 Haifa, Israel
| | - Shoval Tirman
- Savicell Diagnostics Ltd., Matam Advanced Technology Park, Building #23, P.O. Box 15050, 3190501 Haifa, Israel
| | - Nadir Arber
- grid.413449.f0000 0001 0518 6922Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, 6 Weizmann St., 6423906 Tel Aviv, Israel
| | - Amit Katz
- grid.413731.30000 0000 9950 8111Department of General Thoracic Surgery, Rambam Health Care Campus, 8 HaAliya HaShniya St., PO Box 9602, 31096 Haifa, Israel
| | - Yochai Adir
- grid.413469.dPulmonary Division, Faculty of Medicine, Lady Davis Carmel Medical Center, Mikhal Street 7, 3436212 Haifa, Israel
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Aru B, Soltani M, Pehlivanoglu C, Gürlü E, Ganjalikhani-Hakemi M, Yanikkaya Demirel G. Comparison of Laboratory Methods for the Clinical Follow Up of Checkpoint Blockade Therapies in Leukemia: Current Status and Challenges Ahead. Front Oncol 2022; 12:789728. [PMID: 35155232 PMCID: PMC8829140 DOI: 10.3389/fonc.2022.789728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/06/2022] [Indexed: 02/05/2023] Open
Abstract
The development of immune checkpoint inhibitors, the monoclonal antibodies that modulate the interaction between immune checkpoint molecules or their ligands on the immune cells or tumor tissue has revolutionized cancer treatment. While there are various studies proving their efficacy in hematological malignancies, there is also a body of accumulating evidence indicating that immune checkpoint inhibitors’ clinical benefits are limited in such diseases. In addition, due to their regulatory nature that balances the immune responses, blockade of immune checkpoints may lead to toxic side effects and autoimmune responses, and even primary or acquired resistance mechanisms may restrict their success. Thus, the need for laboratory biomarkers to identify and monitor patient populations who are more likely respond to this type of therapy and the management of side effects seem critical. However, guidelines regarding the use of immune checkpoint inhibitors in hematological cancers and during follow-up are limited while there is no consensus on the laboratory parameters to be investigated for safety and efficacy of the treatment. This review aims to provide an insight into recent information on predictive and prognostic value of biomarkers and laboratory tests for the clinical follow up of hematological malignancies, with an emphasis on leukemia.
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Affiliation(s)
- Basak Aru
- Department of Immunology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Mojdeh Soltani
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Cemil Pehlivanoglu
- Department of Emergency Medicine, Hatay Training and Research Hospital, Antakya, Turkey
| | - Ege Gürlü
- Faculty of Medicine 4thYear Student, Yeditepe University, Istanbul, Turkey
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Marsh‐Wakefield FMD, Mitchell AJ, Norton SE, Ashhurst TM, Leman JKH, Roberts JM, Harte JE, McGuire HM, Kemp RA. Making the most of high-dimensional cytometry data. Immunol Cell Biol 2021; 99:680-696. [PMID: 33797774 PMCID: PMC8453896 DOI: 10.1111/imcb.12456] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 01/03/2023]
Abstract
High-dimensional cytometry represents an exciting new era of immunology research, enabling the discovery of new cells and prediction of patient responses to therapy. A plethora of analysis and visualization tools and programs are now available for both new and experienced users; however, the transition from low- to high-dimensional cytometry requires a change in the way users think about experimental design and data analysis. Data from high-dimensional cytometry experiments are often underutilized, because of both the size of the data and the number of possible combinations of markers, as well as to a lack of understanding of the processes required to generate meaningful data. In this article, we explain the concepts behind designing high-dimensional cytometry experiments and provide considerations for new and experienced users to design and carry out high-dimensional experiments to maximize quality data collection.
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Affiliation(s)
- Felix MD Marsh‐Wakefield
- Vascular Immunology UnitDiscipline of PathologyThe University of SydneySydneyNSWAustralia
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
- School of Medical SciencesFaculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
| | - Andrew J Mitchell
- Department of Chemical EngineeringMaterials Characterisation and Fabrication PlatformThe University of MelbourneParkvilleVICAustralia
| | - Samuel E Norton
- Nanix LtdDunedinNew Zealand
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Thomas Myles Ashhurst
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
- Sydney CytometryUniversity of SydneySydneyNSWAustralia
- Ramaciotti Facility for Human Systems BiologyThe University of SydneySydneyNSWAustralia
| | - Julia KH Leman
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | | | - Jessica E Harte
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Helen M McGuire
- Charles Perkins CentreThe University of SydneySydneyNSWAustralia
- Ramaciotti Facility for Human Systems BiologyThe University of SydneySydneyNSWAustralia
- Translational Immunology GroupDiscipline of PathologyThe University of SydneySydneyNSWAustralia
| | - Roslyn A Kemp
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
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Shibru B, Fey K, Fricke S, Blaudszun AR, Fürst F, Weise M, Seiffert S, Weyh MK, Köhl U, Sack U, Boldt A. Detection of Immune Checkpoint Receptors - A Current Challenge in Clinical Flow Cytometry. Front Immunol 2021; 12:694055. [PMID: 34276685 PMCID: PMC8281132 DOI: 10.3389/fimmu.2021.694055] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Immunological therapy principles are increasingly determining modern medicine. They are used to treat diseases of the immune system, for tumors, but also for infections, neurological diseases, and many others. Most of these therapies base on antibodies, but small molecules, soluble receptors or cells and modified cells are also used. The development of immune checkpoint inhibitors is amazingly fast. T-cell directed antibody therapies against PD-1 or CTLA-4 are already firmly established in the clinic. Further targets are constantly being added and it is becoming increasingly clear that their expression is not only relevant on T cells. Furthermore, we do not yet have any experience with the long-term systemic effects of the treatment. Flow cytometry can be used for diagnosis, monitoring, and detection of side effects. In this review, we focus on checkpoint molecules as target molecules and functional markers of cells of the innate and acquired immune system. However, for most of the interesting and potentially relevant parameters, there are still no test kits suitable for routine use. Here we give an overview of the detection of checkpoint molecules on immune cells in the peripheral blood and show examples of a possible design of antibody panels.
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Affiliation(s)
- Benjamin Shibru
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Katharina Fey
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Stephan Fricke
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | | | - Friederike Fürst
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Max Weise
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Sabine Seiffert
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Maria Katharina Weyh
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Institute for Cellular Therapeutics, Hannover Medical School, Hannover, Germany
| | - Ulrich Sack
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Andreas Boldt
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
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9
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Sack U, Fricke S. Can flow cytometry outperform genetic testing in eosinophilia patients? Cytometry A 2021; 99:772-773. [PMID: 33527645 DOI: 10.1002/cyto.a.24311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Ulrich Sack
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Stephan Fricke
- Department of GMP Process Development, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
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