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Hammerich L, Shevchenko Y, Knorr J, Werner W, Bruneau A, Tacke F. Resolving 31 colors on a standard 3-laser full spectrum flow cytometer for immune monitoring of human blood samples. Cytometry B Clin Cytom 2023; 104:367-373. [PMID: 37209003 DOI: 10.1002/cyto.b.22126] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
Immune monitoring of patients on a single-cell level is becoming increasingly important in various diseases. Due to the often very limited availability of human specimens and our increased understanding of the immune systems there is an increasing demand to analyze as many markers as possible simultaneously in one panel. Full spectrum flow cytometry is emerging as a powerful tool for immune monitoring since 5-laser instruments enable characterization of 40 parameters or more in a single sample. Nevertheless, even if only machines with fewer lasers are available, development of novel fluorophore families enables increasing panel sizes. Here, we demonstrate that careful panel design enables the use of 31-color panels on a 3-laser Cytek® Aurora cytometer for analyzing human peripheral blood leukocytes, without the need for custom configuration and using only commercially available fluorochromes. The panel presented here should serve as an example of a 31-fluorochrome combination that can be resolved on a 3-laser full spectrum cytometer and that can be adapted to comprise other (and possibly more) markers of interest depending on the research focus.
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Affiliation(s)
- Linda Hammerich
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Yaroslava Shevchenko
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Jana Knorr
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Wiebke Werner
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Alix Bruneau
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
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2
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Birrer F, Brodie T, Stroka D. OMIP-088: Twenty-target imaging mass cytometry panel for major cell populations in mouse formalin fixed paraffin embedded liver. Cytometry A 2023; 103:189-192. [PMID: 36602064 DOI: 10.1002/cyto.a.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]
Abstract
The purpose of this 20-target imaging mass cytometry (IMC) panel is to identify the main cell types in formalin fixed paraffin embedded (FFPE) mouse liver tissue with the Hyperion™ mass cytometer from Standard BioTools (formerly Fluidigm). The antibody panel includes markers to identify hepatocytes (E-cadherin, HNF4α (hepatocyte nuclear factor 4 alpha), Arginase-1), liver sinusoidal endothelial cells (LSECs; CD206), Kupffer cells (F4/80, CD206), neutrophils (Ly6G, CD11b), bone marrow derived myeloid cells (BMDMs; CD11b), cholangiocytes (E-cadherin high), endothelial cells (CD31, α-SMA), plasmacytoid dendritic cells (CD317), B cells (CD19), T cells (CD3e, CD4, CD8a), NK cells (CD161) as well markers of cell activation (CD44, CD74), proliferation (Ki-67) and to aid in cell segmentation (Pan-Actin, E-cadherin, histone H3). The panel has been tested in other mouse tissues, namely the spleen, colon and lung, and therefore is likely to work across various mouse FFPE samples of interest. It has not been tested using human samples, frozen samples or in suspension mass cytometry because FFPE treatment profoundly changes epitope conformation. In summary, this panel is a powerful tool for pre-clinical research to determine cellular abundance and spatial distribution within mouse tissues and serves as a scaffold, to which more targets can be added for project specific requirements.
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Affiliation(s)
- Fabienne Birrer
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Tess Brodie
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
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3
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Graham A, Korecky J, Schultz E, Gregory M, Asosingh K. Considerations for user consultation in a flow cytometry shared resource laboratory. Cytometry A 2021; 101:228-236. [PMID: 34787950 DOI: 10.1002/cyto.a.24519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/06/2022]
Abstract
User consultation is an essential first step in assuring high-quality flow cytometric data. A central challenge to shared resource laboratory (SRL) staff is how to best guide new and current users to meet each projects' needs. One solution to this challenge is to follow a standard user consultation platform addressing all critical steps between the conception of the experiment and the actual acquisition of samples. Here we describe considerations to help an SRL understand the researcher's goals and how best the SRL staff can provide expert advice in a structured manner. User consultation has an educational nature, informing users about current best practices in cytometry that apply to their specific utilization. A consultation report also improves communication between the SRL, principal investigator, and lab members of the collaborating researcher. Development of best SRL practices is spearheaded by the ISAC SRL committee and this communication sets the foundation to initiate such report for user consultation. Implementation of best practices during user consultation will improve rigor and reproducibility in cytometry.
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Affiliation(s)
- Amy Graham
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jena Korecky
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eric Schultz
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michael Gregory
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, Florida, USA
| | - Kewal Asosingh
- Flow Cytometry Core Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA
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4
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Wang W, Creusot RJ. Orchestrating multiplexity in polychromatic science through OMIPs: A decade-old resource to empower biomedical research. Cytometry A 2021; 99:866-874. [PMID: 34145721 DOI: 10.1002/cyto.a.24471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 05/11/2021] [Accepted: 05/31/2021] [Indexed: 01/20/2023]
Abstract
As the optimized multicolor immunofluorescence panel (OMIP) platform entered its 10th anniversary since its launch, the multicolor flow cytometry landscape has changed significantly. Likewise, OMIPs have continuously evolved to cover larger panel sizes, increasing number of subpopulations profiled in a single panel, and new species. After a decade of contributions to the OMIP platform, a review of this collection, summarizing its content and purpose for the research community, is timely and due. This review provides an overview of OMIPs and a presentation of the depth and diversity of this collection of validated panels, with the expectation that readers will take advantage of them to empower and accelerate their research.
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Affiliation(s)
- Wei Wang
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Remi J Creusot
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
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5
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Elaldi R, Hemon P, Petti L, Cosson E, Desrues B, Sudaka A, Poissonnet G, Van Obberghen-Schilling E, Pers JO, Braud VM, Anjuère F, Meghraoui-Kheddar A. High Dimensional Imaging Mass Cytometry Panel to Visualize the Tumor Immune Microenvironment Contexture. Front Immunol 2021; 12:666233. [PMID: 33936105 PMCID: PMC8085494 DOI: 10.3389/fimmu.2021.666233] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
The integrative analysis of tumor immune microenvironment (TiME) components, their interactions and their microanatomical distribution is mandatory to better understand tumor progression. Imaging Mass Cytometry (IMC) is a high dimensional tissue imaging system which allows the comprehensive and multiparametric in situ exploration of tumor microenvironments at a single cell level. We describe here the design of a 39-antibody IMC panel for the staining of formalin-fixed paraffin-embedded human tumor sections. We also provide an optimized staining procedure and details of the experimental workflow. This panel deciphers the nature of immune cells, their functions and their interactions with tumor cells and cancer-associated fibroblasts as well as with other TiME structural components known to be associated with tumor progression like nerve fibers and tumor extracellular matrix proteins. This panel represents a valuable innovative and powerful tool for fundamental and clinical studies that could be used for the identification of prognostic biomarkers and mechanisms of resistance to current immunotherapies.
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Affiliation(s)
- Roxane Elaldi
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.,Institut Universitaire de la Face et du Cou, Nice, France
| | - Patrice Hemon
- U1227, LBAI, University of Brest, INSERM, CHU de Brest, Brest, France
| | - Luciana Petti
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Estelle Cosson
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | | | - Anne Sudaka
- Centre Antoine Lacassagne, Anatomopathology Laboratory and Human Biobank, Nice, France
| | | | | | | | - Veronique M Braud
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Fabienne Anjuère
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Aïda Meghraoui-Kheddar
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
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6
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Avanzi L, Perinelli E, Bressan M, Balducci C, Lombardi L, Fraccaroli F, van Dick R. The mediational effect of social support between organizational identification and employees' health: a three-wave study on the social cure model. Anxiety Stress Coping 2021; 34:465-478. [PMID: 33403860 DOI: 10.1080/10615806.2020.1868443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Recent research postulated that organizational identification plays an important role in employees' health and well-being. Building on the Social Identity Approach as a framework, we test the so-called social cure hypothesis, according to which group-based processes of social support should reduce employees' psychological distress. DESIGN AND METHODS While there is a considerable amount of cross-sectional evidence concerning the positive role played by organizational identification in this dynamic, there is a lack of full panel studies. This study tries to fill this gap by using data from a sample of technical and administrative staff of a University in Italy at three time points (N = 96). Data were analyzed using Autoregressive Cross-Lagged Panel models. RESULTS We found support for the hypothesized longitudinal mediational model. Specifically, strongly identified employees tend to receive more social support, and this in turn reduces psychological distress over time. CONCLUSIONS This study is the first test of the social cure hypothesis in an organizational context that uses a panel study design. We discuss the theoretical and practical implications for management.
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Affiliation(s)
- Lorenzo Avanzi
- Department of Psychology and Cognitive Science, University of Trento, Italy
| | - Enrico Perinelli
- Department of Psychology and Cognitive Science, University of Trento, Italy
| | - Marco Bressan
- Aix-Marseille University, CNRS, LPC, Marseille, France
| | | | - Luigi Lombardi
- Department of Psychology and Cognitive Science, University of Trento, Italy
| | - Franco Fraccaroli
- Department of Psychology and Cognitive Science, University of Trento, Italy
| | - Rolf van Dick
- Department of Social Psychology, Goethe University Frankfurt, Germany
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7
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Weston SJ, Ritchie SJ, Rohrer JM, Przybylski AK. Recommendations for Increasing the Transparency of Analysis of Preexisting Data Sets. Adv Methods Pract Psychol Sci 2019; 2:214-227. [PMID: 32190814 PMCID: PMC7079740 DOI: 10.1177/2515245919848684] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Secondary data analysis, or the analysis of preexisting data, provides a powerful tool for the resourceful psychological scientist. Never has this been more true than now, when technological advances enable both sharing data across labs and continents and mining large sources of preexisting data. However, secondary data analysis is easily overlooked as a key domain for developing new open-science practices or improving analytic methods for robust data analysis. In this article, we provide researchers with the knowledge necessary to incorporate secondary data analysis into their methodological toolbox. We explain that secondary data analysis can be used for either exploratory or confirmatory work, and can be either correlational or experimental, and we highlight the advantages and disadvantages of this type of research. We describe how transparency-enhancing practices can improve and alter interpretations of results from secondary data analysis and discuss approaches that can be used to improve the robustness of reported results. We close by suggesting ways in which scientific subfields and institutions could address and improve the use of secondary data analysis.
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Affiliation(s)
| | - Stuart J. Ritchie
- Social, Genetic and Developmental Psychiatry Centre, King’s College London
| | - Julia M. Rohrer
- Department of Psychology, University of Leipzig
- International Max Planck Research School on the Life Course, Max Planck Institute for Human Development
- German Institute for Economic Research (DIW Berlin), Berlin, Germany
| | - Andrew K. Przybylski
- Oxford Internet Institute, University of Oxford
- Department of Experimental Psychology, University of Oxford
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8
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Gullaksen SE, Bader L, Hellesøy M, Sulen A, Fagerholt OHE, Engen CB, Skavland J, Gjertsen BT, Gavasso S. Titrating Complex Mass Cytometry Panels. Cytometry A 2019; 95:792-796. [PMID: 30964237 PMCID: PMC6766997 DOI: 10.1002/cyto.a.23751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/20/2022]
Abstract
We describe here a simple and efficient antibody titration approach for cell-surface markers and intracellular cell signaling targets for mass cytometry. The iterative approach builds upon a well-characterized backbone panel of antibodies and analysis using bioinformatic tools such as SPADE. Healthy peripheral blood and bone marrow cells are stained with a pre-optimized "backbone" antibody panel in addition to the progressively diluted (titrated) antibodies. Clustering based on the backbone panel enables the titration of each antibody against a rich hematopoietic background and assures that nonspecific binding and signal spillover can be quantified accurately. Using a slightly expanded backbone panel, antibodies quantifying changes in transcription factors and phosphorylated antigens are titrated on ex vivo stimulated cells to optimize sensitivity and evaluate baseline expression. Based on this information, complex panels of antibodies can be thoroughly optimized for use on healthy whole blood and bone marrow and are easily adaptable to the investigation of samples from for example clinical studies. © 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)
- Stein-Erik Gullaksen
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Lucius Bader
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Bergen group of Epidemiology and Biomarkers in Rheumatic Disease (BEaBIRD), Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Monica Hellesøy
- Department of Internal Medicine, Hematology section, Helse Bergen, Bergen, Norway
| | - André Sulen
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Oda Helen Eck Fagerholt
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Caroline B Engen
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Jørn Skavland
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bjørn Tore Gjertsen
- Centre of Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Internal Medicine, Hematology section, Helse Bergen, Bergen, Norway
| | - Sonia Gavasso
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Neuroimmunology Lab, Haukeland University Hospital, Bergen, Norway
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9
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Abstract
The immune system consists of a complex network of cells, all expressing a wide range of surface and/or intracellular proteins. Using flow cytometry, these cells can be analyzed by labeling with fluorophore-conjugated antibodies. The recent expansion of fluorescence flow cytometry technology, in conjunction with the ever-expanding understanding of the complexity of the immune system, has led to the generation of larger high-dimensional fluorescence flow cytometry panels. However, as panel size and complexity increases, so too does the difficulty involved in constructing high-quality panels, in addition to the challenges of analyzing such high-dimensional datasets. As such, this unit seeks to review the key principles involved in building high-dimensional panels, as well as to guide users through the process of building and analyzing quality panels. Here, cytometer configuration, fluorophore brightness, spreading error, antigen density, choosing the best conjugates, titration, optimization, and data analysis will all be addressed. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Thomas Myles Ashhurst
- Viral Immunopathology Laboratory, Discipline of Pathology, School of Medical Sciences, Sydney Medical School, The University of Sydney, Sydney, Australia.,Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, Australia.,Ramaciotti Facility for Human Systems Biology (RFHSB), The University of Sydney and Centenary Institute, Sydney, Australia.,Marie Bashir Institute for Emerging Infectious Disease (MBI), The University of Sydney, Sydney, Australia
| | - Adrian Lloyd Smith
- Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, Australia.,Ramaciotti Facility for Human Systems Biology (RFHSB), The University of Sydney and Centenary Institute, Sydney, Australia
| | - Nicholas Jonathan Cole King
- Viral Immunopathology Laboratory, Discipline of Pathology, School of Medical Sciences, Sydney Medical School, The University of Sydney, Sydney, Australia.,Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, Australia.,Ramaciotti Facility for Human Systems Biology (RFHSB), The University of Sydney and Centenary Institute, Sydney, Australia.,Marie Bashir Institute for Emerging Infectious Disease (MBI), The University of Sydney, Sydney, Australia.,Australian Institute for Nanoscale Science and Technology, The University of Sydney, Sydney, Australia
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10
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Abstract
BACKGROUND Several studies showed that the waist circumference of US adults has increased over the past 25 y. However, because of the high correlation between waist circumference and body mass index (BMI; in kg/m²) (r ∼ 0.9), it is uncertain if these trends in waist circumference exceed those expected on the basis of BMI changes over this time period. OBJECTIVE We assessed whether the recent trend in waist circumference was independent of changes in BMI, age, and race-ethnicity. DESIGN We analyzed data from the 1999-2000 through 2011-2012 cycles of the NHANES. RESULTS The mean waist circumference increased by ∼2 cm (in men) and ∼4 cm (in women) in adults in the United States over this 12-y period. In men, this increase was very close to what would be expected because of the 0.7 increase in mean BMI over this period. However, in women, most of the secular increase in waist circumference appeared to be independent of changes in BMI (mean: 0.6), age, and race-ethnicity over the 12-y period. We estimated that, independent of changes in these covariates, the mean waist circumference increased by 0.2 cm in men and 2.4 cm in women from 1999-2000 through 2011-2012; only the latter estimate was statistically significant. CONCLUSIONS Our results indicate that, in women but not men, the recent secular trend in waist circumference is greater than what would be expected on the basis of changes in BMI. Possible reasons for this secular increase, along with sex differences, are uncertain.
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Affiliation(s)
- David S Freedman
- From the Divisions of Nutrition, Physical Activity, and Obesity (DSF) and Adult and Community Health (ESF), CDC, Atlanta, GA
| | - Earl S Ford
- From the Divisions of Nutrition, Physical Activity, and Obesity (DSF) and Adult and Community Health (ESF), CDC, Atlanta, GA
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