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Maas SCE, Vidaki A, Wilson R, Teumer A, Liu F, van Meurs JBJ, Uitterlinden AG, Boomsma DI, de Geus EJC, Willemsen G, van Dongen J, van der Kallen CJH, Slagboom PE, Beekman M, van Heemst D, van den Berg LH, Duijts L, Jaddoe VWV, Ladwig KH, Kunze S, Peters A, Ikram MA, Grabe HJ, Felix JF, Waldenberger M, Franco OH, Ghanbari M, Kayser M. Validated inference of smoking habits from blood with a finite DNA methylation marker set. Eur J Epidemiol 2019; 34:1055-1074. [PMID: 31494793 PMCID: PMC6861351 DOI: 10.1007/s10654-019-00555-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/22/2019] [Indexed: 12/18/2022]
Abstract
Inferring a person’s smoking habit and history from blood is relevant for complementing or replacing self-reports in epidemiological and public health research, and for forensic applications. However, a finite DNA methylation marker set and a validated statistical model based on a large dataset are not yet available. Employing 14 epigenome-wide association studies for marker discovery, and using data from six population-based cohorts (N = 3764) for model building, we identified 13 CpGs most suitable for inferring smoking versus non-smoking status from blood with a cumulative Area Under the Curve (AUC) of 0.901. Internal fivefold cross-validation yielded an average AUC of 0.897 ± 0.137, while external model validation in an independent population-based cohort (N = 1608) achieved an AUC of 0.911. These 13 CpGs also provided accurate inference of current (average AUCcrossvalidation 0.925 ± 0.021, AUCexternalvalidation0.914), former (0.766 ± 0.023, 0.699) and never smoking (0.830 ± 0.019, 0.781) status, allowed inferring pack-years in current smokers (10 pack-years 0.800 ± 0.068, 0.796; 15 pack-years 0.767 ± 0.102, 0.752) and inferring smoking cessation time in former smokers (5 years 0.774 ± 0.024, 0.760; 10 years 0.766 ± 0.033, 0.764; 15 years 0.767 ± 0.020, 0.754). Model application to children revealed highly accurate inference of the true non-smoking status (6 years of age: accuracy 0.994, N = 355; 10 years: 0.994, N = 309), suggesting prenatal and passive smoking exposure having no impact on model applications in adults. The finite set of DNA methylation markers allow accurate inference of smoking habit, with comparable accuracy as plasma cotinine use, and smoking history from blood, which we envision becoming useful in epidemiology and public health research, and in medical and forensic applications.
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Affiliation(s)
- Silvana C E Maas
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Walther-Rathenau-Str. 48, 17475, Greifswald, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Greifswald, 17475 Greifswald, Germany
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101 Beijing, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, 100049 Beijing, People's Republic of China
| | - Joyce B J van Meurs
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit, Van der Boechorststraat 7-9, 1081 BT, Amsterdam, The Netherlands
| | - Carla J H van der Kallen
- Department of Internal Medicine, Maastricht University Medical Center, Randwycksingel 35, 6229 EG, Maastricht, The Netherlands.,Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Diana van Heemst
- Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, P.O. box 9600, 2300 RC, Leiden, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Postbus 85500, 3508 GA, Utrecht, The Netherlands
| | | | - Liesbeth Duijts
- Division of Respiratory Medicine and Allergology and Division of Neonatology, Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Karl-Heinz Ladwig
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80802 Munich, Germany.,Institute for Medical Informatics, Biometrics and Epidemiology, Ludwig-Maximilians-Universität (LMU) Munich, Marchioninistr. 15, 81377 Munich, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Ellernholzstraße 1-2, 17475, Greifswald, Germany
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80802 Munich, Germany
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands. .,Department of Genetics, School of Medicine, Mashhad University of Medical Science, PO Box 91735-951, 9133913716 Mashhad, Iran.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
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Arpón A, Milagro FI, Ramos-Lopez O, Mansego ML, Santos JL, Riezu-Boj JI, Martínez JA. Epigenome-wide association study in peripheral white blood cells involving insulin resistance. Sci Rep 2019; 9:2445. [PMID: 30792424 PMCID: PMC6385280 DOI: 10.1038/s41598-019-38980-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/11/2019] [Indexed: 02/06/2023] Open
Abstract
Insulin resistance (IR) is a hallmark of type 2 diabetes, metabolic syndrome and cardiometabolic risk. An epigenetic phenomena such as DNA methylation might be involved in the onset and development of systemic IR. The aim of this study was to explore the genetic DNA methylation levels in peripheral white blood cells with the objective of identifying epigenetic signatures associated with IR measured by the Homeostatic Model Assessment of IR (HOMA-IR) following an epigenome-wide association study approach. DNA methylation levels were assessed using Infinium Methylation Assay (Illumina), and were associated with HOMA-IR values of participants from the Methyl Epigenome Network Association (MENA) project, finding statistical associations for at least 798 CpGs. A stringent statistical analysis revealed that 478 of them showed a differential methylation pattern between individuals with HOMA-IR ≤ 3 and > 3. ROC curves of top four CpGs out of 478 allowed differentiating individuals between both groups (AUC≈0.88). This study demonstrated the association between DNA methylation in some specific CpGs and HOMA-IR values that will help to the understanding and in the development of new strategies for personalized approaches to predict and prevent IR-associated diseases.
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Affiliation(s)
- Ana Arpón
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - Fermín I Milagro
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain
| | - Omar Ramos-Lopez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - M Luisa Mansego
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - José Luis Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José-Ignacio Riezu-Boj
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain. .,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.
| | - J Alfredo Martínez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain.,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.,Madrid Institute for Advanced Studies (IMDEA), IMDEA Food, Madrid, Spain
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