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Choi Y, Cha J, Choi S. Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES). BMC Bioinformatics 2024; 25:56. [PMID: 38308205 PMCID: PMC10837879 DOI: 10.1186/s12859-024-05677-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Genome-wide association studies have successfully identified genetic variants associated with human disease. Various statistical approaches based on penalized and machine learning methods have recently been proposed for disease prediction. In this study, we evaluated the performance of several such methods for predicting asthma using the Korean Chip (KORV1.1) from the Korean Genome and Epidemiology Study (KoGES). RESULTS First, single-nucleotide polymorphisms were selected via single-variant tests using logistic regression with the adjustment of several epidemiological factors. Next, we evaluated the following methods for disease prediction: ridge, least absolute shrinkage and selection operator, elastic net, smoothly clipped absolute deviation, support vector machine, random forest, boosting, bagging, naïve Bayes, and k-nearest neighbor. Finally, we compared their predictive performance based on the area under the curve of the receiver operating characteristic curves, precision, recall, F1-score, Cohen's Kappa, balanced accuracy, error rate, Matthews correlation coefficient, and area under the precision-recall curve. Additionally, three oversampling algorithms are used to deal with imbalance problems. CONCLUSIONS Our results show that penalized methods exhibit better predictive performance for asthma than that achieved via machine learning methods. On the other hand, in the oversampling study, randomforest and boosting methods overall showed better prediction performance than penalized methods.
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Affiliation(s)
- Yongjun Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea
| | - Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
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Gupta MK, Peng H, Li Y, Xu CJ. The role of DNA methylation in personalized medicine for immune-related diseases. Pharmacol Ther 2023; 250:108508. [PMID: 37567513 DOI: 10.1016/j.pharmthera.2023.108508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Epigenetics functions as a bridge between host genetic & environmental factors, aiding in human health and diseases. Many immune-related diseases, including infectious and allergic diseases, have been linked to epigenetic mechanisms, particularly DNA methylation. In this review, we summarized an updated overview of DNA methylation and its importance in personalized medicine, and demonstrated that DNA methylation has excellent potential for disease prevention, diagnosis, and treatment in a personalized manner. The future implications and limitations of the DNA methylation study have also been well-discussed.
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Affiliation(s)
- Manoj Kumar Gupta
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - He Peng
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
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Joglekar MM, Nizamoglu M, Fan Y, Nemani SSP, Weckmann M, Pouwels SD, Heijink IH, Melgert BN, Pillay J, Burgess JK. Highway to heal: Influence of altered extracellular matrix on infiltrating immune cells during acute and chronic lung diseases. Front Pharmacol 2022; 13:995051. [PMID: 36408219 PMCID: PMC9669433 DOI: 10.3389/fphar.2022.995051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/19/2022] [Indexed: 10/31/2023] Open
Abstract
Environmental insults including respiratory infections, in combination with genetic predisposition, may lead to lung diseases such as chronic obstructive pulmonary disease, lung fibrosis, asthma, and acute respiratory distress syndrome. Common characteristics of these diseases are infiltration and activation of inflammatory cells and abnormal extracellular matrix (ECM) turnover, leading to tissue damage and impairments in lung function. The ECM provides three-dimensional (3D) architectural support to the lung and crucial biochemical and biophysical cues to the cells, directing cellular processes. As immune cells travel to reach any site of injury, they encounter the composition and various mechanical features of the ECM. Emerging evidence demonstrates the crucial role played by the local environment in recruiting immune cells and their function in lung diseases. Moreover, recent developments in the field have elucidated considerable differences in responses of immune cells in two-dimensional versus 3D modeling systems. Examining the effect of individual parameters of the ECM to study their effect independently and collectively in a 3D microenvironment will help in better understanding disease pathobiology. In this article, we discuss the importance of investigating cellular migration and recent advances in this field. Moreover, we summarize changes in the ECM in lung diseases and the potential impacts on infiltrating immune cell migration in these diseases. There has been compelling progress in this field that encourages further developments, such as advanced in vitro 3D modeling using native ECM-based models, patient-derived materials, and bioprinting. We conclude with an overview of these state-of-the-art methodologies, followed by a discussion on developing novel and innovative models and the practical challenges envisaged in implementing and utilizing these systems.
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Affiliation(s)
- Mugdha M. Joglekar
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
| | - Mehmet Nizamoglu
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
| | - YiWen Fan
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
| | - Sai Sneha Priya Nemani
- Department of Paediatric Pneumology &Allergology, University Children’s Hospital, Schleswig-Holstein, Campus Lübeck, Germany
- Epigenetics of Chronic Lung Disease, Priority Research Area Chronic Lung Diseases; Leibniz Lung Research Center Borstel; Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Germany
| | - Markus Weckmann
- Department of Paediatric Pneumology &Allergology, University Children’s Hospital, Schleswig-Holstein, Campus Lübeck, Germany
- Epigenetics of Chronic Lung Disease, Priority Research Area Chronic Lung Diseases; Leibniz Lung Research Center Borstel; Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Germany
| | - Simon D. Pouwels
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, Netherlands
| | - Irene H. Heijink
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, Netherlands
| | - Barbro N. Melgert
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, Groningen, Netherlands
| | - Janesh Pillay
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Department of Critical Care, Groningen, Netherlands
| | - Janette K. Burgess
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands
- University of Groningen, University Medical Center Groningen, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, Groningen, Netherlands
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