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Qin ZM, Liang SQ, Long JX, Deng JM, Wei X, Yang ML, Tang SJ, Li HL. Importance of GWAS Risk Loci and Clinical Data in Predicting Asthma Using Machine-learning Approaches. Comb Chem High Throughput Screen 2024; 27:400-407. [PMID: 37278039 DOI: 10.2174/1386207326666230602161939] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 04/17/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
INTRODUCTION To understand the risk factors of asthma, we combined genome-wide association study (GWAS) risk loci and clinical data in predicting asthma using machine-learning approaches. METHODS A case-control study with 123 asthmatics and 100 controls was conducted in the Zhuang population in Guangxi. GWAS risk loci were detected using polymerase chain reaction, and clinical data were collected. Machine-learning approaches were used to identify the major factors that contribute to asthma. RESULTS A total of 14 GWAS risk loci with clinical data were analyzed on the basis of 10 times the 10-fold cross-validation for all machine-learning models. Using GWAS risk loci or clinical data, the best performances exhibited area under the curve (AUC) values of 64.3% and 71.4%, respectively. Combining GWAS risk loci and clinical data, the XGBoost established the best model with an AUC of 79.7%, indicating that the combination of genetics and clinical data can enable improved performance. We then sorted the importance of features and found the top six risk factors for predicting asthma to be rs3117098, rs7775228, family history, rs2305480, rs4833095, and body mass index. CONCLUSION Asthma-prediction models based on GWAS risk loci and clinical data can accurately predict asthma, and thus provide insights into the disease pathogenesis.
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Affiliation(s)
- Zan-Mei Qin
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Si-Qiao Liang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jian-Xiong Long
- Department of Epidemiology and Health Statistics, School of Public Health of Guangxi Medical University, Nanning, Guangxi, China
| | - Jing-Min Deng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xuan Wei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Mei-Ling Yang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shao-Jie Tang
- School of Automation, Xi'an University of Posts and Telecommunications, Xi'an, Shanxi, 710121, China
- Xi'an Key Laboratory of Advanced Controlling and Intelligent Processing (ACIP), Xi'an, Shanxi, 710121, China
| | - Hai-Li Li
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Kim SY, Kim EG, Kim M, Hong JY, Kim GE, Jung JH, Park M, Kim MJ, Kim YH, Sohn MH, Kim KW. Genome-wide association study identifies BTNL2 associated with atopic asthma in children. Medicine (Baltimore) 2021; 100:e27626. [PMID: 34871226 PMCID: PMC8568460 DOI: 10.1097/md.0000000000027626] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/06/2021] [Indexed: 01/05/2023] Open
Abstract
Asthma is a heterogeneous disease characterized by chronic airway inflammation with a genetic predisposition. Butyrophilin-like 2 (BTNL2) is a member of the immunoglobulin superfamily that plays an important role in regulating T cell activation and immune homeostasis. Here, we aimed to investigate the association of the genetic variants of BTNL2 with childhood asthma and asthma-related traits by utilizing extreme asthma phenotypes and employing a genome-wide association study. Our study included 243 children with well-defined moderate to severe atopic asthma and 134 healthy children with no history of allergic diseases and allergic sensitization. DNA from these subjects was genotyped using AxiomTM Genome-Wide Array Plates. Although no single nucleotide polymorphisms (SNPs) reached a genome-wide threshold of significance, 3 SNPs, rs3817971, rs41355746, and rs41441651, at BTNL2 were significantly associated with moderate to severe atopic asthma after performing Bonferroni correction. These SNPs were also associated with the risk of allergic sensitization toward house dust mites and the presence and degree of bronchial hyperresponsiveness. Thus, we identified that BTNL2 was associated with atopic moderate to severe persistent asthma in Korean children, and this may play an important role in disease development and susceptibility.
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Affiliation(s)
- Soo Yeon Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Gyul Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mina Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Yeon Hong
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
- Division of Cardiovascular Disease Research, Department for Chronic Disease Convergence Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Ga Eun Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Pediatrics, Keimyung University School of Medicine, Keimyung University Dongsan Hospital, Daegu, Republic of Korea
| | - Jae Hwa Jung
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mireu Park
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Jung Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yoon Hee Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myung Hyun Sohn
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung Won Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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Liang SQ, Deng JM, Wei X, Chen ZR, Yang ML, Qin HJ, Zhang JQ, He ZY. Association of GWAS-supported noncoding area loci rs404860, rs3117098, and rs7775228 with asthma in Chinese Zhuang population. J Clin Lab Anal 2019; 34:e23066. [PMID: 31605414 PMCID: PMC7031573 DOI: 10.1002/jcla.23066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/08/2019] [Accepted: 09/18/2019] [Indexed: 11/08/2022] Open
Abstract
Background Asthma is a complicated and polygenic inheritance disease, and its prevalence increases worldwide. Recent genome‐wide association studies (GWASs) identified a significant association of single nucleotide polymorphism with asthma in the Japanese population. This study aimed to examine the association of GWAS‐supported noncoding area loci, namely rs404860, rs3117098, and rs7775228, with asthma in Chinese Zhuang population. Methods A case‐control study involving 223 individuals, comprising 123 patients with asthma and 100 healthy controls, was conducted. Genotypes were determined by polymerase chain reaction (PCR)/ligase detection reaction assay. The association between gene polymorphisms and asthma risk was calculated by logistic regression analysis using different genetic models through comparisons of alleles (A vs a), homozygote genotypes (AA vs aa), heterozygote genotypes (Aa vs aa), dominant models (AA+Aa vs aa), and recessive models (AA vs. Aa+aa). Results The distribution of the genotype frequency of rs3117098 was statistically different between the case and control groups. For rs3117098, significant associations were observed through comparisons of alleles (OR: 1.832, 95% CI: 1.048‐3.204, P = .034) and dominant models (OR: 2.065, 95% CI: 1.001‐4.260, P = .050). The statistical analysis showed no significant difference for loci rs404860 and rs7775228 between patients with asthma and controls. Conclusion rs3117098 may be the risk factor for asthma in Chinese Zhuang population.
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Affiliation(s)
- Si-Qiao Liang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jing-Min Deng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xuan Wei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhang-Rong Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Mei-Ling Yang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hua-Jiao Qin
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jian-Quan Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhi-Yi He
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, China
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