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Chen SY, Chen YC, Liu TY, Chang KC, Chang SS, Wu N, Lee Wu D, Dunlap RK, Chan CJ, Yang JS, Liao CC, Tsai FJ. Novel Genes Associated with Atrial Fibrillation and the Predictive Models for AF Incorporating Polygenic Risk Scores and PheWAS-Derived Risk Factors. Can J Cardiol 2024:S0828-282X(24)00851-1. [PMID: 39142603 DOI: 10.1016/j.cjca.2024.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Atrial fibrillation (AF), the most common atrial arrhythmia, presents varied clinical manifestations. Despite the identification of genetic loci associated with AF, particularly in specific populations, research within Asian ethnicities remains limited. This study aimed to develop predictive models for AF using AF-associated single-nucleotide polymorphisms (SNPs) from a Genome-Wide Association Study (GWAS) on a substantial cohort of Taiwanese individuals, evaluating the models' predictive efficacy. METHODS Involving 75,121 subjects, including 5,694 AF patients and 69,427 normal controls with GWAS data, the study merged polygenic risk scores (PRS) from AF-associated SNPs with Phenome-wide association study (PheWAS)-derived risk factors. Advanced statistical and machine learning techniques were employed to develop and evaluate AF predictive models for discrimination and calibration. RESULTS The study identified the top 30 significant SNPs associated with AF, predominantly on chromosomes 10 and 16, implicating genes like NEURL1, SH3PXD2A, INA, NT5C2, STN1, and ZFHX3. Notably, INA, NT5C2, and STN1 were newly linked to AF. The GWAS predictive power using PRS-CS analysis for AF exhibited an area under the curve (AUC) of 0.600 (P < 0.001), improving to 0.855 (P < 0.001) after adjusting for age and gender. PheWAS analysis showed the top 10 diseases associated with these genes were circulatory system diseases. CONCLUSIONS Integrating genetic and phenotypic data enhanced the accuracy and clinical relevance of AF predictive models. The findings suggest promise for refining AF risk assessment, enabling personalized interventions, and reducing AF-related morbidity and mortality burdens.
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Affiliation(s)
- Shih-Yin Chen
- School of Chinese Medicine, China Medical University, Taichung, 404, Taiwan; Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
| | - Yu-Chia Chen
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, 404, Taiwan
| | - Ting-Yuan Liu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, 404, Taiwan
| | - Kuan-Cheng Chang
- Division of Cardiovascular Medicine, Department of Medicine, China Medical University Hospital, Taichung 404, Taiwan; School of Medicine, College of Medicine, China Medical University, Taichung 404, Taiwan
| | - Shih-Sheng Chang
- Division of Cardiovascular Medicine, Department of Medicine, China Medical University Hospital, Taichung 404, Taiwan; School of Medicine, College of Medicine, China Medical University, Taichung 404, Taiwan
| | - Ning Wu
- Department of Biological Sciences, Southeastern Oklahoma State University, Durant, OK 74701, USA
| | - Donald Lee Wu
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Tulsa, OK 74104, USA
| | - Rylee Kay Dunlap
- College of Osteopathic Medicine, Oklahoma State University Center for Health Sciences, Tulsa, OK 74107, USA
| | - Chia-Jung Chan
- Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
| | - Jai-Sing Yang
- Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
| | - Chi Chou Liao
- Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
| | - Fuu-Jen Tsai
- School of Chinese Medicine, China Medical University, Taichung, 404, Taiwan; Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan; Department of Medical Genetics, China Medical University Hospital, Taichung 404, Taiwan.
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Ke ZP, Zhang GF, Guo YH, Sun YM, Wang J, Li N, Qiu XB, Xu YJ, Yang YQ. A novel PRRX1 loss-of-function variation contributing to familial atrial fibrillation and congenital patent ductus arteriosus. Genet Mol Biol 2022; 45:e20210378. [PMID: 35377386 PMCID: PMC8978609 DOI: 10.1590/1678-4685-gmb-2021-0378] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/25/2022] [Indexed: 12/27/2022] Open
Abstract
Atrial fibrillation (AF) represents the most common type of sustained cardiac arrhythmia in humans and confers a significantly increased risk for thromboembolic stroke, congestive heart failure and premature death. Aggregating evidence emphasizes the predominant genetic defects underpinning AF and an increasing number of deleterious variations in more than 50 genes have been involved in the pathogenesis of AF. Nevertheless, the genetic basis underlying AF remains incompletely understood. In the current research, by whole-exome sequencing and Sanger sequencing analysis in a family with autosomal-dominant AF and congenital patent ductus arteriosus (PDA), a novel heterozygous variation in the PRRX1 gene encoding a homeobox transcription factor critical for cardiovascular development, NM_022716.4:c.373G>T;p.(Glu125*), was identified to be in co-segregation with AF and PDA in the whole family. The truncating variation was not detected in 306 unrelated healthy individuals employed as controls. Quantitative biological measurements with a reporter gene analysis system revealed that the Glu125*-mutant PRRX1 protein failed to transactivate its downstream target genes SHOX2 and ISL1, two genes that have been causally linked to AF. Conclusively, the present study firstly links PRRX1 loss-of-function variation to AF and PDA, suggesting that AF and PDA share a common abnormal developmental basis in a proportion of cases.
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Affiliation(s)
| | | | - Yu-Han Guo
- Fudan University, China; Fudan University, China
| | | | | | - Ning Li
- Shanghai Jiao Tong University, China
| | | | - Ying-Jia Xu
- Fudan University, China; Fudan University, China
| | - Yi-Qing Yang
- Fudan University, China; Fudan University, China; Fudan University, China; Fudan University, China
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