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Shen HC, Pan MH, Huang CJ, Yeh HY, Yang HI, Lin YH, Huang CC, Lee KC, Yang YY, Hou MC. Multiple genetic polymorphisms are associated with the risk of metabolic syndrome, fatty liver, and airflow limitation: A Taiwan Biobank study. Gene 2024; 927:148660. [PMID: 38866261 DOI: 10.1016/j.gene.2024.148660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Links have been reported between the airflow limitation and both metabolic syndrome (MetS) and fatty liver (FL). Additionally, associations between genetic factors and risks of MetS, FL, and airflow limitation have been identified separately in different studies. Our study aims to simultaneously explore the association between specific single nucleotide polymorphisms (SNPs) of certain genes and the risk of the three associated diseases. METHODS In this retrospective cross-sectional nationwide study, 150,709 participants from the Taiwan Biobank (TWB) were enrolled. We conducted a genotype-phenotype association analysis of nine SNPs on seven genes (ApoE-rs429358, MBOAT7-rs641738, LEPR-rs1805096, APOC3-rs2854116, APOC3-rs2854117, PPP1R3B-rs4240624, PPP1R3B-rs4841132, TM6SF2-rs58542926, and IFNL4-rs368234815) using data from the TWB1.0 and TWB2.0 genotype dataset. Participants underwent a series of assessments including questionnaires, blood examinations, abdominal ultrasounds, and spirometry examinations. RESULTS MetS was associated with FL and airflow limitation. ApoE-rs429358, LEPR-rs1805096, APOC3-rs2854116, APOC3-rs2854117, PPP1R3B-rs4240624, PPP1R3B-rs4841132, and TM6SF2-rs58542926 were significantly associated with the risk of MetS. The cumulative impact of T alleles of ApoE-rs429358 and TM6SF2-rs58542926 on the risk of FL was observed (p-value for trend < 0.001). Individuals without MetS and airflow limitation carrying LEPR-rs1805096 G_G genotype exhibited a reduction in the forced expiratory volume in 1 s percentage prediction (Coefficient -35, 95 % confidence interval (CI) -69.7- -0.4), low forced vital capacity percentage prediction (Coefficient -41.6, 95 % CI -82.6- -0.6), and low vital capacity percentage prediction (Coefficient -42.2, 95 % CI -84.2- -0.1). CONCLUSIONS MetS significantly correlated with FL and airflow limitation. Multiple SNPs were notably associated with MetS. Specifically, T alleles of ApoE-rs429358 and TM6SF2-rs58542926 cumulatively increased the risk of FL. LEPR-rs1805096 shows a trend-wise association with pulmonary function, which is significant in patients without MetS or airflow limitation.
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Affiliation(s)
- Hsiao-Chin Shen
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan; Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Mei-Hung Pan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Jen Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiao-Yun Yeh
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Taiwan; Doctoral Program of Clinical and Experimental Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Yi-Hsuan Lin
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-Chang Huang
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan; Department of Internal Medicine, Division of Endocrinology and Metabolism, Taipei Veterans General Hospital, Taiwan
| | - Kuei-Chuan Lee
- Faculty of Medicine, School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan; Department of Internal Medicine, Division of Gastroenterology and Hepatology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ying-Ying Yang
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan; Department of Internal Medicine, Division of Gastroenterology and Hepatology, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Ming-Chih Hou
- Faculty of Medicine, School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan; Department of Internal Medicine, Division of Gastroenterology and Hepatology, Taipei Veterans General Hospital, Taipei, Taiwan
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Lim AMW, Lim EU, Chen PL, Fann CSJ. Unsupervised clustering identified clinically relevant metabolic syndrome endotypes in UK and Taiwan Biobanks. iScience 2024; 27:109815. [PMID: 39040048 PMCID: PMC11260869 DOI: 10.1016/j.isci.2024.109815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/02/2024] [Accepted: 04/23/2024] [Indexed: 07/24/2024] Open
Abstract
Metabolic syndrome (MetS) is a collection of cardiovascular risk factors; however, the high prevalence and heterogeneity impede effective clinical management. We conducted unsupervised clustering on individuals from UK Biobank to reveal endotypes. Five MetS subgroups were identified: Cluster 1 (C1): non-descriptive, Cluster 2 (C2): hypertensive, Cluster 3 (C3): obese, Cluster 4 (C4): lipodystrophy-like, and Cluster 5 (C5): hyperglycemic. For all of the endotypes, we identified the corresponding cardiometabolic traits and their associations with clinical outcomes. Genome-wide association studies (GWASs) were conducted to identify associated genotypic traits. We then determined endotype-specific genotypic traits and constructed polygenic risk score (PRS) models specific to each endotype. GWAS of each MetS clusters revealed different genotypic traits. C1 GWAS revealed novel findings of TRIM63, MYBPC3, MYLPF, and RAPSN. Intriguingly, C1, C3, and C4 were associated with genes highly expressed in brain tissues. MetS clusters with comparable phenotypic and genotypic traits were identified in Taiwan Biobank.
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Affiliation(s)
- Aylwin Ming Wee Lim
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112304, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- ASUS Intelligent Cloud Services (AICS), Taipei 112, Taiwan
| | - Evan Unit Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei 10617, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Cathy Shen Jang Fann
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112304, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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Sheu JJC, Lin WY, Liu TY, Chang CYY, Cheng J, Li YH, Chen CM, Tseng CC, Ding WY, Chung C, Hwang T, Chen PH, Tsai FJ. Ethnic-specific genetic susceptibility loci for endometriosis in Taiwanese-Han population: a genome-wide association study. J Hum Genet 2024:10.1038/s10038-024-01270-5. [PMID: 38982179 DOI: 10.1038/s10038-024-01270-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 06/18/2024] [Accepted: 06/23/2024] [Indexed: 07/11/2024]
Abstract
Endometriosis is a common gynecological disorder affecting around 10% of reproductive-age women. Although many hypotheses were proposed, genetic alteration has been considered as one of the key factors promoting pathogenesis. Due to racial/ethnic disparities in the process of hormone regulation and nutrition metabolism, a genome-wide association study (GWAS) with 2794 cases and 27,940 controls was conducted in a Taiwanese-Han population. Our study identified five significant susceptibility loci for endometriosis, and three of them, WNT4 (on the 1p36.12), RMND1 (6q25.1), and CCDC170 (6q25.1), have been previously associated with endometriosis across different populations, including European and Japanese descent cohorts. Other two including C5orf66/C5orf66-AS2 (5q31.1) and STN1 (10q24.33) are newly identified ones. Functional network analysis of potent risk genes revealed the involvement of cancer susceptibility and neurodevelopmental disorders in endometriosis development. In addition, long non-coding RNAs (lncRNAs) C5orf66 and C5orf66-AS2 can interact with many RNA-binding proteins (RBPs) which can influence RNA metabolic process, mRNA stabilization, and mRNA splicing, leading to dysregulation in tumor-promoting gene expression. Those findings support clinical observations of differences in the presentation of endometriosis in Taiwanese-Han population with higher risks of developing deeply infiltrating/invasive lesions and the associated malignancies.
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Affiliation(s)
- Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yatsen University, Kaohsiung, 804201, Taiwan
- Institute of Biopharmaceutical Sciences, National Sun Yatsen University, Kaohsiung, 804201, Taiwan
- Institute of Precision Medicine, National Sun Yatsen University, Kaohsiung, 804201, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, 404333, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, 807378, Taiwan
| | - Wei-Yong Lin
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, 404333, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Ting-Yuan Liu
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Cherry Yin-Yi Chang
- Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung, 404327, Taiwan
- Department of Medicine, School of Medicine, China Medical University, Taichung, 404333, Taiwan
| | - Jack Cheng
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Yau-Hong Li
- Institute of Biomedical Sciences, National Sun Yatsen University, Kaohsiung, 804201, Taiwan
- Department of Obstetrics and Gynecology, Pingtung Veterans General Hospital, Pingtung, 900053, Taiwan
| | - Chih-Mei Chen
- Genetics Center, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Chung-Chen Tseng
- Institute of Biomedical Sciences, National Sun Yatsen University, Kaohsiung, 804201, Taiwan
| | - Wendy Yarou Ding
- Genetics Center, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Ching Chung
- Genetics Center, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Tritium Hwang
- Institute of Biomedical Sciences, National Sun Yatsen University, Kaohsiung, 804201, Taiwan
| | - Ping-Ho Chen
- Institute of Biomedical Sciences, National Sun Yatsen University, Kaohsiung, 804201, Taiwan
- School of Dentistry, Kaohsiung Medical University, Kaohsiung, 807378, Taiwan
| | - Fuu-Jen Tsai
- School of Chinese Medicine, China Medical University, Taichung, 404333, Taiwan.
- Genetics Center, China Medical University Hospital, Taichung, 404327, Taiwan.
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Lin WY. Detecting gene-environment interactions from multiple continuous traits. Bioinformatics 2024; 40:btae419. [PMID: 38917408 PMCID: PMC11254352 DOI: 10.1093/bioinformatics/btae419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 06/27/2024] Open
Abstract
MOTIVATION Genetic variants present differential effects on humans according to various environmental exposures, the so-called "gene-environment interactions" (GxE). Many diseases can be diagnosed with multiple traits, such as obesity, diabetes, and dyslipidemia. I developed a multivariate scale test (MST) for detecting the GxE of a disease with several continuous traits. Given a significant MST result, I continued to search for which trait and which E enriched the GxE signals. Simulation studies were performed to compare MST with the univariate scale test (UST). RESULTS MST can gain more power than UST because of (1) integrating more traits with GxE information and (2) the less harsh penalty on multiple testing. However, if only few traits account for GxE, MST may lose power due to aggregating non-informative traits into the test statistic. As an example, MST was applied to a discovery set of 93 708 Taiwan Biobank (TWB) individuals and a replication set of 25 200 TWB individuals. From among 2 570 487 SNPs with minor allele frequencies ≥5%, MST identified 18 independent variance quantitative trait loci (P < 2.4E-9 in the discovery cohort and P < 2.8E-5 in the replication cohort) and 41 GxE signals (P < .00027) based on eight trait domains (including 29 traits). AVAILABILITY AND IMPLEMENTATION https://github.com/WanYuLin/Multivariate-scale-test-MST.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei 100, Taiwan
- Master of Public Health Degree Program, College of Public Health, National Taiwan University, Taipei 100, Taiwan
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Lin WD, Liao WL, Chen WC, Liu TY, Chen YC, Tsai FJ. Genome-wide association study identifies novel susceptible loci and evaluation of polygenic risk score for chronic obstructive pulmonary disease in a Taiwanese population. BMC Genomics 2024; 25:607. [PMID: 38886662 PMCID: PMC11184693 DOI: 10.1186/s12864-024-10526-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) describes a group of progressive lung diseases causing breathing difficulties. While COPD development typically involves a complex interplay between genetic and environmental factors, genetics play a role in disease susceptibility. This study used genome-wide association studies (GWAS) and polygenic risk score (PRS) to elucidate the genetic basis for COPD in Taiwanese patients. RESULTS GWAS was performed on a Taiwanese COPD case-control cohort with a sample size of 5,442 cases and 17,681 controls. Additionally, the PRS was calculated and assessed in our target groups. GWAS results indicate that although there were no single nucleotide polymorphisms (SNPs) of genome-wide significance, prominent COPD susceptibility loci on or nearby genes such as WWTR1, EXT1, INTU, MAP3K7CL, MAMDC2, BZW1/CLK1, LINC01197, LINC01894, and CFAP95 (C9orf135) were identified, which had not been reported in previous studies. Thirteen susceptibility loci, such as CHRNA4, AFAP1, and DTWD1, previously reported in other populations were replicated and confirmed to be associated with COPD in Taiwanese populations. The PRS was determined in the target groups using the summary statistics from our base group, yielding an effective association with COPD (odds ratio [OR] 1.09, 95% confidence interval [CI] 1.02-1.17, p = 0.011). Furthermore, replication a previous lung function trait PRS model in our target group, showed a significant association of COPD susceptibility with PRS of Forced Expiratory Volume in one second (FEV1)/Forced Vital Capacity (FCV) (OR 0.89, 95% CI 0.83-0.95, p = 0.001). CONCLUSIONS Novel COPD-related genes were identified in the studied Taiwanese population. The PRS model, based on COPD or lung function traits, enables disease risk estimation and enhances prediction before suffering. These results offer new perspectives on the genetics of COPD and serve as a basis for future research.
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Affiliation(s)
- Wei-De Lin
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, 404333, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 404333, Taiwan
- Center for Personalized Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Wei-Cheng Chen
- Department of Internal Medicine, Pulmonary and Critical Care Medicine, China Medical University Hospital, Taichung, 404333, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404327, Taiwan
| | - Ting-Yuan Liu
- Department of Medical Research, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Yu-Chia Chen
- Department of Medical Research, Million-Person Precision Medicine Initiative, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan.
- School of Chinese Medicine, China Medical University, Taichung, 404333, Taiwan.
- Division of Genetics and Metabolism, China Medical University Children's Hospital, Taichung, 404327, Taiwan.
- Department of Medical Genetics, China Medical University Hospital, Taichung, 404327, Taiwan.
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, 413305, Taiwan.
- Department of Medical Research, China Medical University Hospital, No. 2, Yude Road, North District, Taichung, 404327, Taiwan.
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Capalbo A, de Wert G, Mertes H, Klausner L, Coonen E, Spinella F, Van de Velde H, Viville S, Sermon K, Vermeulen N, Lencz T, Carmi S. Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations. Hum Reprod Update 2024:dmae012. [PMID: 38805697 DOI: 10.1093/humupd/dmae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The genetic composition of embryos generated by in vitro fertilization (IVF) can be examined with preimplantation genetic testing (PGT). Until recently, PGT was limited to detecting single-gene, high-risk pathogenic variants, large structural variants, and aneuploidy. Recent advances have made genome-wide genotyping of IVF embryos feasible and affordable, raising the possibility of screening embryos for their risk of polygenic diseases such as breast cancer, hypertension, diabetes, or schizophrenia. Despite a heated debate around this new technology, called polygenic embryo screening (PES; also PGT-P), it is already available to IVF patients in some countries. Several articles have studied epidemiological, clinical, and ethical perspectives on PES; however, a comprehensive, principled review of this emerging field is missing. OBJECTIVE AND RATIONALE This review has four main goals. First, given the interdisciplinary nature of PES studies, we aim to provide a self-contained educational background about PES to reproductive specialists interested in the subject. Second, we provide a comprehensive and critical review of arguments for and against the introduction of PES, crystallizing and prioritizing the key issues. We also cover the attitudes of IVF patients, clinicians, and the public towards PES. Third, we distinguish between possible future groups of PES patients, highlighting the benefits and harms pertaining to each group. Finally, our review, which is supported by ESHRE, is intended to aid healthcare professionals and policymakers in decision-making regarding whether to introduce PES in the clinic, and if so, how, and to whom. SEARCH METHODS We searched for PubMed-indexed articles published between 1/1/2003 and 1/3/2024 using the terms 'polygenic embryo screening', 'polygenic preimplantation', and 'PGT-P'. We limited the review to primary research papers in English whose main focus was PES for medical conditions. We also included papers that did not appear in the search but were deemed relevant. OUTCOMES The main theoretical benefit of PES is a reduction in lifetime polygenic disease risk for children born after screening. The magnitude of the risk reduction has been predicted based on statistical modelling, simulations, and sibling pair analyses. Results based on all methods suggest that under the best-case scenario, large relative risk reductions are possible for one or more diseases. However, as these models abstract several practical limitations, the realized benefits may be smaller, particularly due to a limited number of embryos and unclear future accuracy of the risk estimates. PES may negatively impact patients and their future children, as well as society. The main personal harms are an unindicated IVF treatment, a possible reduction in IVF success rates, and patient confusion, incomplete counselling, and choice overload. The main possible societal harms include discarded embryos, an increasing demand for 'designer babies', overemphasis of the genetic determinants of disease, unequal access, and lower utility in people of non-European ancestries. Benefits and harms will vary across the main potential patient groups, comprising patients already requiring IVF, fertile people with a history of a severe polygenic disease, and fertile healthy people. In the United States, the attitudes of IVF patients and the public towards PES seem positive, while healthcare professionals are cautious, sceptical about clinical utility, and concerned about patient counselling. WIDER IMPLICATIONS The theoretical potential of PES to reduce risk across multiple polygenic diseases requires further research into its benefits and harms. Given the large number of practical limitations and possible harms, particularly unnecessary IVF treatments and discarded viable embryos, PES should be offered only within a research context before further clarity is achieved regarding its balance of benefits and harms. The gap in attitudes between healthcare professionals and the public needs to be narrowed by expanding public and patient education and providing resources for informative and unbiased genetic counselling.
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Affiliation(s)
- Antonio Capalbo
- Juno Genetics, Department of Reproductive Genetics, Rome, Italy
- Center for Advanced Studies and Technology (CAST), Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics & Society, CAPHRI-School for Public Health and Primary Care and GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Ghent University, Ghent, Belgium
- Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
| | - Liraz Klausner
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edith Coonen
- Departments of Clinical Genetics and Reproductive Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - Francesca Spinella
- Eurofins GENOMA Group Srl, Molecular Genetics Laboratories, Department of Scientific Communication, Rome, Italy
| | - Hilde Van de Velde
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
- Brussels IVF, UZ Brussel, Brussel, Belgium
| | - Stephane Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, France
- Laboratoire de Diagnostic Génétique, Unité de Génétique de l'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Karen Sermon
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
| | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Liao WL, Huang YC, Chang YW, Cheng CF, Liu TY, Lu HF, Chen HL, Tsai FJ. Impact of polygenic risk score for triglyceride trajectory and diabetic complications in subjects with type 2 diabetes based on large electronic medical record data from Taiwan: a case control study. J Endocrinol Invest 2024:10.1007/s40618-024-02397-0. [PMID: 38795312 DOI: 10.1007/s40618-024-02397-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/15/2024] [Indexed: 05/27/2024]
Abstract
BACKGROUND The prevalence of diabetic dyslipidemia has gradually increased worldwide and individuals with hypertriglyceridemia often have a high polygenic burden of triglyceride (TG)-increasing variants. However, the contribution of genetic variants to dyslipidemia in patients with type 2 diabetes (T2D) remains limited. Therefore, in this study, we aimed to investigate the genetic characteristics of longitudinal changes in TG levels among patients with T2D and summarize the genetic effects of polygenic risk score (PRS) on TG trajectory and risk of diabetic complications. METHODS We conducted a case-control study. A total of 11,312 patients with T2D with longitudinal TG and genetic data were identified from a large hospital database in Taiwan. We then performed a genome-wide association study and calculated the relative PRS. RESULTS In total, 21 single-nucleotide polymorphisms (SNPs) related to TG trajectory were identified and yielded an area under the receiver operating characteristic curve (ROC) of 0.712 for high TG trajectory risk among Taiwanese patients with T2D. A cumulative genetic effect was observed for high TG trajectory, even when considering the adherence of a lipid-lowering agent in stratified analysis. An increased PRS increases high TG trajectory risk in a logistic regression model (odds ratio = 1.55; 95% confidence interval [CI] = 1.31-1.83 in the validation cohort). The TG-specific PRS was associated with the risk of diabetic microvascular complications, including diabetic retinopathy and nephropathy (with hazard ratios of 1.11 [95% CI = 1.01-1.21, P = 0.027] and 1.05 [95% CI = 1.01-1.1, P = 0.018], respectively). CONCLUSIONS This study may contribute to the identification of patients with T2D who are at risk of abnormal TG levels and diabetic microvascular complications using polygenic information.
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Affiliation(s)
- W-L Liao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
- Center for Personalized Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Y-C Huang
- School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Y-W Chang
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
- Center for Personalized Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - C-F Cheng
- Big Data Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - T-Y Liu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - H-F Lu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - H-L Chen
- Big Data Center, China Medical University Hospital, Taichung, 40447, Taiwan
| | - F-J Tsai
- School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan.
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan.
- Division of Medical Genetics, China Medical University Children's Hospital, Taichung, 40447, Taiwan.
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, 413305, Taiwan.
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Hung SC, Chang LW, Hsiao TH, Lin GC, Wang SS, Li JR, Chen IC. Polygenic risk score predicting susceptibility and outcome of benign prostatic hyperplasia in the Han Chinese. Hum Genomics 2024; 18:49. [PMID: 38778357 PMCID: PMC11110300 DOI: 10.1186/s40246-024-00619-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Given the high prevalence of BPH among elderly men, pinpointing those at elevated risk can aid in early intervention and effective management. This study aimed to explore that polygenic risk score (PRS) is effective in predicting benign prostatic hyperplasia (BPH) incidence, prognosis and risk of operation in Han Chinese. METHODS A retrospective cohort study included 12,474 male participants (6,237 with BPH and 6,237 non-BPH controls) from the Taiwan Precision Medicine Initiative (TPMI). Genotyping was performed using the Affymetrix Genome-Wide TWB 2.0 SNP Array. PRS was calculated using PGS001865, comprising 1,712 single nucleotide polymorphisms. Logistic regression models assessed the association between PRS and BPH incidence, adjusting for age and prostate-specific antigen (PSA) levels. The study also examined the relationship between PSA, prostate volume, and response to 5-α-reductase inhibitor (5ARI) treatment, as well as the association between PRS and the risk of TURP. RESULTS Individuals in the highest PRS quartile (Q4) had a significantly higher risk of BPH compared to the lowest quartile (Q1) (OR = 1.51, 95% CI = 1.274-1.783, p < 0.0001), after adjusting for PSA level. The Q4 group exhibited larger prostate volumes and a smaller volume reduction after 5ARI treatment. The Q1 group had a lower cumulative TURP probability at 3, 5, and 10 years compared to the Q4 group. PRS Q4 was an independent risk factor for TURP. CONCLUSIONS In this Han Chinese cohort, higher PRS was associated with an increased susceptibility to BPH, larger prostate volumes, poorer response to 5ARI treatment, and a higher risk of TURP. Larger prospective studies with longer follow-up are warranted to further validate these findings.
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Affiliation(s)
- Sheng-Chun Hung
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Li-Wen Chang
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Guan-Cheng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shian-Shiang Wang
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Jian-Ri Li
- Division of Urology, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medicine and Nursing, Hungkuang University, Taichung, Taiwan
| | - I-Chieh Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.
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Chang FY, Huang CH, Yang CH, Chang JT, Yang CM, Ho TC, Hsieh YT, Lai TT, Lin CW, Lin CP, Chen YC, Lai YJ, Chen PL, Hsu JS, Chen TC. Genetics in neovascular age-related macular degeneration susceptibility and treatment response to anti-VEGF intravitreal injection: A case series study. Clin Exp Ophthalmol 2024. [PMID: 38757252 DOI: 10.1111/ceo.14388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/24/2024] [Accepted: 05/04/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND To identify genotypes associated with neovascular age-related macular degeneration (nAMD) and investigate the associations between genotype variations and anti-vascular endothelial growth factor (VEGF) treatment response. METHODS This observational, retrospective, case series study enrolled patients diagnosed with nAMD who received anti-VEGF treatment in National Taiwan University Hospital with at least one-year follow-up between 2012 and 2020. A genome-wide association study (GWAS) was conducted on enrolled patients and controls. Correlations between the genotypes identified from GWAS and the treatment response of functional/anatomical biomarkers, including visual acuity (VA), presence of intraretinal or subretinal fluid (SRF), serous or fibrovascular pigmented epithelium detachment (PED), and disruption of the ellipsoid zone (EZ), were analysed. RESULTS In total, 182 patients with nAMD and 1748 controls were enrolled. GWAS revealed 16 single nucleotide polymorphisms (SNPs) as risk loci for nAMD, including seven loci in CFH and ARMS2/HTRA1 and nine novel loci, including rs117517872 and rs79835234(COPB2-DT), rs7525578(RAP1A), rs2123738(LOC105376755), rs1374879(CNTN3), rs3812692(SAR1A), rs117501587(PRKCA), rs9965945(CNDP1), and rs189769231(MATK). Our study revealed rs800292(CFH), rs11200638(HTRA1), and rs2123738(LOC105376755) correlated with poor treatment response in VA (P = 0.005), SRF (P = 0.044), and fibrovascular PED (P = 0.007), respectively. Rs9965945(CNDP1) was correlated with poor response in disruption of EZ (P = 0.046) and serous PED (P = 0.049). CONCLUSIONS Among the 16 SNPs found in the GWAS, four loci-CFH, ARMS2/HTRA1, and two novel loci-were correlated with the susceptibility of nAMD and anatomical/functional responses after anti-VEGF treatment.
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Affiliation(s)
- Fang-Yu Chang
- College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chu-Hsuan Huang
- Department of Ophthalmology, Cathay General Hospital, Taipei, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chang-Hao Yang
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jung-Tzu Chang
- Department of Ophthalmology, Cathay General Hospital, Taipei, Taiwan
| | - Chung-May Yang
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tzzy-Chang Ho
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Ting Hsieh
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tso-Ting Lai
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chao-Wen Lin
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chang-Pin Lin
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Chieh Chen
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ying-Ju Lai
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ta-Ching Chen
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Center of Frontier Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
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10
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Chou WH, Chen LC, Wong HSC, Chao CH, Chu HW, Chang WC. Phenomic landscape and pharmacogenomic implications for HLA region in a Taiwan Han Chinese population. Biomark Res 2024; 12:46. [PMID: 38702819 PMCID: PMC11067262 DOI: 10.1186/s40364-024-00591-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The human leukocyte antigen (HLA) genes, exhibiting significant genetic diversity, are associated with susceptibility to various clinical diseases and diverse in drug responses. High costs of HLA sequencing and the population-specific architecture of this genetic region necessitate the establishment of a population-specific HLA imputation reference panel. Moreover, there is a lack of understanding about the genetic and phenotypic landscape of HLA variations within the Taiwanese population. METHODS We created models for a Taiwanese-specific HLA imputation reference panel. These models were trained with the array genotype data and HLA sequencing data from 845 Taiwanese subjects. HLA imputation was applied for 59,448 Taiwanese subjects to characterize the HLA allele and haplotype frequencies. Additionally, a phenome-wide association study (PheWAS) was conducted to identify the phenotypes associated with HLA variations. The association of the biallelic HLA variants with the binary and quantitative traits were evaluated with additive logistic and linear regression models, respectively. Furthermore, an omnibus test with likelihood-ratio test was applied for each HLA amino acid position in the multiallelic HLA amino acid polymorphisms to compare the difference between a fitted model and a null model following a χ2 distribution of n-1 degree of freedom at a position with n residues. Finally, we estimated the prevalence of adverse drug reactions (ADR)-related HLA alleles in the Taiwanese population. RESULTS In this study, the reference panel models displayed remarkable accuracy, with averages of 99.3%, 98.9%, and 99.1% for 2-, 4-, 6-digit alleles of the eight classical HLA genes, respectively. For PheWAS, a total of 18,136 significant associations with HLA variants across 26 phenotypes are identified (p < 5×10-8), highlighting the pleiotropy feature of the HLA region. Among the independent signals, 15 are novel, including the association of HLA-B pos 138 variation with ankylosing spondylitis (AS), and rs9266290 and rs9266292 with allergy. Through an analysis spanning the entire HLA region, we identified clusters of phenotype correlations. Finally, the carriers of pharmacogenomic related HLA alleles, including HLA-C*01:02 (35.86%), HLA-B*58:01 (20.9%), and HLA-B*15:02 (8.38%), were characterized in the Taiwanese general population. CONCLUSIONS We successfully delivered the HLA imputation for 59,448 Taiwanese subjects and characterized the genetic and phenotypic landscapes of the HLA variations. In addition, we quantified the estimated prevalence of the ADR-related HLA alleles in the Taiwanese population. The developed HLA imputation reference panel could be used for estimation of population HLA allele frequencies, which can facilitate further studies in the role of HLA variants in a wider range of phenotypes in the population.
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Affiliation(s)
- Wan-Hsuan Chou
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Lu-Chun Chen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Henry Sung-Ching Wong
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Ching-Hsuan Chao
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Department of Pharmacology, National Defense Medical Center, Taipei, Taiwan.
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11
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Cahoon JL, Rui X, Tang E, Simons C, Langie J, Chen M, Lo YC, Chiang CWK. Imputation accuracy across global human populations. Am J Hum Genet 2024; 111:979-989. [PMID: 38604166 PMCID: PMC11080279 DOI: 10.1016/j.ajhg.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
Genotype imputation is now fundamental for genome-wide association studies but lacks fairness due to the underrepresentation of references from non-European ancestries. The state-of-the-art imputation reference panel released by the Trans-Omics for Precision Medicine (TOPMed) initiative improved the imputation of admixed African-ancestry and Hispanic/Latino samples, but imputation for populations primarily residing outside of North America may still fall short in performance due to persisting underrepresentation. To illustrate this point, we imputed the genotypes of over 43,000 individuals across 123 populations around the world and identified numerous populations where imputation accuracy paled in comparison to that of European-ancestry populations. For instance, the mean imputation r-squared (Rsq) for variants with minor allele frequencies between 1% and 5% in Saudi Arabians (n = 1,061), Vietnamese (n = 1,264), Thai (n = 2,435), and Papua New Guineans (n = 776) were 0.79, 0.78, 0.76, and 0.62, respectively, compared to 0.90-0.93 for comparable European populations matched in sample size and SNP array content. Outside of Africa and Latin America, Rsq appeared to decrease as genetic distances to European-ancestry reference increased, as predicted. Using sequencing data as ground truth, we also showed that Rsq may over-estimate imputation accuracy for non-European populations more than European populations, suggesting further disparity in accuracy between populations. Using 1,496 sequenced individuals from Taiwan Biobank as a second reference panel to TOPMed, we also assessed a strategy to improve imputation for non-European populations with meta-imputation, but this design did not improve accuracy across frequency spectra. Taken together, our analyses suggest that we must ultimately strive to increase diversity and size to promote equity within genetics research.
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Affiliation(s)
- Jordan L Cahoon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA; Department of Computer Science, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Echo Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Christopher Simons
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Ying-Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA.
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12
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Wang SH, Huang YC, Cheng CW, Chang YW, Liao WL. Impact of the trans-ancestry polygenic risk score on type 2 diabetes risk, onset age and progression among population in Taiwan. Am J Physiol Endocrinol Metab 2024; 326:E547-E554. [PMID: 38363735 DOI: 10.1152/ajpendo.00252.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Type 2 diabetes (T2D) prevalence in adults at a younger age has increased but the disease status may go unnoticed. This study aimed to determine whether the onset age and subsequent diabetic complications can be attributed to the polygenic architecture of T2D in the Taiwan Han population. A total of 9,627 cases with T2D and 85,606 controls from the Taiwan Biobank were enrolled. Three diabetic polygenic risk scores (PRSs), PRS_EAS and PRS_EUR, and a trans-ancestry PRS (PRS_META), calculated using summary statistic from East Asian and European populations. The onset age was identified by linking to the National Taiwan Insurance Research Database, and the incidence of different diabetic complications during follow-up was recorded. PRS_META (7.4%) explained a higher variation for T2D status. And the higher percentile of PRS is also correlated with higher percentage of T2D family history and prediabetes status. More, the PRS was negatively associated with onset age (β = -0.91 yr), and this was more evident among males (β = -1.11 vs. -0.76 for males and females, respectively). The hazard ratio of diabetic retinopathy (DR) and diabetic foot were significantly associated with PRS_EAS and PRS_META, respectively. However, the PRS was not associated with other diabetic complications, including diabetic nephropathy, cardiovascular disease, and hypertension. Our findings indicated that diabetic PRS which combined susceptibility variants from cross-population could be used as a tool for early screening of T2D, especially for high-risk populations, such as individuals with high genetic risk, and may be associated with the risk of complications in subjects with T2D. NEW & NOTEWORTHY Our findings indicated that diabetic polygenic risk score (PRS) which combined susceptibility variants from Asian and European population affect the onset age of type 2 diabetes (T2D) and could be used as a tool for early screening of T2D, especially for individuals with high genetic risk, and may be associated with the risk of diabetic complications among people in Taiwan.
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Affiliation(s)
- Shi-Heng Wang
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Zhunan, Taiwan
- Department of Public Health, China Medical University, Taichung, Taiwan
| | - Yu-Chuen Huang
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chun-Wen Cheng
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Ya-Wen Chang
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Center for Personalized Medicine, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Center for Personalized Medicine, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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13
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Hsu CC, Chuang HK, Hsiao YJ, Chiang PH, Chen SW, Luo WT, Yang YP, Tsai PH, Chen SJ, Hsieh AR, Chiou SH. Predicting Risks of Dry Eye Disease Development Using a Genome-Wide Polygenic Risk Score Model. Transl Vis Sci Technol 2024; 13:13. [PMID: 38767906 PMCID: PMC11114613 DOI: 10.1167/tvst.13.5.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/20/2024] [Indexed: 05/22/2024] Open
Abstract
Purpose The purpose of this study was to conduct a large-scale genome-wide association study (GWAS) and construct a polygenic risk score (PRS) for risk stratification in patients with dry eye disease (DED) using the Taiwan Biobank (TWB) databases. Methods This retrospective case-control study involved 40,112 subjects of Han Chinese ancestry, sourced from the publicly available TWB. Cases were patients with DED (n = 14,185), and controls were individuals without DED (n = 25,927). The patients with DED were further divided into 8072 young (<60 years old) and 6113 old participants (≥60 years old). Using PLINK (version 1.9) software, quality control was carried out, followed by logistic regression analysis with adjustments for sex, age, body mass index, depression, and manic episodes as covariates. We also built PRS prediction models using the standard clumping and thresholding method and evaluated their performance (area under the curve [AUC]) through five-fold cross-validation. Results Eleven independent risk loci were identified for these patients with DED at the genome-wide significance levels, including DNAJB6, MAML3, LINC02267, DCHS1, SIRPB3P, HULC, MUC16, GAS2L3, and ZFPM2. Among these, MUC16 encodes mucin family protein. The PRS model incorporated 932 and 740 genetic loci for young and old populations, respectively. A higher PRS score indicated a greater DED risk, with the top 5% of PRS individuals having a 10-fold higher risk. After integrating these covariates into the PRS model, the area under the receiver operating curve (AUROC) increased from 0.509 and 0.537 to 0.600 and 0.648 for young and old populations, respectively, demonstrating the genetic-environmental interaction. Conclusions Our study prompts potential candidates for the mechanism of DED and paves the way for more personalized medication in the future. Translational Relevance Our study identified genes related to DED and constructed a PRS model to improve DED prediction.
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Affiliation(s)
- Chih-Chien Hsu
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hao-Kai Chuang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Jer Hsiao
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pin-Hsuan Chiang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Szu-Wen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Wei-Ting Luo
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shih-Jen Chen
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei City, Taiwan
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan
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Wang CH, Huang YN, Liao WL, Hsieh AR, Lin WD, Liu KW, Lu WL, Huang CC, Chien YH, Lee NC, Su PH, Tsai FJ. GBA1 as a risk gene for osteoporosis in the specific populations and its role in the development of Gaucher disease. Orphanet J Rare Dis 2024; 19:144. [PMID: 38575988 PMCID: PMC10993575 DOI: 10.1186/s13023-024-03132-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: 08/30/2023] [Accepted: 03/03/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Osteoporosis and its primary complication, fragility fractures, contribute to substantial global morbidity and mortality. Gaucher disease (GD) is caused by glucocerebrosidase (GBA1) deficiency, leading to skeletal complications. This study aimed to investigate the impact of the GBA1 gene on osteoporosis progression in GD patients and the specific populations. METHODS We selected 8115 patients with osteoporosis (T-score ≤ - 2.5) and 55,942 healthy individuals (T-score > - 1) from a clinical database (N = 95,223). Monocytes from GD patients were evaluated in relation to endoplasmic reticulum (ER) stress, inflammasome activation, and osteoclastogenesis. An in vitro model of GD patient's cells treated with adeno-associated virus 9 (AAV9)-GBA1 to assess GBA1 enzyme activity, chitotriosidase activity, ER stress, and osteoclast differentiation. Longitudinal dual-energy X-ray absorptiometry (DXA) data tracking bone density in patients with Gaucher disease (GD) undergoing enzyme replacement therapy (ERT) over an extended period. RESULTS The GBA1 gene variant rs11264345 was significantly associated [P < 0.002, Odds Ratio (OR) = 1.06] with an increased risk of bone disease. Upregulation of Calnexin, NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) and Apoptosis-associated speck-like protein containing a C-terminal caspase recruitment domain (ASC) was positively associated with osteoclastogenesis in patients with GD. In vitro AAV9-GBA1 treatment of GD patient cells led to enhanced GBA1 enzyme activity, reduced chitotriosidase activity, diminished ER stress, and decreased osteoclast differentiation. Long-term bone density data suggests that initiating ERT earlier in GD leads to greater improvements in bone density. CONCLUSIONS Elevated ER stress and inflammasome activation are indicative of osteoporosis development, suggesting the need for clinical monitoring of patients with GD. Furthermore, disease-associated variant in the GBA1 gene may constitute a risk factor predisposing specific populations to osteoporosis.
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Affiliation(s)
- Chung-Hsing Wang
- Division of Genetics and Metabolism, Children's Hospital of China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
- Department of Pediatrics, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., South Dist., Taichung, 402306, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Nan Huang
- Department of Pediatrics, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., South Dist., Taichung, 402306, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Department of Medical Research, Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei City, Taiwan
| | - Wei-De Lin
- Department of Medical Research, Genetic Center, China Medical University Hospital, No. 2 Yuh-Der Road, Taichung, 404, Taiwan
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Kai-Wen Liu
- Division of Genetics and Metabolism, Children's Hospital of China Medical University, Taichung, Taiwan
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Wen-Li Lu
- Division of Genetics and Metabolism, Children's Hospital of China Medical University, Taichung, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pen-Hua Su
- Department of Pediatrics, Chung Shan Medical University Hospital, No. 110, Sec. 1, Jianguo N. Rd., South Dist., Taichung, 402306, Taiwan.
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.
| | - Fuu-Jen Tsai
- Division of Genetics and Metabolism, Children's Hospital of China Medical University, Taichung, Taiwan.
- Department of Medical Research, Genetic Center, China Medical University Hospital, No. 2 Yuh-Der Road, Taichung, 404, Taiwan.
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15
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Shim SM, Lee M, Jeon JP. Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality. Biopreserv Biobank 2024. [PMID: 38563611 DOI: 10.1089/bio.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.
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Affiliation(s)
- Sung-Mi Shim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Meehee Lee
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae-Pil Jeon
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
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16
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Su WC, Juan HL, Lee JI, Huang SP, Chen SC, Geng JH. Secondhand smoke increases the risk of developing chronic obstructive pulmonary disease. Sci Rep 2024; 14:7481. [PMID: 38553570 PMCID: PMC10980762 DOI: 10.1038/s41598-024-58038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Smoking is the most important risk factor for chronic obstructive pulmonary disease (COPD), however evidence from large-scale studies on whether secondhand smoke (SHS) increases the risk of COPD is still lacking. We conducted this large longitudinal study to investigate the association between SHS and the development of COPD. This is a longitudinal study. Data on 6519 subjects who were never-smokers, had no history of COPD, and had complete lung function records were extracted from the Taiwan Biobank. They were divided into two groups according to SHS exposure: no exposure and exposure groups. Data were collected when participants enrolled in the study and during regular follow-up. Cox proportional hazards regression models were used to estimate the relative risk (RR) and 95% confidence interval (CI) for the association between SHS and the risk of developing COPD. At 48 months of follow-up, 260 (4%) participants in the no exposure group and 34 (7%) participants in the exposure group developed COPD. The RR of incident COPD development was significantly higher in the exposure group than that in the no exposure group after adjusting for confounders (RR = 1.49; 95% CI 1.04 to 2.14; P value = 0.031). There is a dose-response relationship between the duration of exposure to SHS and the risk of incident COPD, which demonstrates that an additional hour of exposure to SHS per week was associated with a 1.03-fold increased likelihood of developing COPD after adjusting for confounders (RR = 1.03; 95% CI 1.00 to 1.05; P value = 0.027). SHS exposure contributes to the development of COPD. This finding can help raise awareness of the harms of SHS and provide a reference for formulating anti-smoking policies.
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Affiliation(s)
- Wen-Chi Su
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Huai-Lei Juan
- Department of Internal Medicine, Kaohsiung Municipal Siaogang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jia-In Lee
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Pin Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Ph.D. Program in Environmental and Occupational Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Medical Science and Technology, College of Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Szu-Chia Chen
- Department of Internal Medicine, Kaohsiung Municipal Siaogang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jiun-Hung Geng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Department of Urology, Kaohsiung Municipal Siaogang Hospital, No. 482, Shanming Rd, Xiaogang District, Kaohsiung City, 812, Taiwan.
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17
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Lu HF, Chou CH, Lin YJ, Uchiyama S, Terao C, Wang YW, Yang JS, Liu TY, Wong HSC, Chen SCC, Tsai FJ. The genome-wide association study of serum IgE levels demonstrated a shared genetic background in allergic diseases. Clin Immunol 2024; 260:109897. [PMID: 38199299 DOI: 10.1016/j.clim.2024.109897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Immunoglobulin E (IgE) synthessis is highly related to a variety of atopic diseases, and several genome-wide association studies (GWASs) have demonstrated the association between genes and IgE level. In this study, we conducted the largest genome-wide association study of IgE involving a Taiwanese Han population. Eight independent variants exhibited genome-wide significance. Among them, an intronic SNP of CD28, rs1181388, and an intergenic SNP, rs1002957030, on 11q23.2 were identified as novel signals for IgE. Seven of the loci were replicated successfully in a meta-analysis using data on Japanese population. Among all the human leukocyte antigen (HLA) regions, HLA-DQA1*03:02 - HLA-DQB1*03:03 was the most significant haplotype (OR = 1.25, SE = 0.02, FDR = 1.6 × 10-14), corresponding to HLA-DQA1 Asp160 and HLA-DQB1 Leu87 amino acid residues. The genetic correlation showed significance between IgE and allergic diseases including asthma, atopic dermatitis, and pollinosis. IgE PRS was significantly correlated with total IgE levels. Furthermore, the top decile IgE polygenic risk score (PRS) group had the highest risk of asthma for the Taiwan Biobank and Biobank Japan cohorts. IgE PRS may be used to aid in predicting the occurrence of allergic reactions before symptoms occur and biomarkers are detectable. Our study provided a more comprehensive understanding of the impact of genomic variants, including complex HLA alleles, on serum IgE levels.
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Affiliation(s)
- Hsing-Fang Lu
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chen-Hsing Chou
- PhD Program for Health Science and Industry, College of Health Care, China Medical University, Taichung, Taiwan; Department of Health Services Administration, China Medical University, Taichung, Taiwan
| | - Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Shunsuke Uchiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan; The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yu-Wen Wang
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan
| | - Jai-Sing Yang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 404327, Taiwan
| | - Ting-Yuan Liu
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan
| | - Henry Sung-Ching Wong
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Sean Chun-Chang Chen
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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18
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Chen HA, Hsu RH, Chen LC, Lee NC, Chiu PC, Hwu WL, Chien YH. Twelve-year review of galactosemia newborn screening in Taiwan: Evolving methods and insights. Mol Genet Metab Rep 2024; 38:101048. [PMID: 38469088 PMCID: PMC10926206 DOI: 10.1016/j.ymgmr.2024.101048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 03/13/2024] Open
Abstract
Background Galactosemia was introduced into Taiwan's routine newborn screening (NBS) program in 1985. This study presents a 12-year experience, emphasizing disease diagnosis and screening performance. Method NBS for galactosemia utilized dried blood spot samples taken 48-72 h post-delivery, with total galactose (TGal) level as the primary marker. Newborns with critical TGal levels were referred immediately, while those with borderline TGal underwent a recall test. GALT activity measurement was applied simultaneously as the second-tier marker. Further confirmatory tests, such as whole exome sequencing (WES), were conducted upon referral. Results From January 1st, 2011, to December 31st, 2022, 51 cases were identified from 817,906 newborns. Of these, nine individuals had persistently elevated TGal. Diagnoses included one case of GALT deficiency, one of GALM deficiency, and seven of GALE deficiencies. Notably, the classic galactosemia patient (GALT deficiency) presented with extreme high TGal and was referred to the hospital for diet management immediately. All affected patients were instructed to adopt a galactose-restricted diet. By the median age of 2.5 years, all exhibited normal development and liver function. Conclusion The incidence of classical galactosemia and its variants is extremely low in Taiwan. Incorporating WES into NBS has improved our ability to detect various galactosemia forms, enriching our understanding of the genetic underpinnings. While these newly discovered forms often present with milder initial elevations in TGal, specific biochemical investigations and regular monitoring are essential to understanding the long-term implications and outcomes.
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Affiliation(s)
- Hui-An Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Rai-Hseng Hsu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Chu Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pao-Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung City, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
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19
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Chen CL, Lee NC, Chien YH, Hwu WL, Hung MZ, Lin YL, Lin SY, Lee CN. Ethnically unique disease burden and limitations of current expanded carrier screening panels. Int J Gynaecol Obstet 2024; 164:918-924. [PMID: 37681470 DOI: 10.1002/ijgo.15072] [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: 03/23/2023] [Revised: 07/28/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVES The purpose of the study is to identify the recessive diseases currently affecting real-world pediatric patients in Taiwan, and whether current extended carrier screening panels have the coverage and detective power to identify the pathogenic variants in the carrier parents. METHODS A total of 132 trio-samples were collected from May 2017 to March 2022. The participants were parents of pediatric intensive care unit patients who were critically ill or infants with abnormal newborn screening results. A retrospective carrier screening scheme was applied to analyze only the carrier status of pathogenic or likely pathogenic recessive variants resulting in diseases in their children. The recessive disorders diagnosed in our cohort were compared with the gene content in commercial panels. RESULTS Mutations in COQ4, PEX1, OTC, and IKBKG were the most frequently identified. In the parents of 44 children with confirmed diagnoses of recessive diseases, 47 (53.40%) screened positive for being the carriers of the same recessive disorders diagnosed in their children. The commercial panels covered 35.13% to 54.05% of the disorders diagnosed in this cohort. CONCLUSION Clinicians and genetic counselors should be aware of the limitations of current extended carrier screening and interpret negative screening results with caution. Future panels should also consider genes with ethnically unique mutations such as pathogenic variants of the COQ4 gene in the East Asian population.
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Affiliation(s)
- Chih-Ling Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Miao-Zi Hung
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Shin-Yu Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Nan Lee
- Department of Obstetrics and Gynecology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
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20
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Chen TT, Kim J, Lam M, Chuang YF, Chiu YL, Lin SC, Jung SH, Kim B, Kim S, Cho C, Shim I, Park S, Ahn Y, Okbay A, Jang H, Kim HJ, Seo SW, Park WY, Ge T, Huang H, Feng YCA, Lin YF, Myung W, Chen CY, Won HH. Shared genetic architectures of educational attainment in East Asian and European populations. Nat Hum Behav 2024; 8:562-575. [PMID: 38182883 PMCID: PMC10963262 DOI: 10.1038/s41562-023-01781-9] [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: 03/19/2023] [Accepted: 11/09/2023] [Indexed: 01/07/2024]
Abstract
Educational attainment (EduYears), a heritable trait often used as a proxy for cognitive ability, is associated with various health and social outcomes. Previous genome-wide association studies (GWASs) on EduYears have been focused on samples of European (EUR) genetic ancestries. Here we present the first large-scale GWAS of EduYears in people of East Asian (EAS) ancestry (n = 176,400) and conduct a cross-ancestry meta-analysis with EduYears GWAS in people of EUR ancestry (n = 766,345). EduYears showed a high genetic correlation and power-adjusted transferability ratio between EAS and EUR. We also found similar functional enrichment, gene expression enrichment and cross-trait genetic correlations between two populations. Cross-ancestry fine-mapping identified refined credible sets with a higher posterior inclusion probability than single population fine-mapping. Polygenic prediction analysis in four independent EAS and EUR cohorts demonstrated transferability between populations. Our study supports the need for further research on diverse ancestries to increase our understanding of the genetic basis of educational attainment.
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Affiliation(s)
- Tzu-Ting Chen
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Jaeyoung Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Max Lam
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Division of Psychiatry Research, the Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Research Division Institute of Mental Health Singapore, Singapore, Singapore
| | - Yi-Fang Chuang
- Institute of Public Health and International Health Program, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yen-Ling Chiu
- Graduate Institute of Medicine, Yuan Ze University, Taoyuan City, Taiwan
- Department of Medical Research, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Shu-Chin Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beomsu Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Soyeon Kim
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chamlee Cho
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Injeong Shim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Sanghyeon Park
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Yeeun Ahn
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Aysu Okbay
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hyemin Jang
- Departments of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, South Korea
| | - Hee Jin Kim
- Departments of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, South Korea
| | - Sang Won Seo
- Departments of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tian Ge
- Stanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yen-Chen Anne Feng
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei City, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Yen-Feng Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan.
- Department of Public Health and Medical Humanities, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Woojae Myung
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea.
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, South Korea.
| | | | - Hong-Hee Won
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea.
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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21
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Li MH, Chen IC, Yang HW, Yen HC, Huang YC, Hsu CC, Chen YM, Ke YY. The characterization and comorbidities of heterozygous Bardet-Biedl syndrome carriers. Int J Med Sci 2024; 21:784-794. [PMID: 38617006 PMCID: PMC11008491 DOI: 10.7150/ijms.92766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/10/2024] [Indexed: 04/16/2024] Open
Abstract
Introduction: Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disorder with clinical features of retinal dystrophy, obesity, postaxial polydactyly, renal anomalies, learning disabilities, hypogonadism, and genitourinary abnormalities. Nevertheless, previous studies on the phenotypic traits of BBS heterozygous carriers have generated inconclusive results. The aim of our study was to investigate the impact of BBS heterozygosity on carriers when compared to non-carriers within the Taiwanese population. Materials and Methods: This study follows a hospital-based case-control design. We employed the Taiwan Biobank version 2 (TWBv2) array to identify three specific loci associated with BBS (rs773862084, rs567573386, and rs199910690). In total, 716 patients were included in the case group, and they were compared to a control group of 2,864 patients who lacked BBS alleles. The control group was selected through gender and age matching at a ratio of 1:4. The association between BBS-related loci and comorbidity was assessed using logistic regression models. Results: We found that BBS heterozygous carriers exhibited a significant association with elevated BMI levels, especially the variant rs199910690 in MKS1 (p=0.0037). The prevalence of comorbidities in the carriers' group was not higher than that in the non-carriers' group. Besides, the average values of the biochemistry data showed no significant differences, except for creatinine level. Furthermore, we conducted a BMI-based analysis to identify specific risk factors for chronic kidney disease (CKD). Our findings revealed that individuals carrying the CA/AA genotype of the BBS2 rs773862084 variant or the CT/TT genotype of the MKS1 rs199910690 variant showed a reduced risk of developing CKD, irrespective of their BMI levels. When stratified by BMI level, obese males with the MKS1 rs199910690 variant and obese females with the BBS2 rs773862084 variant exhibited a negative association with CKD development. Conclusion: We found that aside from the association with overweight and obesity, heterozygous BBS mutations did not appear to increase the predisposition of individuals to comorbidities and metabolic diseases. To gain a more comprehensive understanding of the genetic susceptibility associated with Bardet-Biedl Syndrome (BBS), further research is warranted.
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Affiliation(s)
- Meng-Hua Li
- Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - I-Chieh Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hui-Wen Yang
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Hsin-Chien Yen
- Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yung-Chieh Huang
- Division of Nephrology, Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chia-Chi Hsu
- Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Ming Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Institute of Biomedical Science and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taiwan
| | - Yu-Yuan Ke
- Division of Pediatric Genetics and Metabolism, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
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22
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Chien CW, Tang YA, Jeng SL, Pan HA, Sun HS. Blastocyst telomere length predicts successful implantation after frozen-thawed embryo transfer. Hum Reprod Open 2024; 2024:hoae012. [PMID: 38515829 PMCID: PMC10955253 DOI: 10.1093/hropen/hoae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 02/04/2024] [Indexed: 03/23/2024] Open
Abstract
STUDY QUESTION Do embryos with longer telomere length (TL) at the blastocyst stage have a higher capacity to survive after frozen-thawed embryo transfer (FET)? SUMMARY ANSWER Digitally estimated TL using low-pass whole genome sequencing (WGS) data from the preimplantation genetic testing for aneuploidy (PGT-A) process demonstrates that blastocyst TL is the most essential factor associated with likelihood of implantation. WHAT IS KNOWN ALREADY The lifetime TL is established in the early cleavage cycles following fertilization through a recombination-based lengthening mechanism and starts erosion beyond the blastocyst stage. In addition, a telomerase-mediated slow erosion of TL in human fetuses has been observed from a gestational age of 6-11 weeks. Finally, an abnormal shortening of telomeres is likely involved in embryo loss during early development. STUDY DESIGN SIZE DURATION Blastocyst samples were obtained from patients who underwent PGT-A and FET in an IVF center from March 2015 to May 2018. Digitally estimated mitochondrial copy number (mtCN) and TL were used to study associations with the implantation potential of each embryo. PARTICIPANTS/MATERIALS SETTING AND METHODS In total, 965 blastocysts from 232 cycles (164 patients) were available to investigate the biological and clinical relevance of TL. A WGS-based workflow was applied to determine the ploidy of each embryo. Data from low-pass WGS-PGT-A were used to estimate the mtCN and TL for each embryo. Single-variant and multi-variant logistic regression, decision tree, and random forest models were applied to study various factors in association with the implantation potential of each embryo. MAIN RESULTS AND THE ROLE OF CHANCE Of the 965 blastocysts originally available, only 216 underwent FET. While mtCN from the transferred embryos is significantly associated with the ploidy call of each embryo, mtCN has no role in impacting IVF outcomes after an embryo transfer in these women. The results indicate that mtCN is a marker of embryo aneuploidy. On the other hand, digitally estimated TL is the most prominent univariant factor and showed a significant positive association with pregnancy outcomes (P < 0.01, odds ratio 79.1). We combined several maternal and embryo parameters to study the joint effects on successful implantation. The machine learning models, namely decision tree and random forest, were trained and yielded classification accuracy of 0.82 and 0.91, respectively. Taken together, these results support the vital role of TL in governing implantation potential, perhaps through the ability to control embryo survival after transfer. LIMITATIONS REASONS FOR CAUTION The small sample size limits our study as only 216 blastocysts were transferred. The number was further reduced to 153 blastocysts, where pregnancy outcomes could be accurately traced. The other limitation of this study is that all data were collected from a single IVF center. The uniform and controlled operation of IVF cycles in a single center may cause selection bias. WIDER IMPLICATIONS OF THE FINDINGS We present novel findings to show that digitally estimated TL at the blastocyst stage is a predictor of pregnancy capacity after a FET cycle. As elective single-embryo transfer has become the mainstream direction in reproductive medicine, prioritizing embryos based on their implantation potential is crucial for clinical infertility treatment in order to reduce twin pregnancy rate and the time to pregnancy in an IVF center. The AI-powered, random forest prediction model established in this study thus provides a way to improve clinical practice and optimize the chances for people with fertility problems to achieve parenthood. STUDY FUNDING/COMPETING INTERESTS This study was supported by a grant from the National Science and Technology Council, Taiwan (MOST 108-2321-B-006-013 -). There were no competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Chun-Wei Chien
- Center for Genomic Medicine, Innovation Headquarters, National Cheng Kung University, Tainan, Taiwan
| | - Yen-An Tang
- Center for Genomic Medicine, Innovation Headquarters, National Cheng Kung University, Tainan, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shuen-Lin Jeng
- Department of Statistics, Institute of Data Science, National Cheng Kung University, Tainan, Taiwan
- Center for Innovative FinTech Business Models, National Cheng Kung University, Tainan, Taiwan
| | - Hsien-An Pan
- IVF center, An-An Women and Children Clinic, Tainan, Taiwan
- Department of Obstetrics and Gynecology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - H Sunny Sun
- Center for Genomic Medicine, Innovation Headquarters, National Cheng Kung University, Tainan, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Chen CS, Hung KS, Jian MJ, Chung HY, Chang CK, Perng CL, Chen HC, Chang FY, Wang CH, Hung YJ, Shang HS. Host-Pathogen Interactions in K. pneumoniae Urinary Tract Infections: Investigating Genetic Risk Factors in the Taiwanese Population. Diagnostics (Basel) 2024; 14:415. [PMID: 38396454 PMCID: PMC10888217 DOI: 10.3390/diagnostics14040415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae (K. pneumoniae) urinary tract infections pose a significant challenge in Taiwan. The significance of this issue arises because of the growing concerns about the antibiotic resistance of K. pneumoniae. Therefore, this study aimed to uncover potential genomic risk factors in Taiwanese patients with K. pneumoniae urinary tract infections through genome-wide association studies (GWAS). METHODS Genotyping data are obtained from participants with a history of urinary tract infections enrolled at the Tri-Service General Hospital as part of the Taiwan Precision Medicine Initiative (TPMI). A case-control study employing GWAS is designed to detect potential susceptibility single-nucleotide polymorphisms (SNPs) in patients with K. pneumoniae-related urinary tract infections. The associated genes are determined using a genome browser, and their expression profiles are validated via the GTEx database. The GO, Reactome, DisGeNET, and MalaCards databases are also consulted to determine further connections between biological functions, molecular pathways, and associated diseases between these genes. RESULTS The results identified 11 genetic variants with higher odds ratios compared to controls. These variants are implicated in processes such as adhesion, protein depolymerization, Ca2+-activated potassium channels, SUMOylation, and protein ubiquitination, which could potentially influence the host immune response. CONCLUSIONS This study implies that certain risk variants may be linked to K. pneumoniae infections by affecting diverse molecular functions that can potentially impact host immunity. Additional research and follow-up studies are necessary to elucidate the influence of these risk variants on infectious diseases and develop targeted interventions for mitigating the spread of K. pneumoniae urinary tract infections.
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Affiliation(s)
- Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan (H.-Y.C.)
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan (H.-Y.C.)
| | - Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan (H.-Y.C.)
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan (H.-Y.C.)
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan (H.-Y.C.)
| | - Hsiang-Cheng Chen
- Division of Rheumatology/Immunology and Allergy, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan;
| | - Chih-Hung Wang
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan (H.-Y.C.)
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Huang YC, Lee MC, Huang SY, Chou CM, Yang HW, Chen IC. Polygenic Risk Score in Predicting Esophageal, Oropharyngeal, and Hypopharynx Cancer Risk among Taiwanese Population. Cancers (Basel) 2024; 16:707. [PMID: 38398100 PMCID: PMC10886704 DOI: 10.3390/cancers16040707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Esophageal cancer shares strong associations with oropharyngeal and hypopharyngeal cancers, primarily due to shared risk factors like excessive tobacco and alcohol use. This retrospective study at Taichung Veterans General Hospital involved 54,692 participants, including 385 with squamous cell carcinoma (SCC) of the esophagus, oropharynx, or hypopharynx. Using a polygenic risk score (PRS) derived from 8353 single-nucleotide polymorphisms, researchers aimed to assess its correlation with cancer incidence and prognosis. The study found a 1.83-fold higher risk of esophageal, oropharyngeal, and hypopharyngeal SCCs in participants with a high PRS (Q4) compared to the low-PRS group (Q1). Esophageal cancer risk demonstrated a significant positive association with the PRS, as did hypopharyngeal cancer. Clinical parameters and staging showed limited associations with PRS quartiles, and the PRS did not significantly impact recurrence or mortality rates. The research highlighted that a higher PRS is linked to increased susceptibility to esophageal and hypopharyngeal cancer. Notably, a specific polygenic risk score, PGS001087, exhibited a discernible association with SCC risk, particularly in specific subtypes and advanced disease stages. However, it was not significantly linked to clinical cancer staging, emphasizing the multifactorial nature of cancer development. This hospital study reveals that a higher PRS correlates with increased susceptibility to esophageal and hypopharyngeal cancers. Notably, PGS001087 shows a discernible association with SCC risk in specific subtypes and advanced stages, although not significantly linked to clinical cancer staging. These findings enhance our understanding of genetic factors in upper aerodigestive tract cancers, particularly esophageal SCC, guiding future research and risk assessment strategies.
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Affiliation(s)
- Yu-Che Huang
- Division of Thoracic Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
- Department of Critical Care Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Ming-Ching Lee
- Division of Thoracic Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
- Department of Medical Education, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Sheng-Yang Huang
- Division of Pediatric Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung 40705, Taiwan; (S.-Y.H.); (C.-M.C.)
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11267, Taiwan
| | - Chia-Man Chou
- Division of Pediatric Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung 40705, Taiwan; (S.-Y.H.); (C.-M.C.)
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11267, Taiwan
| | - Hui-Wen Yang
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
| | - I-Chieh Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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Kuo MC, Chu YT, Su YA, Chen ML, Wu RM. Prosaposin variants in sporadic, familial, and early-onset Parkinson's disease: a Taiwanese case-control study and meta-analysis. Sci Rep 2024; 14:2225. [PMID: 38278831 PMCID: PMC10817969 DOI: 10.1038/s41598-024-51646-y] [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: 08/07/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
Polymorphisms in the PSAP gene, which encodes prosaposin and is involved in the lysosomal function, yielded conflicting results regarding the association with Parkinson's disease (PD). Therefore, this study aims to investigate the role of PSAP in familial PD (FPD), early onset PD (EOPD) with age at onset before 50 years old, and sporadic PD (SPD) among Taiwanese population, and summarize relevant studies via meta-analysis. By sequencing exon 1 to 14 in 183 FPD and 219 EOPD, two novel exonic variants were found in EOPD, including p.A146E (c.437C > A) on exon 5 and p.Y248C (c.743A > G) on exon 7. Furthermore, four previously reported intronic variants (rs142614739/rs74733861), rs749823, rs4747203 and rs885828) in intron 11 and 12 were analyzed in 485 SPD and 712 in-hospital controls, in addition to the aforementioned FPD and EOPD groups. The adjusted odd ratios (ORs) by age and sex, only rs142614739 was significantly associated with higher risk of EOPD (OR = 1.85, 95% CI = 1.33-2.58). The risk effect was further confirmed by the meta-analysis of the association between rs142614739 and the risk of PD in both common effect (OR = 1.29, 95% CI = 1.11-1.50) and random effect (OR = 1.29, 95% CI = 1.11-1.50). Our findings suggest that the PSAP rs142614739 variant is associated with the risk of EOPD. Further functional studies are warranted to elucidate the biochemical mechanisms.
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Affiliation(s)
- Ming-Che Kuo
- Department of Neurology, Centre for Parkinson and Movement Disorder, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medicine, National Taiwan University Cancer Center, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yung-Tsai Chu
- Department of Neurology, Centre for Parkinson and Movement Disorder, National Taiwan University Hospital, Taipei, Taiwan
- Department of Neurology, National Taiwan University Hospital Jinshan Branch, New Taipei City, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Yu-An Su
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Ling Chen
- Department of Neurology, Centre for Parkinson and Movement Disorder, National Taiwan University Hospital, Taipei, Taiwan
| | - Ruey-Meei Wu
- Department of Neurology, Centre for Parkinson and Movement Disorder, National Taiwan University Hospital, Taipei, Taiwan.
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Department of Neurology, College of Medicine, National Taiwan University, No.7, Chung Shan South. Road, Taipei, 10002, Taiwan.
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Chung CW, Chou SC, Hsiao TH, Zhang GJ, Chung YF, Chen YM. Machine learning approaches to identify systemic lupus erythematosus in anti-nuclear antibody-positive patients using genomic data and electronic health records. BioData Min 2024; 17:1. [PMID: 38183082 PMCID: PMC10770905 DOI: 10.1186/s13040-023-00352-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Although the 2019 EULAR/ACR classification criteria for systemic lupus erythematosus (SLE) has required at least a positive anti-nuclear antibody (ANA) titer (≥ 1:80), it remains challenging for clinicians to identify patients with SLE. This study aimed to develop a machine learning (ML) approach to assist in the detection of SLE patients using genomic data and electronic health records. METHODS Participants with a positive ANA (≥ 1:80) were enrolled from the Taiwan Precision Medicine Initiative cohort. The Taiwan Biobank version 2 array was used to detect single nucleotide polymorphism (SNP) data. Six ML models, Logistic Regression, Random Forest (RF), Support Vector Machine, Light Gradient Boosting Machine, Gradient Tree Boosting, and Extreme Gradient Boosting (XGB), were used to identify SLE patients. The importance of the clinical and genetic features was determined by Shapley Additive Explanation (SHAP) values. A logistic regression model was applied to identify genetic variations associated with SLE in the subset of patients with an ANA equal to or exceeding 1:640. RESULTS A total of 946 SLE and 1,892 non-SLE controls were included in this analysis. Among the six ML models, RF and XGB demonstrated superior performance in the differentiation of SLE from non-SLE. The leading features in the SHAP diagram were anti-double strand DNA antibodies, ANA titers, AC4 ANA pattern, polygenic risk scores, complement levels, and SNPs. Additionally, in the subgroup with a high ANA titer (≥ 1:640), six SNPs positively associated with SLE and five SNPs negatively correlated with SLE were discovered. CONCLUSIONS ML approaches offer the potential to assist in diagnosing SLE and uncovering novel SNPs in a group of patients with autoimmunity.
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Affiliation(s)
- Chih-Wei Chung
- Department of Information Management, National Taiwan University, Taipei, Taiwan
| | - Seng-Cho Chou
- Department of Information Management, National Taiwan University, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Grace Joyce Zhang
- Department of Cellular and Physiological Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Yu-Fang Chung
- Department of Electrical Engineering, Tunghai University, Taichung, Taiwan
| | - Yi-Ming Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.
- Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, 1650, Section 4, Taiwan Boulevard, Xitun Dist., Taichung City, 407, Taiwan.
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan.
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Rong Hsing Research Center for Translational Medicine & Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.
- Precision Medicine Research Center, College of Medicine, National Chung Hsing University, Taichung, Taiwan.
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Hsu YC, Chen HL, Cheng CF, Chattopadhyay A, Chen PS, Lin CC, Chiang HY, Liu TY, Huang CH, Kuo CC, Chuang EY, Lu TP, Tsai FJ. The largest genome-wide association study for breast cancer in Taiwanese Han population. Breast Cancer Res Treat 2024; 203:291-306. [PMID: 37851288 DOI: 10.1007/s10549-023-07133-5] [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: 06/22/2023] [Accepted: 09/23/2023] [Indexed: 10/19/2023]
Abstract
PURPOSE Breast cancer is a molecularly heterogeneous disease, and multiple genetic variants contribute to its development and prognosis. Most of previous genome-wide association studies (GWASs) and polygenic risk scores (PRSs) analyses focused on studying breast cancers of Caucasian populations, which may not be applicable to other population. Therefore, we conducted the largest breast cancer cohort of Taiwanese population to fill in the knowledge gap. METHODS A total of 152,534 Participants recruited by China Medical University Hospital between 2003 and 2019 were filtered by several patient selection criteria and GWAS quality control steps, resulting in the inclusion of 2496 cases and 9984 controls for this study. We then conducted GWAS for all breast cancers and PRS analyses for all breast cancers and the four breast cancer subtypes, including luminal A, luminal B, basal-like, and HER2-enriched. RESULTS The GWAS analyses identified 113 SNPs, 50 of which were novel. The PRS models for all breast cancers and the luminal A subtype showed positively correlated trends between the PRS and the risk of developing breast cancer. The odds ratios (95% confidence intervals) for the groups with the highest PRS in all breast cancers and the luminal A subtype were 5.33 (3.79-7.66) and 3.55 (2.13-6.14), respectively. CONCLUSION In summary, we explored the association of genetic variants with breast cancer in the largest Taiwanese cohort and developed two PRS models that can predict the risk of developing any breast cancer and the luminal A subtype in Taiwanese women.
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Affiliation(s)
- Yu-Ching Hsu
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Statistical Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Health Data Analytics and Statistics, Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Hung-Lin Chen
- Big Data Center, China Medical University Hospital, Taichung, Taiwan
| | - Chi-Fung Cheng
- Big Data Center, China Medical University Hospital, Taichung, Taiwan
| | - Amrita Chattopadhyay
- Center for Translational Genomic Research, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Pei-Shan Chen
- Big Data Center, China Medical University Hospital, Taichung, Taiwan
| | - Che-Chen Lin
- Big Data Center, China Medical University Hospital, Taichung, Taiwan
| | - Hsiu-Yin Chiang
- Big Data Center, China Medical University Hospital, Taichung, Taiwan
| | - Ting-Yuan Liu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chi-Hao Huang
- Division of Breast Surgery, Department of Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Chin-Chi Kuo
- Big Data Center, China Medical University Hospital, Taichung, Taiwan
- Division of Nephrology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Tzu-Pin Lu
- Institute of Health Data Analytics and Statistics, Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan.
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
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Lin HJ, Chen CH, Su MW, Lin CW, Cheng YW, Tang SC, Jeng JS. Modifiable vascular risk factors contribute to stroke in 1080 NOTCH3 R544C carriers in Taiwan Biobank. Int J Stroke 2024; 19:105-113. [PMID: 37485895 DOI: 10.1177/17474930231191991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
BACKGROUND AND AIM Previous studies have suggested cardiovascular risk factors increase the risk of not only common sporadic stroke but also of stroke in patients with monogenic stroke disorders including CADASIL. We investigated the effects of the NOTCH3 Arg544Cys (R544C) variant and associated vascular risk factors on stroke in the Taiwanese population. METHODS This study was conducted using data from the Taiwan Biobank, consisting of at least 130,000 Han Chinese participants. The genotype was derived from customized genome-wide arrays for 650,000 to 750,000 single-nucleotide polymorphisms (SNPs). Individuals with NOTCH3 R544C were subsequently matched with noncarriers based on the propensity score at a 1:10 ratio by demographic and cardiovascular risk factors. The odds ratio (OR) for stroke or other phenotypes in NOTCH3 R544C carriers and matched noncarriers was then calculated. Univariate and multivariate regression analyses were performed on cardiovascular risk factors in NOTCH3 R544C carriers with and without stroke. The polygenic risk score (PRS) model, adopted from the UK Biobank, was then applied to evaluate the role of NOTCH3 R544C in stroke. RESULTS From the 114,282 participants with both genotype and questionnaire results, 1080 (0.95%) harbored the pathogenic NOTCH3 R544C variant. When compared to the matched controls (n = 10,800), the carriers presented with a history of stroke (OR: 2.52, 95% confidence interval (CI) (1.45, 4.37)), dementia (OR: 30.1, 95% CI (3.13, 289.43)), and sibling history of stroke (OR: 2.48, 95% CI (1.85, 3.34)) phenotypes. The risk of stroke increased with every 10-year increase in age (p = 0.006, Cochran-Mantel-Haenszel test). Among NOTCH3 R544C carriers, 16 (1.3%) of the 1080 carriers with a stroke history were older, male, and more likely to have hypertension, diabetes, dyslipidemia, and a family history of stroke. In the stepwise multivariate analysis, hypertension (OR: 11.28, 95% CI (3.54, 43.3)) and diabetes mellitus (OR: 4.10, 95% CI (1.31, 12.4)) were independently associated with stroke. Harboring the NOTCH3 R544C variant in the Taiwan Biobank is comparable with a 6.74 standard deviations increase in individual's polygenic risk score for stroke. CONCLUSION While the NOTCH3 R544C variant alone increased the risk of stroke, modifiable vascular risk factors also played a role in the occurrence of stroke in Taiwanese community-dwelling individuals carrying the NOTCH3 variant.
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Affiliation(s)
- Hung-Jen Lin
- Department of Medical Education, National Taiwan University Hospital, Taipei
| | - Chih-Hao Chen
- Department of Neurology, National Taiwan University Hospital, Taipei
| | - Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei
| | - Chien-Wei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei
| | - Yu-Wen Cheng
- Department of Neurology, National Taiwan University Hospital, Taipei
| | - Sung-Chun Tang
- Department of Neurology, National Taiwan University Hospital, Taipei
| | - Jiann-Shing Jeng
- Department of Neurology, National Taiwan University Hospital, Taipei
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Hsu JS, Wu DC, Shih SH, Liu JF, Tsai YC, Lee TL, Chen WA, Tseng YH, Lo YC, Lin HY, Chen YC, Chen JY, Chou TH, Chang DTH, Su MW, Guo WH, Mao HH, Chen CY, Chen PL. Complete genomic profiles of 1496 Taiwanese reveal curated medical insights. J Adv Res 2023:S2090-1232(23)00405-8. [PMID: 38159844 DOI: 10.1016/j.jare.2023.12.018] [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: 08/14/2023] [Revised: 12/03/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
INTRODUCTION The population of Taiwan has a long history of ethno-cultural evolution. The Taiwanese population was isolated from other large populations such as the European, Han Chinese, and Japanese population. The Taiwan Biobank (TWB) project has built a nationwide database, particularly for personal whole-genome sequence (WGS) to facilitate basic and clinical collaboration nationally and internationally, making it one of the most valuable public datasets of the East Asian population. OBJECTIVES This study provides comprehensive medical genomic findings from TWB WGS data, for better characterization of disease susceptibility and the choice of ideal treatment regimens in Taiwanese population. METHODS We reanalyzed 1496 WGS using a PrecisionFDA Truth challenge winner method Sentieon DNAscope. Single nucleotide variants (SNV) and small insertions/deletions (INDEL) were benchmarked. We also analyzed pharmacogenomic (PGx) drug-associated alleles, and copy number variants (CNV). Multiple practicing clinicians reviewed and curated the clinically significant variants. Variant annotations can be browsed at TaiwanGenomes (https://genomes.tw). RESULTS We found that each participant had an average of 6,870.7 globally novel variants and 75.3% (831/1103) of the participants harbored at least one PharmGKB-selected high evidence level human leukocyte antigen (HLA) risk allele. 54 PharmGKB-reported high-level instances of evidence of Cytochrome P450 variant-drug pairs, with a population frequency of over 13.2%. We also identified 23 variants in the ACMG secondary finding V3 gene list from 25 participants, suggesting that 1.67% (25/1496) of the population is harboring at least one medical actionable variant. Our carrier status analyses suggest that one in 25 couples (3.94%) would risk having offspring with at least one pathogenic variant, which is in line with rates found in Japan and Singapore. For pathogenic CNV, we detected 6.88% and 2.02% carrier rates for alpha thalassemia and spinal muscular atrophy, respectively. CONCLUSION Our study highlights the overall medical insights of a complete Taiwanese genomic profile.
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Affiliation(s)
- Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Dung-Chi Wu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Shang-Hung Shih
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Jen-Feng Liu
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Ya-Chen Tsai
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Tung-Lin Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan
| | - Wei-An Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan
| | - Yi-Hsuan Tseng
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Yi-Chung Lo
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan
| | - Hong-Ye Lin
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chieh Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Jing-Yi Chen
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan
| | - Ting-Hsuan Chou
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Darby Tien-Hao Chang
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan; Digital Technology Division, SinoPac Holdings, Taiwan
| | - Ming Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Wei-Hong Guo
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Hsiang Mao
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Yu Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan.
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Ho CY, Lee JI, Huang SP, Chen SC, Geng JH. A Genome-Wide Association Study of Metabolic Syndrome in the Taiwanese Population. Nutrients 2023; 16:77. [PMID: 38201907 PMCID: PMC10780952 DOI: 10.3390/nu16010077] [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: 11/08/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The purpose of this study was to investigate genetic factors associated with metabolic syndrome (MetS) by conducting a large-scale genome-wide association study (GWAS) in Taiwan, addressing the limited data on Asian populations compared to Western populations. Using data from the Taiwan Biobank, comprehensive clinical and genetic information from 107,230 Taiwanese individuals was analyzed. Genotyping data from the TWB1.0 and TWB2.0 chips, including over 650,000 single nucleotide polymorphisms (SNPs), were utilized. Genotype imputation using the 1000 Genomes Project was performed, resulting in more than 9 million SNPs. MetS was defined based on a modified version of the Adult Treatment Panel III criteria. Among all participants (mean age: 50 years), 23% met the MetS definition. GWAS analysis identified 549 SNPs significantly associated with MetS, collectively mapping to 10 genomic risk loci. Notable risk loci included rs1004558, rs3812316, rs326, rs4486200, rs2954038, rs10830963, rs662799, rs62033400, rs183130, and rs34342646. Gene-set analysis revealed 22 associated genes: CETP, LPL, APOA5, SIK3, ZPR1, APOC1, BUD13, MLXIPL, TOMM40, GCK, YKT6, RPS6KB1, FTO, VMP1, TUBD1, BCL7B, C19orf80 (ANGPTL8), SIDT2, SENP7, PAFAH1B2, DOCK6, and FOXA2. This study identified genomic risk loci for MetS in a large Taiwanese population through a comprehensive GWAS approach. These associations provide novel insights into the genetic basis of MetS and hold promise for the potential discovery of clinical biomarkers.
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Affiliation(s)
- Chih-Yi Ho
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Jia-In Lee
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shu-Pin Huang
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Ph.D. Program in Environmental and Occupational Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Medical Science and Technology, College of Medicine, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Szu-Chia Chen
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Internal Medicine, Kaohsiung Municipal Siaogang Hospital, Kaohsiung Medical University, Kaohsiung 812, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jiun-Hung Geng
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Urology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung 812, Taiwan
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Chen CY, Chen TT, Feng YCA, Yu M, Lin SC, Longchamps RJ, Wang SH, Hsu YH, Yang HI, Kuo PH, Daly MJ, Chen WJ, Huang H, Ge T, Lin YF. Analysis across Taiwan Biobank, Biobank Japan, and UK Biobank identifies hundreds of novel loci for 36 quantitative traits. CELL GENOMICS 2023; 3:100436. [PMID: 38116116 PMCID: PMC10726425 DOI: 10.1016/j.xgen.2023.100436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/21/2021] [Accepted: 10/09/2023] [Indexed: 12/21/2023]
Abstract
Genome-wide association studies (GWASs) have identified tens of thousands of genetic loci associated with human complex traits. However, the majority of GWASs were conducted in individuals of European ancestries. Failure to capture global genetic diversity has limited genomic discovery and has impeded equitable delivery of genomic knowledge to diverse populations. Here we report findings from 102,900 individuals across 36 human quantitative traits in the Taiwan Biobank (TWB), a major biobank effort that broadens the population diversity of genetic studies in East Asia. We identified 968 novel genetic loci, pinpointed novel causal variants through statistical fine-mapping, compared the genetic architecture across TWB, Biobank Japan, and UK Biobank, and evaluated the utility of cross-phenotype, cross-population polygenic risk scores in disease risk prediction. These results demonstrated the potential to advance discovery through diversifying GWAS populations and provided insights into the common genetic basis of human complex traits in East Asia.
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Affiliation(s)
- Chia-Yen Chen
- Biogen, Cambridge, MA 02142, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tzu-Ting Chen
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Yen-Chen Anne Feng
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100025, Taiwan
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei 100025, Taiwan
| | - Mingrui Yu
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shu-Chin Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Ryan J. Longchamps
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shi-Heng Wang
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Miaoli 35053, Taiwan
- Department of Public Health, College of Public Health, China Medical University, Taichung 40678, Taiwan
| | - Yi-Hsiang Hsu
- Marcus Institute for Aging Research and Harvard Medical School, Boston, MA 02131, USA
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Harvard School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hwai-I. Yang
- Genomics Research Center, Academia Sinica, Taipei 115201, Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei 112304, Taiwan
- Doctoral Program of Clinical and Experimental Medicine, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei 115021, Taiwan
| | - Po-Hsiu Kuo
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100025, Taiwan
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei 106319, Taiwan
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, Finland
| | - Wei J. Chen
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100025, Taiwan
- Department of Psychiatry, College of Medicine and National Taiwan University Hospital, Taipei 106319, Taiwan
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Yen-Feng Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
- Department of Public Health & Medical Humanities, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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Chen JJ, Chen IC, Wei CY, Lin SY, Chen YM. Utilize polygenic risk score to enhance fracture risk estimation and improve the performance of FRAX in patients with osteoporosis. Arch Osteoporos 2023; 18:147. [PMID: 38036866 DOI: 10.1007/s11657-023-01357-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
This study examined the use of polygenic risk scores (PGS) in combination with the Fracture Risk Assessment Tool (FRAX) to enhance fragility fractures risk estimation in osteoporosis patients. Analyzing data from over 57,000 participants, PGS improved fracture risk estimation, especially for individuals with intermediate to low risks, allowing personalized preventive strategies. INTRODUCTION Osteoporosis and fragility fractures are multifactorial, with contributions from both clinical and genetic determinants. However, whether using polygenic risk scores (PGS) may enhance the risk estimation of osteoporotic fracture in addition to Fracture Risk Assessment Tool (FRAX) remains unknown. This study investigated the collective association of PGS and FRAX with fragility fracture. METHODS We conducted a cohort study from the Taiwan Precision Medicine Initiative (TPMI) at Taichung Veterans General Hospital, Taiwan. Genotyping was performed to compute PGS associated with bone mineral density (BMD). Phenome-wide association studies were executed to pinpoint phenotypes correlated with the PGS. Logistic regression analysis was conducted to ascertain factors associated with osteoporotic fractures. RESULTS Among all 57,257 TPMI participants, 3744 (904 men and 2840 women, with a mean age of 66.7) individuals had BMD testing, with 540 (14.42%) presenting with fractures. The 3744 individuals who underwent BMD testing were categorized into four quartiles (Q1-Q4) based on PGS; 540 (14.42%) presented with fractures. Individuals with PGS-Q1 exhibited lower BMD, a higher prevalence of major fractures, and elevated FRAX-major and FRAX-hip than those with PGS-Q4. PGS was associated with major fractures after adjusting age, sex, and FRAX scores. Notably, the risk of major fractures (PGS-Q1 vs. Q4) was significantly higher in the subgroups of FRAX-major scores < 10% and 10-20%, but not in participants with a FRAX-major score ≧ 20%. CONCLUSIONS Our study highlights the potential of PGS to augment fracture risk estimation in conjunction with FRAX, particularly in individuals with middle to low risks. Incorporating genetic testing could empower physicians to tailor personalized preventive strategies for osteoporosis.
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Affiliation(s)
- Jian-Jiun Chen
- Department of Orthopedics, Taipei Veterans General Hospital, Taipei, Taiwan
| | - I-Chieh Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chia-Yi Wei
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shih-Yi Lin
- Center for Geriatrics and Gerontology, Taichung Veterans General Hospital, Taichung, Taiwan.
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung-Hsing University, Taichung, Taiwan.
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan.
| | - Yi-Ming Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung-Hsing University, Taichung, Taiwan.
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan.
- Division of Allergy, Immunology and Rheumatology, Taichung Veterans General Hospital, Taichung, Taiwan.
- Institute of Biomedical Science and Rong-Hsing Research Center for Translational Medicine, Chung-Hsing University, Taichung, Taiwan.
- Precision Medicine Research Center, College of Medicine, National Chung Hsing University, Taichung, Taiwan.
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Yang L, Lin Z, Gao Y, Zhang J, Peng H, Li Y, Che J, Zhao L, Zhang J. Populational pan-ethnic screening panel enabled by deep whole genome sequencing. NPJ Genom Med 2023; 8:38. [PMID: 37985665 PMCID: PMC10661700 DOI: 10.1038/s41525-023-00383-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
Birth defect is a global threat to the public health systems. Mitigating neonatal anomalies is hampered by elusive molecular mechanisms of pathogenic mutations and poor subsequent translation into preventative measures. Applying appropriate strategies in China to promote reproductive health is particularly challenging, as the Chinese population compromises complex genomic diversity due to the inclusion of many ethnic groups with distinct genetic backgrounds. To investigate and evaluate the feasibility of implementing a pan-ethnic screening strategy, and guide future reproductive counselling, high-quality variants associated with autosome recessive (AR) diseases derived from the largest publicly available cohort of the Chinese population were re-analysed using a bottom-up approach. The analyses of gene carrier rates (GCRs) across distinct ethnic groups revealed that substantial heterogeneity existed potentially due to diverse evolutionary selection. The sampling population, sequencing coverage and underlying population structure contributed to the differential variants observed between ChinaMAP and the East Asian group in gnomAD. Beyond characteristics of GCR, potential druggable targets were additionally explored according to genomic features and functional roles of investigated genes, demonstrating that phase separation could be a therapeutic target for autosomal recessive diseases. A further examination of estimated GCR across ethnic groups indicated that most genes shared by at least two populations could be utilised to direct the design of a pan-ethnic screening application once sequencing and interpreting costs become negligible. To this end, a list of autosomal recessive disease genes is proposed based on the prioritised rank of GCR to formulate a tiered screening strategy.
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Affiliation(s)
- Linfeng Yang
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhe Lin
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yong Gao
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Yaqing Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Lijian Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.
- Medical Technology College of Hebei Medical University, Shijiazhuang, China.
| | - Jilin Zhang
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong S.A.R, China.
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China.
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong S.A.R, China.
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Lee CT, Tsai WH, Chang CC, Chen PC, Fann CSJ, Chang HK, Liu SY, Wu MZ, Chiu PC, Hsu WM, Yang WS, Lai LP, Tsai WY, Yang SB, Chen PL. Genotype-phenotype correlation in Taiwanese children with diazoxide-unresponsive congenital hyperinsulinism. Front Endocrinol (Lausanne) 2023; 14:1283907. [PMID: 38033998 PMCID: PMC10687152 DOI: 10.3389/fendo.2023.1283907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Objective Congenital hyperinsulinism (CHI) is a group of clinically and genetically heterogeneous disorders characterized by dysregulated insulin secretion. The aim of the study was to elucidate genetic etiologies of Taiwanese children with the most severe diazoxide-unresponsive CHI and analyze their genotype-phenotype correlations. Methods We combined Sanger with whole exome sequencing (WES) to analyze CHI-related genes. The allele frequency of the most common variant was estimated by single-nucleotide polymorphism haplotype analysis. The functional effects of the ATP-sensitive potassium (KATP) channel variants were assessed using patch clamp recording and Western blot. Results Nine of 13 (69%) patients with ten different pathogenic variants (7 in ABCC8, 2 in KCNJ11 and 1 in GCK) were identified by the combined sequencing. The variant ABCC8 p.T1042QfsX75 identified in three probands was located in a specific haplotype. Functional study revealed the human SUR1 (hSUR1)-L366F KATP channels failed to respond to intracellular MgADP and diazoxide while hSUR1-R797Q and hSUR1-R1393C KATP channels were defective in trafficking. One patient had a de novo dominant mutation in the GCK gene (p.I211F), and WES revealed mosaicism of this variant from another patient. Conclusion Pathogenic variants in KATP channels are the most common underlying cause of diazoxide-unresponsive CHI in the Taiwanese cohort. The p.T1042QfsX75 variant in the ABCC8 gene is highly suggestive of a founder effect. The I211F mutation in the GCK gene and three rare SUR1 variants associated with defective gating (p.L366F) or traffic (p.R797Q and p.R1393C) KATP channels are also associated with the diazoxide-unresponsive phenotype.
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Affiliation(s)
- Cheng-Ting Lee
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Hao Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Pei-Chun Chen
- Department of Physiology, National Cheng-Kung University, Tainan, Taiwan
| | | | - Hsueh-Kai Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shih-Yao Liu
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mu-Zon Wu
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pao-Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wen-Ming Hsu
- Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ling-Ping Lai
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Yu Tsai
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shi-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Lung Chen
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
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Lin E, Kuo PH, Liu YL, Wang TJ, Yang AC, Tsai SJ. The cysteine-altering p.R544C variant in the NOTCH3 gene is a probable candidate for blood pressure and relevant traits in the Taiwan Biobank. J Neurol 2023; 270:5536-5544. [PMID: 37526664 DOI: 10.1007/s00415-023-11909-6] [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: 12/05/2022] [Revised: 06/17/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND The cysteine-altering variants in NOTCH3 have been suggested to be associated with stroke, dementia, and cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), where aberrant blood pressure levels represent the characteristics of these diseases. We aimed to assess whether the cysteine-altering p.Arg544Cys (p.R544C; rs201118034) variant and common single nucleotide variants (SNVs) in NOTCH3 could contribute to systolic and diastolic blood pressure and related phenotypes in the Taiwan Biobank. METHODS We employed a discovery sample of 68,925 individuals, an independent replication sample of 45,676 individuals, and a combined/total sample of 114,601 individuals; all from the Taiwan Biobank. Blood pressure, such as systolic and diastolic blood pressure, was measured for all participants. Association was evaluated using a general linear model, where results were considered statistically significant if the P value < 0.05 divided by the number of independent tests per model. RESULTS From our analysis, we identified and replicated three novel candidates for blood pressure that have not previously been reported: the cysteine-altering p.R544C variant for systolic blood pressure, the common SNV rs11669950 for diastolic blood pressure, and the common SNV rs4808235 for diastolic blood pressure. We also generalized two previously identified SNVs (i.e., rs10418305 and rs7408868) in NOTCH3 for blood pressure in European and non-Taiwanese East Asian populations to the Taiwanese population. Moreover, the participants with NOTCH3 p.R544C had an increased stroke frequency (P < 1.0 × 10-5) and a higher dementia frequency (P = 2.0 × 10-4) compared with the whole Taiwan Biobank population in the combined/total sample. CONCLUSION NOTCH3 is a strong candidate for a role in stroke, dementia, and CADASIL, which has previously been linked to blood pressure changes. While our preliminary study suggests that NOTCH3 p.R544C may influence blood pressure, stroke, and dementia in the Taiwan Biobank, replication in a well-powered external sample is required. This study also underlines considerable prospects of detecting novel genetic biomarkers in underrepresented worldwide populations.
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Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, 3980 15th Avenue NE, Box 351617, Seattle, WA, 98195, USA.
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA.
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan.
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10617, Taiwan
- Department of Psychiatry, National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, 35053, Taiwan
| | - Tso-Jen Wang
- Taoyuan Psychiatric Center, Ministry of Health and Welfare, Taoyuan, 33058, Taiwan
| | - Albert C Yang
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, No. 201, Shih-Pai Road, Sec. 2, Taipei, 11217, Taiwan.
- Division of Psychiatry, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan.
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Yen TT, Chen IC, Cho S, Chang TG, Shih KH, Hua MW, Li JL, Hsu CY, Hsiao TH, Chen YM. GJB2 p.V37I Mutation Associated With Moderate Nonsyndromic Hearing Loss in an Adult Taiwanese Population. Ear Hear 2023; 44:1423-1429. [PMID: 37271870 DOI: 10.1097/aud.0000000000001384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
BACKGROUND Gap junction protein beta 2 ( GJB2 ) p.V37I mutations are the most important hereditary cause of sensorineural hearing loss (SNHL) in Taiwan. Hearing outcomes are associated with hearing levels at baseline and the duration of follow-up. However, the audiological features of GJB2 p.V37I mutations in the adult population are unknown. The objectives of the present study were to investigate the audiological features, progression rate, and allele frequency of GJB2 p.V37I mutations among an adult Taiwanese population. METHODS Subjects of this case-control study were chosen from 13,580 participants of the Taiwan Precision Medicine Initiative. The genetic variations of GJB2 p.V37I were determined by polymerase chain reaction. We analyzed existing pure-tone threshold data from 38 individuals who were homozygous or compound heterozygotes for GJB2 p.V37I, 129 who were heterozygotes, and 602 individuals who were wild-type. Phenome-wide association studies (PheWAS) analysis was also performed to identify phenotypes associated with GJB2 p.V37I. RESULTS The minor allele frequency of GJB2 p.V37I was 0.92% in our study population. The mean hearing level of participants with a p.V37I mutation indicated moderate to severe hearing loss with 38.2% ± 22.3% binaural hearing impairment. GJB2 p.V37I was associated with an increased risk of hearing disability (odds ratio: 21.46, 95% confidence interval: 8.62 to 53.44, p < 0.001) in an autosomal recessive pattern. In addition, PheWAS discovered a significant association between GJB2 p.V37I and fracture of the humerus. GJB2 p.V37I is a pathogenic and prevalent variant of SNHL among the adult population. CONCLUSIONS The present study recommends patients with known GJB2 p.V37I mutations receive regular audiometric evaluation and genetic counseling. Early assistive listening device intervention is suggested to improve the quality of hearing.
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Affiliation(s)
- Ting-Ting Yen
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
| | - I-Chieh Chen
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Sudi Cho
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, University of California, Davis, California, USA
| | - Ting-Gang Chang
- Department of Psychiatry, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Psychology, School of Psychology,Chung Shan Medical University, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Kai-Hsiang Shih
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Men-Wei Hua
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jui-Lin Li
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chiann-Yi Hsu
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ming Chen
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine and Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taiwan
- Precision Medicine Research Center, College of Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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Chiang YT, Lin PH, Lo MY, Chen HL, Lee CY, Tsai CY, Lin YH, Tsai SF, Liu TC, Hsu CJ, Chen PL, Hsu JSJ, Wu CC. Genetic Factors Contribute to the Phenotypic Variability in GJB2-Related Hearing Impairment. J Mol Diagn 2023; 25:827-837. [PMID: 37683890 DOI: 10.1016/j.jmoldx.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 09/10/2023] Open
Abstract
Recessive variants in GJB2 are the most important genetic cause of sensorineural hearing impairment (SNHI) worldwide. Phenotypes vary significantly in GJB2-related SNHI, even in patients with identical variants. For instance, patients homozygous for the GJB2 p.V37I variant, which is highly prevalent in the Asian populations, usually present with mild-to-moderate SNHI; yet severe-to-profound SNHI is occasionally observed in approximately 10% of p.V37I homozygotes. To investigate the genomic underpinnings of the phenotypic variability, we performed next-generation sequencing of GJB2 and other deafness genes in 63 p.V37I homozygotes with extreme phenotypic severities. Additional pathogenic variants of other deafness genes were identified in five of the 35 patients with severe-to-profound SNHI. Furthermore, case-control association analyses were conducted for 30 unrelated p.V37I homozygotes with severe-to-profound SNHI against 28 p.V37I homozygotes with mild-to-moderate SNHI, and 120 population controls from the Taiwan Biobank. The severe-to-profound group exhibited a higher frequency of the crystallin lambda 1 (CRYL1) variant (rs14236), located upstream of GJB2, than the mild-to-moderate and Taiwan Biobank groups. Our results demonstrated that pathogenic variants in other deafness genes and a possible modifier, the CRYL1 rs14236 variant, may contribute to phenotypic variability in GJB2-realted SNHI, highlighting the importance of comprehensive genomic surveys to delineate the genotype-phenotype correlations.
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Affiliation(s)
- Yu-Ting Chiang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Hsuan Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Otolaryngology Head and Neck Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Yu Lo
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Lin Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Surgical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Chen-Yu Lee
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Cheng-Yu Tsai
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yin-Hung Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Feng Tsai
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Tien-Chen Liu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chuan-Jen Hsu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Otolaryngology Head and Neck Surgery, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Jacob Shu-Jui Hsu
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Chen-Chi Wu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
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Liao Y, Chen Y, Hsiao T, Lin C, Wu M, Hsu C, Chen Y, Hsu C. CYP2C19 genotypes and osteoporotic fractures in long-term users of proton pump inhibitors: A hospital-based study. Clin Transl Sci 2023; 16:2198-2208. [PMID: 37641483 PMCID: PMC10651637 DOI: 10.1111/cts.13620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/25/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
Proton pump inhibitors (PPIs) are commonly prescribed medications. The existing data suggest that individuals at a high risk of fractures have been exposed to high doses of PPIs for prolonged durations. CYP2C19 plays a pivotal role in metabolism of PPIs and thereby influences their pharmacokinetic profile. Hence, we hypothesize that CYP2C19 genotypes may be associated with fragility fracture among PPIs users due to PPI exposure. This study aimed to investigate the association between CYP2C19 genotypes, bone mineral density (BMD), and osteoporotic fracture in a hospital-based population. This retrospective cohort study enrolled patients who were prescribed long-term PPIs at Taichung Veterans General Hospital using data extracted from the Taiwan Precision Medicine Initiative between January 2010 and April 2021. Associations between CYP2C19 phenotypes, comorbidities, and fractures in PPI users were analyzed. We enrolled 1518 long-term PPI users; 571 (38%), 727 (48%), and 220 (14%) CYP2C19 normal metabolizers (NMs), intermediate metabolizers (IMs), and poor metabolizers (PMs), respectively. Among them, 49 (3.2%) patients developed fractures within the 1-year follow-up period; 20 (3.5%) fractures in NMs, 24 (3.3%) in IMs, and 5 (2.3%) in PMs, respectively. No significant difference was observed among CYP2C19 genotypes and fracture. Additionally, BMD measurements during the 1-year follow-up period were made available among 75 participants. No significant difference in BMD between CYP2C19 PMs and non-PMs was found. This real-world, hospital-based study concludes that CYP2C19 PMs/IMs are not associated with an increased risk for fractures or reduced BMD in individuals on long-term PPI therapy.
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Affiliation(s)
- Yi‐Ju Liao
- Department of PharmacyTaichung Veterans General HospitalTaichungTaiwan
- Department of PharmacyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yu‐Ting Chen
- Department of PharmacyTaichung Veterans General HospitalTaichungTaiwan
| | - Tzu‐Hung Hsiao
- Department of Medical ResearchTaichung Veterans General HospitalTaichungTaiwan
- Department of Public HealthFu Jen Catholic UniversityNew TaipeiTaiwan
- Institute of Public Health and Community Medicine Research CenterNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Ching‐Heng Lin
- Department of Medical ResearchTaichung Veterans General HospitalTaichungTaiwan
- Department of Public HealthFu Jen Catholic UniversityNew TaipeiTaiwan
- Institute of Public Health and Community Medicine Research CenterNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
- Department of Industrial Engineering and Enterprise InformationTunghai UniversityTaichungTaiwan
| | - Ming‐Fen Wu
- Department of PharmacyTaichung Veterans General HospitalTaichungTaiwan
| | - Chiann‐Yi Hsu
- Department of Medical ResearchTaichung Veterans General HospitalTaichungTaiwan
- Biostatistics Task Force of Taichung Veterans General HospitalTaichungTaiwan
| | - Yi‐Ming Chen
- Department of Medical ResearchTaichung Veterans General HospitalTaichungTaiwan
- Division of Allergy, Immunology and Rheumatology, Department of Internal MedicineTaichung Veterans General HospitalTaichungTaiwan
- Department of Post‐Baccalaureate Medicine, College of MedicineNational Chung Hsing UniversityTaichungTaiwan
- School of MedicineNational Yang‐Ming Chiao Tung UniversityTaipeiTaiwan
- Rong Hsing Research Center for Translational Medicine & Ph.D. Program in Translational MedicineNational Chung Hsing UniversityTaichungTaiwan
- Precision Medicine Research Center, College of MedicineNational Chung Hsing UniversityTaichungTaiwan
| | - Chun‐Sheng Hsu
- Department of Post‐Baccalaureate Medicine, College of MedicineNational Chung Hsing UniversityTaichungTaiwan
- Department of Physical Medicine and RehabilitationTaichung Veterans General HospitalTaichungTaiwan
- School of MedicineNational Defense Medical CenterTaipeiTaiwan
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Wu P, Liu Z, Tian Z, Wu B, Shao J, Li Q, Geng Z, Pan Y, Lu K, Wang Q, Xu T, Zhou K. CYP2C19 Loss-of-Function Variants Associated With Long-Term Ischemic Stroke Events During Clopidogrel Treatment in the Chinese Population. Clin Pharmacol Ther 2023; 114:1126-1133. [PMID: 37607302 DOI: 10.1002/cpt.3028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/12/2023] [Indexed: 08/24/2023]
Abstract
This study aims to determine whether CYP2C19 loss-of-function (LoF) variants were associated with long-term ischemic stroke risk in Chinese primary care patients treated with clopidogrel. Patients treated with clopidogrel were ascertained from Chinese electronic medical records linked with a biobank for a retrospective cohort study. Their medical information was examined for the period from January 2018 to December 2021. Two CYP2C19 major loss of function variants (*2:rs4244285 and *3: rs4986893) were genotyped. The clinical outcome was ischemic stroke event. Cox regression analysis was used to evaluate the association between the occurrence of ischemic stroke events and CYP2C19 LoF variants. Covariates included age, gender, body mass index, prior ischemic stroke, transient ischemic attack, hypertension, diabetes mellitus, hyperlipoidemia, smoke status, aspirin use, proton-pump inhibitor use, and statin use. Of the 1,141 patients included in the clopidogrel therapy cohort, 61.9% carried at least one CYP2C19 LoF variant. During a median follow-up period of 12 months, 103 patients (9.0%) had an ischemic stroke. After adjusting for other risk factors, carriers of CYP2C19 LoF variants had significantly higher risk of ischemic stroke compared with non-carriers (hazard ratio: 1.64, 95% confidence interval: 1.06-2.53, P = 0.025). This pharmacogenetic study of clopidogrel provides novel insights into the association between the CYP2C19 LoF variant and long-term stroke risk. We established that there is still a need for CYP2C19 genotype-guided personalized antiplatelet therapy in those who have returned to the primary care setting for clopidogrel prescription.
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Affiliation(s)
- Peng Wu
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Ziqing Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zijian Tian
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Benrui Wu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jian Shao
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Qian Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoxu Geng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Pan
- Department of General Practice, Kunshan Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, China
| | - Ke Lu
- Department of General Practice, Kunshan Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, China
| | - Qiang Wang
- Department of General Practice, Kunshan Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, China
| | - Tao Xu
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kaixin Zhou
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
- College of Public Health, Guangzhou Medical University, Guangzhou, China
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Cahoon JL, Rui X, Tang E, Simons C, Langie J, Chen M, Lo YC, Chiang CWK. Imputation Accuracy Across Global Human Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541241. [PMID: 37292811 PMCID: PMC10245797 DOI: 10.1101/2023.05.22.541241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Genotype imputation is now fundamental for genome-wide association studies but lacks fairness due to the underrepresentation of populations with non-European ancestries. The state-of-the-art imputation reference panel released by the Trans-Omics for Precision Medicine (TOPMed) initiative contains a substantial number of admixed African-ancestry and Hispanic/Latino samples to impute these populations with nearly the same accuracy as European-ancestry cohorts. However, imputation for populations primarily residing outside of North America may still fall short in performance due to persisting underrepresentation. To illustrate this point, we curated genome-wide array data from 23 publications published between 2008 to 2021. In total, we imputed over 43k individuals across 123 populations around the world. We identified a number of populations where imputation accuracy paled in comparison to that of European-ancestry populations. For instance, the mean imputation r-squared (Rsq) for 1-5% alleles in Saudi Arabians (N=1061), Vietnamese (N=1264), Thai (N=2435), and Papua New Guineans (N=776) were 0.79, 0.78, 0.76, and 0.62, respectively. In contrast, the mean Rsq ranged from 0.90 to 0.93 for comparable European populations matched in sample size and SNP content. Outside of Africa and Latin America, Rsq appeared to decrease as genetic distances to European reference increased, as predicted. Further analysis using sequencing data as ground truth suggested that imputation software may over-estimate imputation accuracy for non-European populations than European populations, suggesting further disparity between populations. Using 1496 whole genome sequenced individuals from Taiwan Biobank as a reference, we also assessed a strategy to improve imputation for non-European populations with meta-imputation, which can combine results from TOPMed with smaller population-specific reference panels. We found that meta-imputation in this design did not improve Rsq genome-wide. Taken together, our analysis suggests that with the current size of alternative reference panels, meta-imputation alone cannot improve imputation efficacy for underrepresented cohorts and we must ultimately strive to increase diversity and size to promote equity within genetics research.
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Affiliation(s)
- Jordan L. Cahoon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Echo Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Christopher Simons
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ying-Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Charleston W. K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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Yang TL, Ting J, Lin MR, Chang WC, Shih CM. Identification of Genetic Variants Associated with Severe Myocardial Bridging through Whole-Exome Sequencing. J Pers Med 2023; 13:1509. [PMID: 37888120 PMCID: PMC10608235 DOI: 10.3390/jpm13101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Myocardial bridging (MB) is a congenital coronary artery anomaly and an important cause of angina. The genetic basis of MB is currently unknown. This study used a whole-exome sequencing technique and analyzed genotypic differences. Eight coronary angiography-confirmed cases of severe MB and eight age- and sex-matched control patients were investigated. In total, 139 rare variants that are potentially pathogenic for severe MB were identified in 132 genes. Genes with multiple rare variants or co-predicted by ClinVar and CADD/REVEL for severe MB were collected, from which heart-specific genes were selected under the guidance of tissue expression levels. Functional annotation indicated significant genetic associations with abnormal skeletal muscle mass, cardiomyopathies, and transmembrane ion channels. Candidate genes were reviewed regarding the functions and locations of each individual gene product. Among the gene candidates for severe MB, rare variants in DMD, SGCA, and TTN were determined to be the most crucial. The results suggest that altered anchoring proteins on the cell membrane and intracellular sarcomere unit of cardiomyocytes play a role in the development of the missed trajectory of coronary vessels. Additional studies are required to support the diagnostic application of cardiac sarcoglycan and dystroglycan complexes in patients with severe MB.
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Affiliation(s)
- Tsung-Lin Yang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Cardiovascular Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Taipei Heart Institute, Taipei Medical University, Taipei 11031, Taiwan
| | - Jafit Ting
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (J.T.); (M.-R.L.)
| | - Min-Rou Lin
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (J.T.); (M.-R.L.)
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan; (J.T.); (M.-R.L.)
- Master’ Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
| | - Chun-Ming Shih
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Cardiovascular Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Taipei Heart Institute, Taipei Medical University, Taipei 11031, Taiwan
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Jiang RS, Chen IC, Chen YM, Hsiao TH, Chen YC. Risk Prediction of Chronic Rhinosinusitis with or without Nasal Polyps in Taiwanese Population Using Polygenic Risk Score for Nasal Polyps. Biomedicines 2023; 11:2729. [PMID: 37893103 PMCID: PMC10603974 DOI: 10.3390/biomedicines11102729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/30/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
The association between single nucleotide polymorphisms and chronic rhinosinusitis (CRS) has been determined. However, it was not known whether the polygenic risk score (PRS) for nasal polyps (NP) could predict CRS with NP (CRSwNP) or without NP (CRSsNP). The aim of this study was to investigate the association between PRSs for NP and the risk of CRS with or without NP. Data from 535 individuals with CRS and 5350 control subjects in the Taiwan Precision Medicine Initiative project were collected. Four PRSs for NP, including PGS000933, PGS000934, PGS001848, and PGS002060 from UK Biobank, were tested in these participants. They were divided into four groups according to quartiles of PRSs. The logistic regression model was performed to evaluate CRSwNP and CRSsNP risk according to PRSs for NP. The PGS002060 had the highest area under the curve at 0.534 for CRSsNP prediction and at 0.588 for CRSwNP prediction. Compared to subjects in the lowest PRS category, the PGS002060 significantly increased the odds for CRSsNP by 1.48 at the highest quintile (p = 0.003) and by 2.32 at the highest quintile for CRSwNP (p = 0.002). In addition, the odds for CRSwNP increased by 3.01 times in female CRSwNP patients (p = 0.009) at the highest quintile compared with those in the lowest PRS category. The PRSs for NP developed from European populations could be applied to the Taiwanese population to predict CRS risk, especially for female CRSwNP.
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Affiliation(s)
- Rong-San Jiang
- Departments of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan; (R.-S.J.); (I.-C.C.); (Y.-M.C.); (T.-H.H.)
- Departments of Otolaryngology, Taichung Veterans General Hospital, Taichung 407219, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan
- RongHsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402202, Taiwan
| | - I-Chieh Chen
- Departments of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan; (R.-S.J.); (I.-C.C.); (Y.-M.C.); (T.-H.H.)
| | - Yi-Ming Chen
- Departments of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan; (R.-S.J.); (I.-C.C.); (Y.-M.C.); (T.-H.H.)
- RongHsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402202, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
- Division of Allergy, Immunology and Rheumatology, Taichung Veterans General Hospital, Taichung 407219, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Biomedical Science, National Chung Hsing University, Taichung 402202, Taiwan
- Precision Medicine Research Center, College of Medicine, National Chung Hsing University, Taichung 402202, Taiwan
| | - Tzu-Hung Hsiao
- Departments of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan; (R.-S.J.); (I.-C.C.); (Y.-M.C.); (T.-H.H.)
- Department of Public Health, Fu Jen Catholic University, New Taipei City 242062, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402202, Taiwan
| | - Yi-Chen Chen
- Departments of Medical Research, Taichung Veterans General Hospital, Taichung 407219, Taiwan; (R.-S.J.); (I.-C.C.); (Y.-M.C.); (T.-H.H.)
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Tsai MJM, Hung MZ, Lin YL, Lee NC, Chien YH, Hwu WL. Curated incidence of lysosomal storage diseases from the Taiwan Biobank. NPJ Genom Med 2023; 8:27. [PMID: 37741878 PMCID: PMC10517920 DOI: 10.1038/s41525-023-00372-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/04/2023] [Indexed: 09/25/2023] Open
Abstract
Lysosomal storage diseases (LSDs) are a group of metabolic disorders resulting from a deficiency in one of the lysosomal hydrolases. Most LSDs are inherited in an autosomal or X-linked recessive manner. As LSDs are rare, their true incidence in Taiwan remains unknown. In this study, we used high-coverage whole-genome sequencing data from 1,495 Taiwanese individuals obtained from the Taiwan Biobank. We found 3826 variants in 71 genes responsible for autosomal recessive LSDs. We first excluded benign variants by allele frequency and other criteria. As a result, 270 variants were considered disease-causing. We curated these variants using published guidelines from the American College of Medical Genetics and Genomics (ACMG). Our results revealed a combined incidence rate of 13 per 100,000 (conservative estimation by pathologic and likely pathogenic variants; 95% CI 6.92-22.23) to 94 per 100,000 (extended estimation by the inclusion of variants of unknown significance; 95% CI 75.96-115.03) among 71 autosomal recessive disease-associated genes. The conservative estimations were similar to those in published clinical data. No disease-causing mutations were found for 18 other diseases; thus, these diseases are likely extremely rare in Taiwan. The study results are important for designing screening and treatment methods for LSDs in Taiwan and demonstrate the importance of mutation curation to avoid overestimating disease incidences from genomic data.
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Affiliation(s)
- Meng-Ju Melody Tsai
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Miao-Zi Hung
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan.
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Chen YC, Liaw YC, Nfor ON, Hsiao CH, Zhong JH, Wu SL, Liaw YP. Epigenetic regulation of Parkinson's disease risk variant GPNMB cg17274742 methylation by sex and exercise from Taiwan Biobank. Front Aging Neurosci 2023; 15:1235840. [PMID: 37744396 PMCID: PMC10513104 DOI: 10.3389/fnagi.2023.1235840] [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: 06/06/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Background Parkinson's disease (PD) is a complex neurodegenerative disease with an elusive etiology that involves the interaction between genetic, behavioral, and environmental factors. Recently, epigenetic modifications, particularly DNA methylation, have been recognized to play an important role in the onset of PD. Glycoprotein non-metastatic melanoma protein B (GPNMB), a type I transmembrane protein crucial for immune cell activation and maturation, has emerged as a potential biomarker for the risk of PD. This research aims to investigate the influence of exercise and gender on the regulation of methylation levels of GPNMB cg17274742 in individuals. Methods We analyze data from 2,474 participants in the Taiwan Biobank, collected from 2008 and 2016. Methylation levels at the GPNMB cg17274742 CpG site were measured using Illumina Infinium MethylationEPIC beads. After excluding individuals with incomplete data or missing information on possible risk factors, our final analysis included 1,442 participants. We used multiple linear regression models to assess the association between sex and exercise with adjusted levels of GPNMB cg17274742 for age, BMI, smoking, drinking, coffee consumption, serum uric acid levels, and hypertension. Results Our results demonstrated that exercise significantly influenced the methylation levels of GPNMB cg17274742 in males (β = -0.00242; p = 0.0026), but not in females (β = -0.00002362; p = 0.9785). Furthermore, male participants who exercised showed significantly lower levels of methylation compared to the reference groups of the female and non-exercising reference groups (β = -0.00357; p = 0.0079). The effect of the interaction between gender and exercise on the methylation of GPNMB cg17274742 was statistically significant (p = 0.0078). Conclusion This study suggests that gender and exercise can modulate GPNMB cg17274742, with hypomethylation observed in exercise men. More research is needed to understand the underlying mechanisms and implications of these epigenetic changes in the context of risk and prevention strategies.
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Affiliation(s)
- Yen-Chung Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Chia Liaw
- Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Shey-Lin Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Electrical Engineering, Changhua National University of Education, Changhua, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
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Rodriguez Llorian E, Kopac N, Waliji LA, Borle K, Dragojlovic N, Elliott AM, Lynd LD. A Rapid Review on the Value of Biobanks Containing Genetic Information. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2023; 26:1286-1295. [PMID: 36921900 DOI: 10.1016/j.jval.2023.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVES Increasing access to health data through biobanks containing genetic information has the potential to expand the knowledge base and thereby improve screening, diagnosis, and treatment options for many diseases. Nevertheless, although privacy concerns and risks surrounding genetic data sharing are well documented, direct evidence in favor of the hypothesized benefits of data integration is scarce, which complicates decision making in this area. Therefore, the objective of this study is to summarize the available evidence on the research and clinical impacts of biobanks containing genetic information, so as to better understand how to quantify the value of expanding genomic data access. METHODS Using a rapid review methodology, we performed a search of MEDLINE/PubMed and Embase databases; and websites of biobanks and genomic initiatives published from 2010 to 2022. We classified findings into 11 indicators including outputs (a direct product of the biobank activities) and outcomes (changes in scientific and clinical capacity). RESULTS Of 8479 abstracts and 101 gray literature sources were reviewed, 96 records were included. Although most records did not report key indicators systematically, the available evidence concentrated on research indicators such as publications and gene-disorder association discoveries (63% of studies), followed by research infrastructure (26%), and clinical indicators (11%) such as supporting the diagnosis of individual patients. CONCLUSIONS Existing evidence on the benefits of biobanks is skewed toward easily quantifiable research outputs. Measuring a comprehensive set of outputs and outcomes inspired by value frameworks is necessary to generate better evidence on the benefits of genomic data sharing.
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Affiliation(s)
- Elisabet Rodriguez Llorian
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Nicola Kopac
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Louloua Ashikhusein Waliji
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kennedy Borle
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada; Centre for Health Evaluation and Outcome Sciences (CHÉOS), St. Paul's Hospital, Vancouver, BC, Canada
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Huang LC, Lee MY, Chien CF, Chang YP, Li KY, Yang YH. Age and sex differences in the association between APOE genotype and Alzheimer's disease in a Taiwan Chinese population. Front Aging Neurosci 2023; 15:1246592. [PMID: 37680541 PMCID: PMC10481952 DOI: 10.3389/fnagi.2023.1246592] [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: 06/24/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction The Apolipoprotein E (APOE) epsilon (ε) 4 allele is a well-established risk factor for late-onset Alzheimer's disease (AD). Reports on white ancestry populations have showed that age, sex, and ethnicity have different effects on the association between APOE genotype and AD. However, studies on Asian populations such as Taiwan Chinese populations are limited. This study aimed to evaluate the association between APOE genotype and AD in a Taiwan Chinese population, and to explore if the association varies by age and sex. Methods We conducted a case-control study in 725 patients with AD and 1,067 age- and sex- matched controls without dementia from a Taiwan Chinese population. Logistic regression models were used to test the association between AD and APOE genotypes. Secondary analyses considered age (<75 or ≥75 years old), and sex stratified models. Results The risk of AD was significantly increased for people with at least one copy of APOE ε4 (OR = 2.52, 95% CI = 2.01-3.17, p < 0.001) and in a dose-dependent manner. Our results did not show an statistically significance different in AD risk when women and men carrying APOEε4 were compared. Despite not reaching statistical significance, the risk of APOE ε4 for AD was higher among younger participants (OR = 3.21, 95% CI = 2.26-4.56, p < 0.001) compared to older ones (OR = 2.13, 95% CI = 1.53-2.97, p < 0.001). When considering both sex and age, the risk of AD was higher among older men carrying APOE ε4 (OR = 2.64, 95% CI = 1.51-4.60 in men; OR = 1.90, 95% CI = 1.26-2.86 in women), while women carrying APOE ε4 appeared to have an increased risk at a younger age (OR = 3.29, 95% CI = 2.20-4.93 in women; OR = 2.91, 95% CI = 1.40-6.05 in men). Discussion The APOE ε4 allele represents a major risk factor for AD in the Taiwanese population. The effect of APOE ε4 allele on AD risk appeared to be stronger among men aged 75 years or more and among younger women.
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Affiliation(s)
- Ling-Chun Huang
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mei-Yueh Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Fang Chien
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yang-Pei Chang
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuan-Ying Li
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuan-Han Yang
- Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Fan HY, Chien KL, Huang YT, Hsu JB, Chen YY, Lai EY, Su JY, Lu TP, Li HY, Hsu SY, Chen YC. Hypertension as a Novel Link for Shared Heritability in Age at Menarche and Cardiometabolic Traits. J Clin Endocrinol Metab 2023; 108:2389-2399. [PMID: 36810613 DOI: 10.1210/clinem/dgad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
CONTEXT Extremely early age at menarche, also called precocious puberty, has been associated with various cardiometabolic traits, but their shared heritability remains unclear. OBJECTIVES This work aimed to identify new shared genetic variants and their pathways for age at menarche and cardiometabolic traits and to investigate the influence of central precocious puberty on childhood cardiometabolic traits. METHODS Using the conjunction false discovery rate method, this study analyzed genome-wide association study data from the menarche-cardiometabolic traits among 59 655 females of Taiwanese ancestry and systemically investigated pleiotropy between age at menarche and cardiometabolic traits. To support the novel hypertension link, we used the Taiwan Puberty Longitudinal Study (TPLS) to investigate the influence of precocious puberty on childhood cardiometabolic traits. RESULTS We discovered 27 novel loci, with an overlap between age at menarche and cardiometabolic traits, including body fat and blood pressure. Among the novel genes discovered, SEC16B, CSK, CYP1A1, FTO, and USB1 are within a protein interaction network with known cardiometabolic genes, including traits for obesity and hypertension. These loci were confirmed through demonstration of significant changes in the methylation or expression levels of neighboring genes. Moreover, the TPLS provided evidence regarding a 2-fold higher risk of early-onset hypertension that occurred in girls with central precocious puberty. CONCLUSION Our study highlights the usefulness of cross-trait analyses for identifying shared etiology between age at menarche and cardiometabolic traits, especially early-onset hypertension. The menarche-related loci may contribute to early-onset hypertension through endocrinological pathways.
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Affiliation(s)
- Hsien-Yu Fan
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Kuo-Liong Chien
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Yen-Tsung Huang
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan
- Department of Mathematics, National Taiwan University, Taipei 106, Taiwan
| | - Justin BoKai Hsu
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan
| | - Yun-Yu Chen
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 407, Taiwan
- Cardiovascular Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
- Heart Rhythm Center, Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Cardiovascular Research Center, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - En-Yu Lai
- Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan
| | - Jia-Ying Su
- Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Hung-Yuan Li
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Shih-Yuan Hsu
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Yang-Ching Chen
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Family Medicine, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan
- Graduate Institute of Metabolism and Obesity Sciences, Taipei Medical University, Taipei 110, Taiwan
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Liu TY, Hsu HY, You YS, Hsieh YW, Lin TC, Peng CW, Huang HY, Chang SS, Tsai FJ. Efficacy of Warfarin Therapy Guided by Pharmacogenetics: A Real-world Investigation Among Han Taiwanese. Clin Ther 2023; 45:662-670. [PMID: 37301690 DOI: 10.1016/j.clinthera.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/01/2023] [Accepted: 04/10/2023] [Indexed: 06/12/2023]
Abstract
PURPOSE The anticoagulation activity of warfarin in populations with CYP2C9, VKORC1, and CYP4F2 variants differs between individuals and is correlated with poor international normalized ratio (INR) control. Pharmacogenetics-guided warfarin dosing has been successfully developed for patients with genetic variations in recent years. However, few real-world data have been used to investigate the INR and warfarin dosage and the time to target INR. This study examined the largest collection of genetic and clinical real-world data related to warfarin to provide further evidence supporting the benefits of pharmacogenetics in clinical outcomes. METHODS We retrieved a total of 69,610 INR-warfarin records after the index date from 2,613 patients in the China Medical University Hospital database between January 2003 and December 2019. Each INR reading was obtained from the latest laboratory data after the hospital visit date. Patients with a history of malignant neoplasms or pregnancy before the index date were excluded, as were patients without data on INR measurements after the fifth day of prescription, genetic information, or gender variables. The primary outcomes were the INR and warfarin dosage during days 7, 14, 28, 56, and 84 after prescription. The secondary outcome was the time required to reach the INR ranges of 1.5 to 3.0 and >4.0. FINDINGS A total of 59,643 INR-warfarin records from 2188 patients were retrieved. The average INR was higher for homozygous carriers of the minor allele at CYP2C9 and VKORC1 during the first 7 days (1.83 [1.03] [CYP2C9*1] and 2.46 [1.44] [CYP2C9*3], P < 0.001; 1.39 [0.36] [rs9923231 G/G], 1.55 [0.79] [rs9923231 G/A], and 1.96 [1.13] [rs9923231 A/A], P < 0.001) than for the wild-type allele. These patients with variants required lower warfarin doses than those with the wild-type allele during the first 28 days. CYP4F2 variant patients seemed to require higher doses of warfarin than those in the wild-type group; however, no significant difference in the average INR was observed (1.95 [1.14] [homozygous V433 carriers], 1.78 [0.98] [heterozygous V433M carriers], and 1.66 [0.91] [homozygous M433 carriers], P = 0.016). IMPLICATIONS Our study indicates that genetic variants in the Han population may enhance warfarin responsiveness, which holds clinical relevance. An increased warfarin dosage was not linked to a shorter time to therapeutic INR between CYP4F2 variant patients and those with a wild-type allele. Assessing CYP2C9 and VKORC1 genetic polymorphisms before initiating warfarin treatment in real-world practice is essential for potentially vulnerable patients and is likely to optimize therapeutic dosing.
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Affiliation(s)
- Ting-Yuan Liu
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
| | - Hsing-Yu Hsu
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan.
| | - Ying-Shu You
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.
| | - Yow-Wen Hsieh
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan.
| | - Tzu-Ching Lin
- Department of Pharmacy, China Medical University Hospital, Taichung, Taiwan.
| | - Chun-Wei Peng
- Artificial Intelligence and Data Science, National Chung Hsing University, Taichung, Taiwan.
| | - Hsin-Yi Huang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, Taiwan.
| | - Shih-Sheng Chang
- Division of Cardiovascular Medicine, China Medical University Hospital, Taichung, Taiwan; School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan.
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan; Division of Pediatric Genetics, Children's Hospital of China Medical University, Taichung, Taiwan; Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
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50
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Wall JD, Sathirapongsasuti JF, Gupta R, Rasheed A, Venkatesan R, Belsare S, Menon R, Phalke S, Mittal A, Fang J, Tanneeru D, Deshmukh M, Bassi A, Robinson J, Chaudhary R, Murugan S, Ul-Asar Z, Saleem I, Ishtiaq U, Fatima A, Sheikh SS, Hameed S, Ishaq M, Rasheed SZ, Memon FUR, Jalal A, Abbas S, Frossard P, Fuchsberger C, Forer L, Schoenherr S, Bei Q, Bhangale T, Tom J, Gadde SGK, B V P, Naik NK, Wang M, Kwok PY, Khera AV, Lakshmi BR, Butterworth AS, Chowdhury R, Danesh J, di Angelantonio E, Naheed A, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Ramprasad VL, Kukkle PL, Seshagiri S, Kathiresan S, Ghosh A, Mohan V, Saleheen D, Stawiski EW, Peterson AS. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity. Nat Commun 2023; 14:3377. [PMID: 37291107 PMCID: PMC10250394 DOI: 10.1038/s41467-023-38766-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
- Dept of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - J Fah Sathirapongsasuti
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
| | - Ravi Gupta
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Asif Rasheed
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Radha Venkatesan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Saurabh Belsare
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | - Ramesh Menon
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Sameer Phalke
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - John Fang
- Thermo Fisher Scientific, Santa Clara, CA, 95051, USA
| | - Deepak Tanneeru
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - Akshi Bassi
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | | | | | - Zameer Ul-Asar
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Imran Saleem
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Unzila Ishtiaq
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Areej Fatima
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | | | | | | | | | | | - Anjum Jalal
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Shahid Abbas
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Philippe Frossard
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Qixin Bei
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, 94080, USA
| | - Jennifer Tom
- Product Development Data Sciences, Genentech, South San Francisco, CA, 94080, USA
| | | | - Priya B V
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | | | - Minxian Wang
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
- Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Amit V Khera
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, MA, 02115, Boston, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
| | - B R Lakshmi
- MDCRC, Royal Care Super Speciality Hospital 1/520, Neelambur, Coimbatore, Tamil Nadu, 641062, India
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Emanuele di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Aliya Naheed
- Initiative for Non Communicable Diseases, Health Systems and Population Studies Division, icddr,b, Dhaka, Bangladesh
| | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | | | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Soaham Desai
- Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Karamsad, Gujarat, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
| | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod Kumar Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Uday B Muthane
- Parkinson and Ageing Research Foundation, Bengaluru, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Prashanth L Kukkle
- All India Institute of Medical Sciences, Rishikesh, India
- Manipal Hospital, Miller Road, Bengaluru, India
- Parkinson's Disease and Movement Disorders Clinic, Bengaluru, India
| | - Somasekar Seshagiri
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Arkasubhra Ghosh
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | - V Mohan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Danish Saleheen
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
- Seymour, Paul and Gloria Milstein Division of Cardiology at Columbia University, New York, NY, 10032, USA
| | - Eric W Stawiski
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
- Caribou Biosciences, Berkeley, CA, 94710, USA
| | - Andrew S Peterson
- MedGenome Inc., Foster City, CA, 94404, USA.
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.
- Broadwing Bio, South San Francisco, CA, 94080, USA.
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