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da Silva RGL. The advancement of artificial intelligence in biomedical research and health innovation: challenges and opportunities in emerging economies. Global Health 2024; 20:44. [PMID: 38773458 PMCID: PMC11107016 DOI: 10.1186/s12992-024-01049-5] [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: 11/10/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
The advancement of artificial intelligence (AI), algorithm optimization and high-throughput experiments has enabled scientists to accelerate the discovery of new chemicals and materials with unprecedented efficiency, resilience and precision. Over the recent years, the so-called autonomous experimentation (AE) systems are featured as key AI innovation to enhance and accelerate research and development (R&D). Also known as self-driving laboratories or materials acceleration platforms, AE systems are digital platforms capable of running a large number of experiments autonomously. Those systems are rapidly impacting biomedical research and clinical innovation, in areas such as drug discovery, nanomedicine, precision oncology, and others. As it is expected that AE will impact healthcare innovation from local to global levels, its implications for science and technology in emerging economies should be examined. By examining the increasing relevance of AE in contemporary R&D activities, this article aims to explore the advancement of artificial intelligence in biomedical research and health innovation, highlighting its implications, challenges and opportunities in emerging economies. AE presents an opportunity for stakeholders from emerging economies to co-produce the global knowledge landscape of AI in health. However, asymmetries in R&D capabilities should be acknowledged since emerging economies suffers from inadequacies and discontinuities in resources and funding. The establishment of decentralized AE infrastructures could support stakeholders to overcome local restrictions and opens venues for more culturally diverse, equitable, and trustworthy development of AI in health-related R&D through meaningful partnerships and engagement. Collaborations with innovators from emerging economies could facilitate anticipation of fiscal pressures in science and technology policies, obsolescence of knowledge infrastructures, ethical and regulatory policy lag, and other issues present in the Global South. Also, improving cultural and geographical representativeness of AE contributes to foster the diffusion and acceptance of AI in health-related R&D worldwide. Institutional preparedness is critical and could enable stakeholders to navigate opportunities of AI in biomedical research and health innovation in the coming years.
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Affiliation(s)
- Renan Gonçalves Leonel da Silva
- Health Ethics and Policy Lab, Department of Health Sciences and Technology, ETH Zurich, Hottingerstrasse 10, HOA 17, Zurich, 8092, Switzerland.
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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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Yaoita H, Kawai E, Takayama J, Iwasawa S, Saijo N, Abiko M, Suzuki K, Kimura M, Ozawa A, Tamiya G, Kure S, Kikuchi A. Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population. J Hum Genet 2024; 69:177-183. [PMID: 38351237 PMCID: PMC11043042 DOI: 10.1038/s10038-024-01223-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: 10/23/2023] [Revised: 01/05/2024] [Accepted: 01/25/2024] [Indexed: 02/19/2024]
Abstract
Truncus Arteriosus (TA) is a congenital heart disease characterized by a single common blood vessel emerging from the right and left ventricles instead of the main pulmonary artery and aorta. TA accounts for 4% of all critical congenital heart diseases. The most common cause of TA is 22q11.2 deletion syndrome, accounting for 12-35% of all TA cases. However, no major causes of TA other than 22q11.2 deletion have been reported. We performed whole-genome sequencing of 11 Japanese patients having TA without 22q11.2 deletion. Among five patients, we identified pathogenic variants in TMEM260; the biallelic loss-of-function variants of which have recently been associated with structural heart defects and renal anomalies syndrome (SHDRA). In one patient, we identified a de novo pathogenic variant in GATA6, and in another patient, we identified a de novo probably pathogenic variant in NOTCH1. Notably, we identified a prevalent variant in TMEM260 (ENST00000261556.6), c.1617del (p.Trp539Cysfs*9), in 8/22 alleles among the 11 patients. The c.1617del variant was estimated to occur approximately 23 kiloyears ago. Based on the allele frequency of the c.1617del variant in the Japanese population (0.36%), approximately 26% of Japanese patients afflicted with TA could harbor homozygous c.1617del variants. This study highlights TMEM260, especially c.1617del, as a major genetic cause of TA in the Japanese population.
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Affiliation(s)
- Hisao Yaoita
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Eiichiro Kawai
- Department of Pediatric Cardiology, Miyagi Children's Hospital, Sendai, Japan
| | - Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank organization, Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shinya Iwasawa
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoya Saijo
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Abiko
- Department of Pediatrics, Yamagata University Graduate School of Medicine, Yamagata, Japan
| | - Kouta Suzuki
- Department of Pediatrics, Yamagata University Graduate School of Medicine, Yamagata, Japan
| | - Masato Kimura
- Department of Pediatric Cardiology, Miyagi Children's Hospital, Sendai, Japan
| | - Akira Ozawa
- Department of Pediatric Cardiology, Miyagi Children's Hospital, Sendai, Japan
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank organization, Tohoku University, Sendai, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan
- Miyagi Children's Hospital, Sendai, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan.
- Department of Rare Disease Genomics, Tohoku University Graduate School of Medicine, Sendai, Japan.
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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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Pan YW, Ou TY, Chou YY, Kuo PL, Hsiao HP, Chiu PC, Lin JL, Lo FS, Wang CH, Chen PC, Tsai MC. Syndromic ciliopathy: a taiwanese single-center study. BMC Med Genomics 2024; 17:106. [PMID: 38671463 PMCID: PMC11046915 DOI: 10.1186/s12920-024-01880-0] [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: 10/12/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Syndromic ciliopathies are a group of congenital disorders characterized by broad clinical and genetic overlap, including obesity, visual problems, skeletal anomalies, mental retardation, and renal diseases. The hallmark of the pathophysiology among these disorders is defective ciliary functions or formation. Many different genes have been implicated in the pathogenesis of these diseases, but some patients still remain unclear about their genotypes. METHODS The aim of this study was to identify the genetic causes in patients with syndromic ciliopathy. Patients suspected of or meeting clinical diagnostic criteria for any type of syndromic ciliopathy were recruited at a single diagnostic medical center in Southern Taiwan. Whole exome sequencing (WES) was employed to identify their genotypes and elucidate the mutation spectrum in Taiwanese patients with syndromic ciliopathy. Clinical information was collected at the time of patient enrollment. RESULTS A total of 14 cases were molecularly diagnosed with syndromic ciliopathy. Among these cases, 10 had Bardet-Biedl syndrome (BBS), comprising eight BBS2 patients and two BBS7 patients. Additionally, two cases were diagnosed with Alström syndrome, one with Oral-facial-digital syndrome type 14, and another with Joubert syndrome type 10. A total of 4 novel variants were identified. A recurrent splice site mutation, BBS2: c.534 + 1G > T, was present in all eight BBS2 patients, suggesting a founder effect. One BBS2 patient with homozygous c.534 + 1G > T mutations carried a third ciliopathic allele, TTC21B: c.264_267dupTAGA, a nonsense mutation resulting in a premature stop codon and protein truncation. CONCLUSIONS Whole exome sequencing (WES) assists in identifying molecular pathogenic variants in ciliopathic patients, as well as the genetic hotspot mutations in specific populations. It should be considered as the first-line genetic testing for heterogeneous disorders characterized by the involvement of multiple genes and diverse clinical manifestations.
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Affiliation(s)
- Yu-Wen Pan
- Department of Pediatrics, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China
| | - Tsung-Ying Ou
- Department of Pediatrics, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No. 2, Minsheng Rd., Dalin Township, Chiayi County, Chiayi, 62247, Taiwan, Republic of China
| | - Yen-Yin Chou
- Department of Pediatrics, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China
- Department of Genomic Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China
| | - Pao-Lin Kuo
- Department of Genomic Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China
- Department of Gynecology and Obstetrics, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China
- Department of Obstetrics and Gynecology, E-Da Hospital, No. 1, Yida Rd., Yanchao Dist, Kaohsiung, 824005, Taiwan, Republic of China
| | - Hui-Pin Hsiao
- Department of Pediatrics, Kaohsiung Medical University Chung Ho Memorial Hospital, No. 100, Ziyou 1st Rd., Sanmin Dist, Kaohsiung, 80756, Taiwan, Republic of China
| | - Pao-Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, No. 386, Dazhong 1st Rd., Zuoying Dist, Kaohsiung, 813414, Taiwan, Republic of China
| | - Ju-Li Lin
- Department of Pediatrics, Chang Gung Children's Hospital, No. 5, Fuxing St., Guishan Dist, Taoyuan, 333423, Taiwan, Republic of China
| | - Fu-Sung Lo
- Department of Pediatrics, Chang Gung Children's Hospital, No. 5, Fuxing St., Guishan Dist, Taoyuan, 333423, Taiwan, Republic of China
| | - Chung-Hsing Wang
- Division of Genetics and Metabolism, Children's Hospital of China Medical University, No. 2, Yude Rd., North Dist, Taichung, 404327, Taiwan, Republic of China
- School of Medicine, China Medical University, No. 91, Xueshi Rd., North Dist, Taichung, 404328, Taiwan, Republic of China
| | - Peng-Chieh Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China.
- Center of Clinical Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China.
| | - Meng-Che Tsai
- Department of Pediatrics, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China.
- Department of Genomic Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China.
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 138, Shengli Rd., North Dist, Tainan, 70403, Taiwan, Republic of China.
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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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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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8
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Wang MT, Weng KP, Chang SK, Huang WC, Chen LW. Hemodynamic and Clinical Profiles of Pulmonary Arterial Hypertension Patients with GDF2 and BMPR2 Variants. Int J Mol Sci 2024; 25:2734. [PMID: 38473983 DOI: 10.3390/ijms25052734] [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: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Asians have a higher carrier rate of pulmonary arterial hypertension (PAH)-related genetic variants than Caucasians do. This study aimed to identify PAH-related genetic variants using whole exome sequencing (WES) in Asian idiopathic and heritable PAH cohorts. A WES library was constructed, and candidate variants were further validated by polymerase chain reaction and Sanger sequencing in the PAH cohort. In a total of 69 patients, the highest incidence of variants was found in the BMPR2, ATP13A3, and GDF2 genes. Regarding the BMPR2 gene variants, there were two nonsense variants (c.994C>T, p. Arg332*; c.1750C>T, p. Arg584*), one missense variant (c.1478C>T, p. Thr493Ile), and one novel in-frame deletion variant (c.877_888del, p. Leu293_Ser296del). Regarding the GDF2 variants, there was one likely pathogenic nonsense variant (c.259C>T, p. Gln87*) and two missense variants (c.1207G>A, p. Val403Ile; c.38T>C, p. Leu13Pro). The BMPR2 and GDF2 variant subgroups had worse hemodynamics. Moreover, the GDF2 variant patients were younger and had a significantly lower GDF2 value (135.6 ± 36.2 pg/mL, p = 0.002) in comparison to the value in the non-BMPR2/non-GDF2 mutant group (267.8 ± 185.8 pg/mL). The BMPR2 variant carriers had worse hemodynamics compared to the patients with the non-BMPR2/non-GDF2 mutant group. Moreover, there was a significantly lower GDF2 value in the GDF2 variant carriers compared to the control group. GDF2 may be a protective or corrected modifier in certain genetic backgrounds.
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Affiliation(s)
- Mei-Tzu Wang
- Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Critical Care Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | - Ken-Pen Weng
- Congenital Structural Heart Disease Center, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | | | - Wei-Chun Huang
- Department of Critical Care Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
- Department of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Physical Therapy, Fooyin University, Kaohsiung 813, Taiwan
| | - Lee-Wei Chen
- Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 813, Taiwan
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9
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Maliko M, Su FH, Kamiza AB, Su MJ, Yeh CC. The association between hepatic viral infections and cancers: a cross-sectional study in the Taiwan adult population. Clin Exp Med 2024; 24:20. [PMID: 38279980 PMCID: PMC10821961 DOI: 10.1007/s10238-023-01292-x] [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: 10/04/2023] [Accepted: 12/28/2023] [Indexed: 01/29/2024]
Abstract
BACKGROUND Hepatitis B (HBV) and hepatitis C (HCV) viruses are diseases of global public health concern and are associated with liver cancer. Recent studies have revealed associations between hepatic viral infections and extrahepatic cancers. This study aimed to explore the associations between hepatitis B and C viruses and cancer at baseline in the Taiwan Biobank database while controlling for a wide range of confounding variables. METHODS In a cross-sectional study of adults aged > 20 years, we compared the distribution of demographic factors, lifestyle, and comorbidities between viral and nonviral hepatic groups using the chi-square test. Univariate and multivariate logistic regressions were performed to observe the associations between hepatitis B and C viral infections and cancers by estimating the odds ratio (OR) and 95% confidence interval (CI). Multivariate regression analysis was adjusted for sociodemographic factors, lifestyle, and comorbidities. RESULTS From the database, 2955 participants were identified as having HCV infection, 15,305 as having HBV infection, and 140,108 as the nonviral group. HBV infection was associated with an increased likelihood of liver cancer (adjusted OR (aOR) = 6.60, 95% CI = 3.21-13.57, P < 0.001) and ovarian cancer (aOR = 4.63, 95% CI = 1.98-10.83, P = 0.001). HCV infection was observed to increase the likelihood of liver cancer (aOR = 4.90, 95% CI = 1.37-17.53, P = 0.015), ovarian cancer (aOR = 8.50, 95% CI = 1.78-40.69, P = 0.007), and kidney cancer (aOR = 12.89, 95% CI = 2.41-69.01, P = 0.003). CONCLUSION Our findings suggest that hepatic viral infections are associated with intra- and extrahepatic cancers. However, being cross-sectional, causal inferences cannot be made. A recall-by-genotype study is recommended to further investigate the causality of these associations.
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Affiliation(s)
- Moreen Maliko
- School of Public Health, College of Public Health, Taipei Medical University, 10F Biomedical Technology Building, No.301, Yuantong Rd., Zhonghe Dist., New Taipei City, 235603, Taiwan
| | - Fu-Hsiung Su
- Department of Family Medicine, Cardinal Tien Hospital, Fu Jen Catholic University, New Taipei City, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Abram Bunya Kamiza
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- The African Computational Genomic (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
| | - Ming-Jang Su
- School of Public Health, College of Public Health, Taipei Medical University, 10F Biomedical Technology Building, No.301, Yuantong Rd., Zhonghe Dist., New Taipei City, 235603, Taiwan
- Department of Clinical Pathology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, 235041, Taiwan
| | - Chih-Ching Yeh
- School of Public Health, College of Public Health, Taipei Medical University, 10F Biomedical Technology Building, No.301, Yuantong Rd., Zhonghe Dist., New Taipei City, 235603, Taiwan.
- Department of Public Health, College of Public Health, China Medical University, Taichung, 406, Taiwan.
- Cancer Center, Wan Fang Hospital, Taipei Medical University, New Taipei City, 116, Taiwan.
- Master Program in Applied Epidemiology, College of Public Health, Taipei Medical University, New Taipei City, 235603, Taiwan.
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10
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Tsai HH, Tantoh DM, Lu WY, Chen CY, Liaw YP. Cigarette smoking and PM 2.5 might jointly exacerbate the risk of metabolic syndrome. Front Public Health 2024; 11:1234799. [PMID: 38288423 PMCID: PMC10822970 DOI: 10.3389/fpubh.2023.1234799] [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: 06/05/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024] Open
Abstract
Background Cigarette smoking and particulate matter (PM) with aerodynamic diameter < 2.5 μm (PM2.5) are major preventable cardiovascular mortality and morbidity promoters. Their joint role in metabolic syndrome (MS) pathogenesis is unknown. We determined the risk of MS based on PM2.5 and cigarette smoking in Taiwanese adults. Methods The study included 126,366 Taiwanese between 30 and 70 years old with no personal history of cancer. The Taiwan Biobank (TWB) contained information on MS, cigarette smoking, and covariates, while the Environmental Protection Administration (EPA), Taiwan, contained the PM2.5 information. Individuals were categorized as current, former, and nonsmokers. PM2.5 levels were categorized into quartiles: PM2.5 ≤ Q1, Q1 < PM2.5 ≤ Q2, Q2 < PM2.5 ≤ Q3, and PM2.5 > Q3, corresponding to PM2.5 ≤ 27.137, 27.137 < PM2.5 ≤ 32.589, 32.589 < PM2.5 ≤ 38.205, and PM2.5 > 38.205 μg/m3. Results The prevalence of MS was significantly different according to PM2.5 exposure (p-value = 0.0280) and cigarette smoking (p-value < 0.0001). Higher PM2.5 levels were significantly associated with a higher risk of MS: odds ratio (OR); 95% confidence interval (CI) = 1.058; 1.014-1.104, 1.185; 1.134-1.238, and 1.149; 1.101-1.200 for 27.137 < PM2.5 ≤ 32.589, 32.589 < PM2.5 ≤ 38.205, and PM2.5 > 38.205 μg/m3, respectively. The risk of MS was significantly higher among former and current smokers with OR; 95% CI = 1.062; 1.008-1.118 and 1.531; 1.450-1.616, respectively, and a dose-dependent p-value < 0.0001. The interaction between both exposures regarding MS was significant (p-value = 0.0157). Stratification by cigarette smoking revealed a significant risk of MS due to PM2.5 exposure among nonsmokers: OR (95% CI) = 1.074 (1.022-1.128), 1.226 (1.166-1.290), and 1.187 (1.129-1.247) for 27.137 < PM2.5 ≤ 32.589, 32.589 < PM2.5 ≤ 38.205, and PM2.5 > 38.205 μg/m3, respectively. According to PM2.5 quartiles, current smokers had a higher risk of MS, regardless of PM2.5 levels (OR); 95% CI = 1.605; 1.444-1.785, 1.561; 1.409-1.728, 1.359; 1.211-1.524, and 1.585; 1.418-1.772 for PM2.5 ≤ 27.137, 27.137 < PM2.5 ≤ 32.589, 32.589 < PM2.5 ≤ 38.205, and PM2.5 > 38.205 μg/m3, respectively. After combining both exposures, the group, current smokers; PM2.5 > 38.205 μg/m3 had the highest odds (1.801; 95% CI =1.625-1.995). Conclusion PM2.5 and cigarette smoking were independently and jointly associated with a higher risk of MS. Stratified analyses revealed that cigarette smoking might have a much higher effect on MS than PM2.5. Nonetheless, exposure to both PM2.5 and cigarette smoking could compound the risk of MS.
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Affiliation(s)
- Hao-Hung Tsai
- Institute of Medicine, Chung Shan Medical University, Taichung City, Taiwan
- College of Medicine, Chung Shan Medical University, Taichung City, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, Taiwan
- Department of Medical Imaging, School of Medicine, Chung Shan Medical University, Taichung City, Taiwan
- Department of Medical Imaging and Radiological Sciences, Chung Shan Medical University, Taichung City, Taiwan
| | - Disline Manli Tantoh
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, Taiwan
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
| | - Wen Yu Lu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
| | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, Taichung City, Taiwan
- Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung City, Taiwan
| | - Yung-Po Liaw
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, Taiwan
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
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11
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Chung RH, Chuang SY, Zhuang YS, Jhang YS, Huang TH, Li GH, Chang IS, Hsiung CA, Chiou HY. Evaluating polygenic risk scores for predicting cardiometabolic traits and disease risks in the Taiwan Biobank. HGG ADVANCES 2024; 5:100260. [PMID: 38053338 PMCID: PMC10777116 DOI: 10.1016/j.xhgg.2023.100260] [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: 08/07/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023] Open
Abstract
Type 2 diabetes (T2D) and hypertension are common comorbidities and, along with hyperlipidemia, serve as risk factors for cardiovascular diseases. This study aimed to evaluate the predictive value of polygenic risk scores (PRSs) on cardiometabolic traits related to T2D, hypertension, and hyperlipidemia and the incidence of these three diseases in Taiwan Biobank samples. Using publicly available, large-scale genome-wide association studies summary statistics, we constructed cross-ethnic PRSs for T2D, hypertension, body mass index, and nine quantitative traits typically used to define the three diseases. A composite PRS (cPRS) for each of the nine traits was constructed by aggregating the significant PRSs of its genetically correlated traits. The associations of each of the nine traits at baseline as well as the change of trait values during a 3- to 6-year follow-up period with its cPRS were evaluated. The predictive performances of cPRSs in predicting future incidences of T2D, hypertension, and hyperlipidemia were assessed. The cPRSs had significant associations with baseline and changes of trait values in 3-6 years and explained a higher proportion of variance for all traits than individual PRSs. Furthermore, models incorporating disease-related cPRSs, along with clinical features and relevant trait measurements achieved area under the curve values of 87.8%, 83.7%, and 75.9% for predicting future T2D, hypertension, and hyperlipidemia in 3-6 years, respectively.
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Affiliation(s)
- Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan.
| | - Shao-Yuan Chuang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yong-Sheng Zhuang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Syuan Jhang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Tsung-Hsien Huang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Guo-Hung Li
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Hung-Yi Chiou
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan; School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
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12
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Cheng YF, Yang CY, Tsai MC. Shared Genetics between Age at Menarche and Type 2 Diabetes Mellitus: Genome-Wide Genetic Correlation Study. Biomedicines 2024; 12:157. [PMID: 38255262 PMCID: PMC10813301 DOI: 10.3390/biomedicines12010157] [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: 12/19/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Background: Age at menarche (AAM) has been associated with type 2 diabetes mellitus (T2DM). However, little is known about their shared heritability. Methods: Our data comes from the Taiwan Biobank. Genome-wide association studies (GWASs) were conducted to identify single-nucleotide polymorphisms (SNPs) related to AAM-, T2DM-, and T2DM-related phenotypes, such as body fat percentage (BFP), fasting blood glucose (FBG), and hemoglobin A1C (HbA1C). Further, the conditional false discovery rate (cFDR) method was applied to examine the shared genetic signals. Results: Conditioning on AAM, Quantile-quantile plots showed an earlier departure from the diagonal line among SNPs associated with BFP and FBG, indicating pleiotropic enrichments among AAM and these traits. Further, the cFDR analysis found 39 independent pleiotropic loci that may underlie the AAM-T2DM association. Among them, FN3KRP rs1046896 (cFDR = 6.84 × 10-49), CDKAL1 rs2206734 (cFDR = 6.48 × 10-10), B3GNTL1 rs58431774 (cFDR = 2.95 × 10-10), G6PC2 rs1402837 (cFDR = 1.82 × 10-8), and KCNQ1 rs60808706 (cFDR = 9.49 × 10-8) were highlighted for their significant genetic enrichment. The protein-protein interaction analysis revealed a significantly enriched network among novel discovered genes that were mostly found to be involved in the insulin and glucagon signaling pathways. Conclusions: Our study highlights potential pleiotropic effects across AAM and T2DM. This may shed light on identifying the genetic causes of T2DM.
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Affiliation(s)
- Yuan-Fang Cheng
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Cheng-Yi Yang
- Department of Statistics, College of Management, National Cheng Kung University, Tainan 70101, Taiwan
| | - Meng-Che Tsai
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, 138 Shengli Road, Tainan 70403, Taiwan
- Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Medical Humanities and Social Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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13
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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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14
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Tsai HH, Tantoh DM, Hsiao CH, Zhong JH, Chen CY, Liaw YP. Risk of gout in Taiwan Biobank participants pertaining to their sex and family history of gout among first-degree relatives. Clin Exp Med 2023; 23:5315-5325. [PMID: 37668883 DOI: 10.1007/s10238-023-01167-1] [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: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Family history of gout and sex are independently associated with gout. However, there is a paucity of research regarding the joint role of both factors in gout pathogenesis. Therefore, we assessed the independent and combined association of family history of gout and sex with gout. METHODS Our analysis included 132,311 Taiwan Biobank (TWB)-enrolled individuals comprising 21,159 gout cases and 111,152 controls. We subcategorized the family history of gout as (1) both siblings and parents had gout), (2) only parents had gout, and (3) only siblings had gout. RESULTS Generally, sex (men compared to women) and family history of gout were independently associated with a higher risk of gout. The odds ratio (OR); 95% confidence interval (CI) was 9.175; 8.801-9.566 for sex, and 2.306; 2.206-2.410 for family history. For the subcategories 'both siblings and had gout,' 'only parents had gout,' and 'only siblings had gout,' the odds ratios (ORs); 95% confidence intervals (CIs) were 4.944; 4.414-5.538, 2.041; 1.927-2.161, and 2.162; 2.012-2.323, respectively. The interaction between sex and family history was significant (p value = 0.0001). After stratification by sex, family history of gout remained significantly associated with a higher risk of gout in both sexes, even though the odds ratios were higher in men. For the subcategories 'both siblings and parents had gout,' 'only parent had gout,' and 'only siblings had gout,' the corresponding ORs; 95% CIs were 6.279; 5.243-7.520, 2.211; 2.062-2.371, and 2.148; 1.955-2.361 in men and 4.199; 3.566-4.945, 1.827; 1.640-2.035, and 2.093; 1.876-2.336 in women. After integrating sex and family history (reference: women with no family history), the highest risk of gout was observed in men who had at least one parent and sibling with a history of gout (OR; 95% CI 55.774; 46.360-67.101). CONCLUSION Sex and family history of gout were independently and interactively associated with gout. Sex-wise, men had a higher risk of gout than women. Family history was associated with a higher risk of gout in both sexes, but men had a higher risk. Notably, men having both siblings and parents with gout had the highest risk of gout.
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Affiliation(s)
- Hao-Hung Tsai
- Institute of Medicine, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
- College of Medicine, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
- Department of Medical Imaging, School of Medicine, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
- Department of Medical Imaging and Radiological Sciences, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
| | - Disline Manli Tantoh
- Department of Medical Imaging, Chung Shan Medical University Hospital, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan
| | - Chih-Yi Chen
- Institute of Medicine, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan.
- Division of Thoracic Surgery, Department of Surgery, Chung Shan Medical University Hospital, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan.
| | - Yung-Po Liaw
- Institute of Medicine, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan.
- Department of Medical Imaging, Chung Shan Medical University Hospital, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan.
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110, Sec. 1 Jianguo N. Rd., Taichung City, 40201, Taiwan.
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15
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Ruderman A. Population diversity and equity in the genomic era: going global to return to the local. J Community Genet 2023; 14:519-525. [PMID: 37670200 PMCID: PMC10725358 DOI: 10.1007/s12687-023-00669-5] [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: 06/21/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Advances in precision medicine depend on the quantity and quality of available genomic information. Various articles alert about the current disparities between the world's regions regarding the amount of genomic information available and the negative impact this will have on global health. The objective of this paper is to review these articles to describe what aspects they emphasize and highlight some issues that remain to be analyzed from the perspective of a "peripheral" country. Most of these articles come from central countries, where the need for more diversity in genomics is already detected. Several authors analyze lack of human diversity with focus on national, while others analyze the problem from a global perspective. Depending on the country of origin of the research, the claim for greater diversity has different meanings. Broadly, high-income countries advocate for better coverage looking within the boundaries of their own countries. In other regions of the world, where this field of research has not yet been massively developed, the same need for greater inclusiveness of origins in population genomics studies is not detected. An under-analyzed aspect is the unequal starting point between regions regarding the economic resources available for the development of this field of medicine, and for science and health in general. Although this macroeconomic and social aspect is usually absent in scientific analyses, without it solved, it will be impossible to guarantee that all world populations are equally represented in the panels or genomic databases that serve as input for precision medicine development.
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Affiliation(s)
- Anahí Ruderman
- Patagonian Institute of Social and Human Science. CONICET. Bv. Almirante Brown 2915, Puerto Madryn, Argentina.
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16
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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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17
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Campos AI, Namba S, Lin SC, Nam K, Sidorenko J, Wang H, Kamatani Y, Wang LH, Lee S, Lin YF, Feng YCA, Okada Y, Visscher PM, Yengo L. Boosting the power of genome-wide association studies within and across ancestries by using polygenic scores. Nat Genet 2023; 55:1769-1776. [PMID: 37723263 DOI: 10.1038/s41588-023-01500-0] [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: 12/15/2022] [Accepted: 08/14/2023] [Indexed: 09/20/2023]
Abstract
Genome-wide association studies (GWASs) have been mostly conducted in populations of European ancestry, which currently limits the transferability of their findings to other populations. Here, we show, through theory, simulations and applications to real data, that adjustment of GWAS analyses for polygenic scores (PGSs) increases the statistical power for discovery across all ancestries. We applied this method to analyze seven traits available in three large biobanks with participants of East Asian ancestry (n = 340,000 in total) and report 139 additional associations across traits. We also present a two-stage meta-analysis strategy whereby, in contributing cohorts, a PGS-adjusted GWAS is rerun using PGSs derived from a first round of a standard meta-analysis. On average, across traits, this approach yields a 1.26-fold increase in the number of detected associations (range 1.07- to 1.76-fold increase). Altogether, our study demonstrates the value of using PGSs to increase the power of GWASs in underrepresented populations and promotes such an analytical strategy for future GWAS meta-analyses.
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Affiliation(s)
- Adrian I Campos
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shu-Chin Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Kisung Nam
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Huanwei Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Ling-Hua Wang
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Yen-Feng Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yen-Chen Anne Feng
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei, Taiwan
- Division of Biostatistics and Data Science, Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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18
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Chuang HK, Hsieh AR, Ang TY, Chen SW, Yang YP, Huang HJ, Chiou SH, Lin TC, Chen SJ, Hsu CC, Hwang DK. TMEM132D and VIPR2 Polymorphisms as Genetic Risk Loci for Retinal Detachment: A Genome-Wide Association Study and Polygenic Risk Score Analysis. Invest Ophthalmol Vis Sci 2023; 64:17. [PMID: 37695605 PMCID: PMC10501492 DOI: 10.1167/iovs.64.12.17] [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: 02/14/2023] [Accepted: 07/12/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose Retinal detachment (RD) is a sight-threatening ocular disease caused by separation of the neurosensory retina from the underlying retinal pigment epithelium layer. Its genetic basis is unclear because of a limited amount of data. In this study, we aimed to identify genetic risk loci associated with RD in participants without diabetes mellitus and to construct a polygenic risk score (PRS) to predict the risk of RD. Methods A genome-wide association study was conducted using data from the Taiwan Biobank to identify RD risk loci. A total of 1533 RD cases and 106,270 controls were recruited, all of whom were Han Chinese. Replication studies were performed using data from the UK Biobank and Biobank Japan. To construct the PRS, a traditional clumping and thresholding method was performed and validated by fivefold cross-validation. Results Two novel loci with significant associations were identified. These two genes were TMEM132D (lead single nucleotide polymorphism [SNP]: rs264498, adjusted-P = 7.18 × 10-9) and VIPR2 (lead SNP: rs3812305, adjusted-P = 8.38 × 10-9). The developed PRS was effective in discriminating individuals at high risk of RD with a dose-response relationship. The quartile with the highest risk had an odds ratio of 1244.748 compared to the lowest risk group (95% confidence interval, 175.174-8844.892). Conclusions TMEM132D and VIPR2 polymorphisms are genetic candidates linked to RD in Han Chinese populations. Our proposed PRS was effective at discriminating high-risk from low-risk individuals.
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Affiliation(s)
- Hao-Kai Chuang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei City, Taiwan
| | - Tien-Yap Ang
- Department of Statistics, Tamkang University, New Taipei City, Taiwan
| | - Szu-Wen Chen
- Department of Statistics, Tamkang University, New Taipei City, 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
| | - Hung-Juei Huang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of General Medicine, Taipei Medical University Hospital, Taipei, 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
| | - Tai-Chi Lin
- 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
| | - 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
| | - De-Kuang Hwang
- 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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19
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Yuan K, Longchamps RJ, Pardiñas AF, Yu M, Chen TT, Lin SC, Chen Y, Lam M, Liu R, Xia Y, Guo Z, Shi W, Shen C, Daly MJ, Neale BM, Feng YCA, Lin YF, Chen CY, O'Donovan M, Ge T, Huang H. Fine-mapping across diverse ancestries drives the discovery of putative causal variants underlying human complex traits and diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.07.23284293. [PMID: 36711496 PMCID: PMC9882563 DOI: 10.1101/2023.01.07.23284293] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Genome-wide association studies (GWAS) of human complex traits or diseases often implicate genetic loci that span hundreds or thousands of genetic variants, many of which have similar statistical significance. While statistical fine-mapping in individuals of European ancestries has made important discoveries, cross-population fine-mapping has the potential to improve power and resolution by capitalizing on the genomic diversity across ancestries. Here we present SuSiEx, an accurate and computationally efficient method for cross-population fine-mapping, which builds on the single-population fine-mapping framework, Sum of Single Effects (SuSiE). SuSiEx integrates data from an arbitrary number of ancestries, explicitly models population-specific allele frequencies and LD patterns, accounts for multiple causal variants in a genomic region, and can be applied to GWAS summary statistics. We comprehensively evaluated SuSiEx using simulations, a range of quantitative traits measured in both UK Biobank and Taiwan Biobank, and schizophrenia GWAS across East Asian and European ancestries. In all evaluations, SuSiEx fine-mapped more association signals, produced smaller credible sets and higher posterior inclusion probability (PIP) for putative causal variants, and captured population-specific causal variants.
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Affiliation(s)
- Kai Yuan
- 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
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ryan J Longchamps
- 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
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - Mingrui Yu
- 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
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Tzu-Ting Chen
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Shu-Chin Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yu Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
| | - 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
| | - Ruize Liu
- 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
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yan Xia
- 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
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Zhenglin Guo
- Stanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wenzhao Shi
- Digital Health China Technologies Corp. Ltd., Beijing, China
| | - Chengguo Shen
- Digital Health China Technologies Corp. Ltd., Beijing, China
| | - Mark J Daly
- 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
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Benjamin M Neale
- 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
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yen-Chen A Feng
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yen-Feng Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
- Department of Public Health & Medical Humanities, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University
| | | | - Michael O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, UK
| | - 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
- Stanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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20
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Mohammadi-Shemirani P, Sood T, Paré G. From 'Omics to Multi-omics Technologies: the Discovery of Novel Causal Mediators. Curr Atheroscler Rep 2023; 25:55-65. [PMID: 36595202 PMCID: PMC9807989 DOI: 10.1007/s11883-022-01078-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW 'Omics studies provide a comprehensive characterisation of a biological entity, such as the genome, epigenome, transcriptome, proteome, metabolome, or microbiome. This review covers the unique properties of these types of 'omics and their roles as causal mediators in cardiovascular disease. Moreover, applications and challenges of integrating multiple types of 'omics data to increase predictive power, improve causal inference, and elucidate biological mechanisms are discussed. RECENT FINDINGS Multi-omics approaches are growing in adoption as they provide orthogonal evidence and overcome the limitations of individual types of 'omics data. Studies with multiple types of 'omics data have improved the diagnosis and prediction of disease states and afforded a deeper understanding of underlying pathophysiological mechanisms, beyond any single type of 'omics data. For instance, disease-associated loci in the genome can be supplemented with other 'omics to prioritise causal genes and understand the function of non-coding variants. Alternatively, techniques, such as Mendelian randomisation, can leverage genetics to provide evidence supporting a causal role for disease-associated molecules, and elucidate their role in disease pathogenesis. As technologies improve, costs for 'omics studies will continue to fall and datasets will become increasingly accessible to researchers. The intrinsically unbiased nature of 'omics data is well-suited to exploratory analyses that discover causal mediators of disease, and multi-omics is an emerging discipline that leverages the strengths of each type of 'omics data to provide insights greater than the sum of its parts.
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Affiliation(s)
- Pedrum Mohammadi-Shemirani
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
| | - Tushar Sood
- Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Guillaume Paré
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON Canada
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON Canada
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21
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Tsai MC, Hsu CH, Chu SK, Roy-Gagnon MH, Lin SH. Genome-wide association study of age at menarche in the Taiwan Biobank suggests NOL4 as a novel associated gene. J Hum Genet 2023; 68:339-345. [PMID: 36710296 DOI: 10.1038/s10038-023-01124-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 01/31/2023]
Abstract
Sexual maturation is a complex physiological process that involves multiple variables, such as genetic and environmental factors. Among females, age at menarche (AM) is a critical milestone for sexual maturation. This study aimed to identify genetic markers of AM using nationwide population cohort data in Taiwan. Females with self-reported AM between 10 and 16 years (N = 39,827) were eligible for the final analysis. To identify genetic signals related to AM, we conducted a genome-wide association study using a linear regression model and split-half meta-analysis method to verify our findings. The Functional Mapping and Annotation web-based platform was used for positional mapping and gene-based and gene-set analyses. The meta-analysis identified four significant loci, i.e., LIN28B (pooled P = 1.39 × 10-21), NOL4 (pooled P = 8.94 × 10-9), GPR45 (pooled P = 4.19 × 10-11), and LOC105373831 (pooled P = 4.37 × 10-8), that were associated with AM. MAGMA gene-based analysis revealed that LIN28B (P = 1.13 × 10-8), NOL4 (P = 2.27 × 10-7), RXRG (P = 4.34 × 10-7), ETV5 (P = 1.75 × 10-6), and HACE1 (P = 1.82 × 10-6) were significantly associated with AM, while the gene-set analysis identified a significantly enriched pathway involving mTOR signaling complex (FDR corrected P = 1.28 × 10-2). The results replicated evidence for several genetic markers associated with AM in the Taiwanese female population. Our analysis identified a novel locus (rs7239368) in NOL4 associated with AM (β = 0.051 ± 0.009 years, pooled P = 8.94 × 10-9), whereas additional research is needed to validate its molecular role in sexual maturation.
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Affiliation(s)
- Meng-Che Tsai
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Genomic Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medical Humanities and Social Medicine, Collage of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Hui Hsu
- Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Kai Chu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.,Clinical Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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22
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Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J Pers Med 2022; 12:jpm12122040. [PMID: 36556260 PMCID: PMC9783756 DOI: 10.3390/jpm12122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.
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Affiliation(s)
- Tatyana E. Lazareva
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
| | - Anton I. Changalidis
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | - Alexander A. Tkachenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Evgeniia M. Maksiutenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
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