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Lai EY, Huang YT. Identifying pleiotropic genes via the composite test amidst the complexity of polygenic traits. Brief Bioinform 2024; 25:bbae327. [PMID: 39007593 PMCID: PMC11247409 DOI: 10.1093/bib/bbae327] [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: 04/09/2024] [Revised: 05/29/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Identifying the causal relationship between genotype and phenotype is essential to expanding our understanding of the gene regulatory network spanning the molecular level to perceptible traits. A pleiotropic gene can act as a central hub in the network, influencing multiple outcomes. Identifying such a gene involves testing under a composite null hypothesis where the gene is associated with, at most, one trait. Traditional methods such as meta-analyses of top-hit $P$-values and sequential testing of multiple traits have been proposed, but these methods fail to consider the background of genome-wide signals. Since Huang's composite test produces uniformly distributed $P$-values for genome-wide variants under the composite null, we propose a gene-level pleiotropy test that entails combining the aforementioned method with the aggregated Cauchy association test. A polygenic trait involves multiple genes with different functions to co-regulate mechanisms. We show that polygenicity should be considered when identifying pleiotropic genes; otherwise, the associations polygenic traits initiate will give rise to false positives. In this study, we constructed gene-trait functional modules using the results of the proposed pleiotropy tests. Our analysis suite was implemented as an R package PGCtest. We demonstrated the proposed method with an application study of the Taiwan Biobank database and identified functional modules comprising specific genes and their co-regulated traits.
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Affiliation(s)
- En-Yu Lai
- Institute of Statistical Science, Academia Sinica, No.128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, No.128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
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Chiu CT, Lee JI, Lu CC, Huang SP, Chen SC, Geng JH. The association between body mass index and osteoporosis in a Taiwanese population: a cross-sectional and longitudinal study. Sci Rep 2024; 14:8509. [PMID: 38605101 PMCID: PMC11009266 DOI: 10.1038/s41598-024-59159-4] [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: 01/14/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
This study investigates the correlation between body mass index (BMI) and osteoporosis utilizing data from the Taiwan Biobank. Initially, a comprehensive analysis of 119,009 participants enrolled from 2008 to 2019 was conducted to assess the association between BMI and osteoporosis prevalence. Subsequently, a longitudinal cohort of 24,507 participants, initially free from osteoporosis, underwent regular follow-ups every 2-4 years to analyze the risk of osteoporosis development, which was a subset of the main cohort. Participants were categorized into four BMI groups: underweight (BMI < 18.5 kg/m2), normal weight (18.5 kg/m2 ≤ BMI < 24 kg/m2), overweight (24 kg/m2 ≤ BMI < 27 kg/m2), and obese groups (BMI ≥ 27 kg/m2). A T-score ≤ - 2.5 standard deviations below that of a young adult was defined as osteoporosis. Overall, 556 (14.1%), 5332 (9.1%), 2600 (8.1%) and 1620 (6.7%) of the participants in the underweight, normal weight, overweight and obese groups, respectively, had osteoporosis. A higher prevalence of osteoporosis was noted in the underweight group compared with the normal weight group (odds ratio [OR], 2.20; 95% confidence interval [95% CI], 1.99 to 2.43; p value < 0.001) in multivariable binary logistic regression analysis. Furthermore, in the longitudinal cohort during a mean follow-up of 47 months, incident osteoporosis was found in 61 (9%), 881 (7.2%), 401 (5.8%) and 213 (4.6%) participants in the underweight, normal weight, overweight and obese groups, respectively. Multivariable Cox proportional hazards analysis revealed that the risk of incident osteoporosis was higher in the underweight group than in the normal weight group (hazard ratio [HR], 1.63; 95% CI 1.26 to 2.12; p value < 0.001). Our results suggest that BMI is associated with both the prevalence and the incidence of osteoporosis. In addition, underweight is an independent risk factor for developing osteoporosis. These findings highlight the importance of maintaining normal weight for optimal bone health.
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Affiliation(s)
- Chao-Tse Chiu
- Department of Orthopaedics, Kaohsiung Municipal Siaogang Hospital, Kaohsiung, Taiwan
- Department of Orthopaedics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jia-In Lee
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cheng-Chang Lu
- Department of Orthopaedics, Kaohsiung Municipal Siaogang Hospital, Kaohsiung, Taiwan
- Department of Orthopaedics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Pin Huang
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, 807, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Ph.D. Program in Environmental and Occupational Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Institute of Medical Science and Technology, College of Medicine, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Szu-Chia Chen
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Department of Internal Medicine, Kaohsiung Municipal Siaogang Hospita, l, Kaohsiung Medical University, 812, Kaohsiung, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Jiun-Hung Geng
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, 807, Kaohsiung, Taiwan.
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Urology, Kaohsiung Municipal Siaogang Hospital, No. 482, Shanming Rd, Xiaogang District, Kaohsiung, 812, Taiwan.
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Slušná ĽK, Balog M. Review of Indicators in the Context of Biobanking. Biopreserv Biobank 2023; 21:318-326. [PMID: 36099204 DOI: 10.1089/bio.2022.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Biobanks that intend to serve as high-performing and stable elements of an innovative research ecosystem must have an established system for regular measurement and evaluation using appropriately set indicators. The main objective of this study was to provide a comprehensive overview of indicators in the context of biobanking, with new perspectives to highlight the existence of numerous options and introduce indicators that could help overcome problems associated with the difficult assessment of the impact of biobanks. Methods: A literature review was performed to identify publications relevant to the topic of indicators in biobanking. The Web of Science Core Collection and PubMed databases were searched using specific keywords. In addition, three articles that focused on indicators designed for the evaluation of research infrastructures were included in the review. Results: Based on the scientific literature for the biobanking field, many types of quantitative and qualitative indicators exist. They are mainly related to the quantity and quality of data and samples, their distribution, the monitoring of research projects, and subsequent publication outputs. The indicators identified in the biobanking literature primarily focus on the outcome, not the impact. Conclusions: Indicators identified in the biobanking literature may be further expanded with suggestions designed for other types of research infrastructures, while considering the context where biobanks operate and the needs of individual biobanking stakeholders. The establishment of a comprehensive monitoring system that captures all necessary elements is crucial for modern biobanks.
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Affiliation(s)
| | - Miroslav Balog
- Centre of Social and Psychological Sciences, SAS, Bratislava, Slovakia
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Berger B, Yu YW. Navigating bottlenecks and trade-offs in genomic data analysis. Nat Rev Genet 2023; 24:235-250. [PMID: 36476810 DOI: 10.1038/s41576-022-00551-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
Abstract
Genome sequencing and analysis allow researchers to decode the functional information hidden in DNA sequences as well as to study cell to cell variation within a cell population. Traditionally, the primary bottleneck in genomic analysis pipelines has been the sequencing itself, which has been much more expensive than the computational analyses that follow. However, an important consequence of the continued drive to expand the throughput of sequencing platforms at lower cost is that often the analytical pipelines are struggling to keep up with the sheer amount of raw data produced. Computational cost and efficiency have thus become of ever increasing importance. Recent methodological advances, such as data sketching, accelerators and domain-specific libraries/languages, promise to address these modern computational challenges. However, despite being more efficient, these innovations come with a new set of trade-offs, both expected, such as accuracy versus memory and expense versus time, and more subtle, including the human expertise needed to use non-standard programming interfaces and set up complex infrastructure. In this Review, we discuss how to navigate these new methodological advances and their trade-offs.
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Affiliation(s)
- Bonnie Berger
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Yun William Yu
- Department of Computer and Mathematical Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Tri-Campus Department of Mathematics, University of Toronto, Toronto, Ontario, Canada
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Angeles NAC, Catap ES. Challenges on the Development of Biodiversity Biobanks: The Living Archives of Biodiversity. Biopreserv Biobank 2023; 21:5-13. [PMID: 35133889 DOI: 10.1089/bio.2021.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biodiversity biobanks or ex situ biodiversity biorepositories tend to receive less attention compared with their biomedical counterparts. In this review, we highlight the necessity for these biorepositories by presenting their significant role in health, biodiversity, linking of big data, other translational research, and biodiversity conservation efforts. Moreover, the significant challenges in developing and maintaining biodiversity biobanks based on successful biobanks in some megadiverse developing countries are examined to provide insights into what needs to be done and what can be improved by up-and-coming biodiversity biobanks. These challenges include lack of financial support and political will; availability of experts; development of standard policies; and information management system. In addition, issues regarding access and benefit sharing and Digital Sequence Information must be addressed by biodiversity biobanks.
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Affiliation(s)
- Nestly Anne C Angeles
- Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines.,Department of Science and Technology-Science Education Institute, Taguig, Philippines
| | - Elena S Catap
- Functional Bioactivity Screening Lab, Institute of Biology, College of Science National Science Complex, University of the Philippines-Diliman, Quezon City, Philippines
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Liao CC, Chien CH, Shih YH, Tsai FJ, Li JM. Acupuncture Is Effective at Reducing the Risk of Stroke in Patients with Migraines: A Real-World, Large-Scale Cohort Study with 19-Years of Follow-Up. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1690. [PMID: 36767053 PMCID: PMC9914783 DOI: 10.3390/ijerph20031690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Migraines are common headache disorders and risk factors for subsequent strokes. Acupuncture has been widely used in the treatment of migraines; however, few studies have examined whether its use reduces the risk of strokes in migraineurs. This study explored the long-term effects of acupuncture treatment on stroke risk in migraineurs using national real-world data. We collected new migraine patients from the Taiwan National Health Insurance Research Database (NHIRD) from 1 January 2000 to 31 December 2017. Using 1:1 propensity-score matching, we assigned patients to either an acupuncture or non-acupuncture cohort and followed up until the end of 2018. The incidence of stroke in the two cohorts was compared using the Cox proportional hazards regression analysis. Each cohort was composed of 1354 newly diagnosed migraineurs with similar baseline characteristics. Compared with the non-acupuncture cohort, the acupuncture cohort had a significantly reduced risk of stroke (adjusted hazard ratio, 0.4; 95% confidence interval, 0.35-0.46). The Kaplan-Meier model showed a significantly lower cumulative incidence of stroke in migraine patients who received acupuncture during the 19-year follow-up (log-rank test, p < 0.001). Acupuncture confers protective benefits on migraineurs by reducing the risk of stroke. Our results provide new insights for clinicians and public health experts.
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Affiliation(s)
- Chung-Chih Liao
- Department of Post-Baccalaureate Veterinary Medicine, Asia University, Taichung 41354, Taiwan
| | - Chi-Hsien Chien
- Department of Post-Baccalaureate Veterinary Medicine, Asia University, Taichung 41354, Taiwan
| | - Ying-Hsiu Shih
- Management Office for Health Data, China Medical University Hospital, Taichung 40201, Taiwan
- College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Fuu-Jen Tsai
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
- Division of Medical Genetics, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Biotechnology and Bioinformatics, Asia University, Taichung 41354, Taiwan
| | - Jung-Miao Li
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
- Department of Chinese Medicine, China Medical University Hospital, Taichung 40447, Taiwan
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Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing. Nat Struct Mol Biol 2022; 29:1043-1055. [PMID: 36303034 DOI: 10.1038/s41594-022-00844-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 08/23/2022] [Indexed: 12/24/2022]
Abstract
It is estimated that 10%-30% of disease-associated genetic variants affect splicing. Splicing variants may generate deleteriously altered gene product and are potential therapeutic targets. However, systematic diagnosis or prediction of splicing variants is yet to be established, especially for the near-exon intronic splice region. The major challenge lies in the redundant and ill-defined branch sites and other splicing motifs therein. Here, we carried out unbiased massively parallel splicing assays on 5,307 disease-associated variants that overlapped with branch sites and collected 5,884 variants across the 5' splice region. We found that strong splice sites and exonic features preserve splicing from intronic sequence variation. Whereas the splice-altering mechanism of the 3' intronic variants is complex, that of the 5' is mainly splice-site destruction. Statistical learning combined with these molecular features allows precise prediction of altered splicing from an intronic variant. This statistical model provides the identity and ranking of biological features that determine splicing, which serves as transferable knowledge and out-performs the benchmarking predictive tool. Moreover, we demonstrated that intronic splicing variants may associate with disease risks in the human population. Our study elucidates the mechanism of splicing response of intronic variants, which classify disease-associated splicing variants for the promise of precision medicine.
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Ochieng J, Kwagala B, Barugahare J, Mwaka E, Ekusai-Sebatta D, Ali J, Sewankambo NK. Perspectives and experiences of researchers regarding feedback of incidental genomic research findings: A qualitative study. PLoS One 2022; 17:e0273657. [PMID: 36037169 PMCID: PMC9423610 DOI: 10.1371/journal.pone.0273657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
Background
There is a plethora of unanswered ethical questions about sharing incidental findings in genetics and genomics research. Yet understanding and addressing such issues is necessary for communicating incidental findings with participants. We explored researchers’ perspectives and experiences regarding feedback of incidental genomics findings to participants.
Methods
This was a qualitative study using semi-structured interview schedules for In-depth interviews. Thirty respondents were purposively selected based on role as genetics and genomics researchers in Uganda. Data were analysed through content analysis to identify emerging themes using a comprehensive thematic matrix. QSR International NVivo software was used to support data analysis.
Results
a). On perceptions, sharing of incidental findings was acceptable and four themes emerged including role of professional judgement; role of ethics committees and ethical guidelines; optimal disclosure practices; limits to professional duty and uncertainty and; b). on practices, sharing had been carried out by some researchers and a theme on experience and practices emerged.
Conclusion
Feedback of incidental genomics research findings to participants is generally acceptable to researchers. Some researchers. Challenges include lack of ethical guidelines and uncertainty about the findings.
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Affiliation(s)
- Joseph Ochieng
- Makerere University School of Biomedical Sciences, Kampala, Uganda
- * E-mail:
| | - Betty Kwagala
- Makerere University School of Business and Management Studies, Kampala, Uganda
| | - John Barugahare
- Makerere University School of Liberal and Performing Arts, Kampala, Uganda
| | - Erisa Mwaka
- Makerere University School of Biomedical Sciences, Kampala, Uganda
| | | | - Joseph Ali
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Johns Hopkins Berman Institute of Bioethics, Baltimore, MD, United States of America
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Hsiao WWW, Lin JC, Fan CT, Chen SSS. Precision Health in Taiwan: A Data-Driven Diagnostic Platform for the Future of Disease Prevention. Comput Struct Biotechnol J 2022; 20:1593-1602. [PMID: 35495110 PMCID: PMC9019916 DOI: 10.1016/j.csbj.2022.03.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
“Precision medicine” has revolutionized how we respond to diseases by using an individual’s genomic data and lifestyle and environment-related information to create an effective personalized treatment. However, issues surrounding regulations, medical insurance payments and the use of patients’ medical data, have delayed the development of precision medicine and made it difficult to achieve “true” personalization. We therefore recommend that precision medicine be transformed into precision health: a novel and generalized platform of tools and methods that could prevent, manage, and treat disease at a population level. “Precision health,” one of six core strategic industries highlighted in Taiwan’s vision for 2030, uses various physiological data, genomic data, and external factors, to develop unique “preventative” solutions or therapeutic strategies. For Taiwan to implement precision health, it has to address three challenges: (1) the high-cost issue of precision health; (2) the harmonization issues surrounding integration and transmission of specimen and data; (3) the legal issue of combining information and communications technology (ICT) with Artificial Intelligence (AI) for medical use. In this paper, we propose an innovative framework with six recommendations for facilitating the development of precision health in Taiwan, including a novel model of precise telemedicine with AI-aided technology. We then describe how these tools can be proactively applied in early response to the COVID-19 crisis. We believe that precision health represents an important shift to more proactive and preventive healthcare that enables people to lead healthier lives.
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Affiliation(s)
- Wesley Wei-Wen Hsiao
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei, Taiwan, ROC
| | - Jui-Chu Lin
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei, Taiwan, ROC
- College of Liberal Arts and Social Sciences, National Taiwan University of Science and Technology, Taipei, Taiwan, ROC
- Corresponding authors at: Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei, Taiwan, ROC (J.-C Lin). Division of Urology, Taipei City Hospital Zhong Xiao Branch, Taipei, Taiwan, ROC (S.S.-S. Chen).
| | - Chien-Te Fan
- Institute of Law for Science and Technology, National Tsing Hua University, Hsin-Chu, Taiwan, ROC
| | - Saint Shiou-Sheng Chen
- Division of Urology, Taipei City Hospital Zhong Xiao Branch, Taipei, Taiwan, ROC
- Commission for General Education, National Taiwan University of Science and Technology, Taipei, Taiwan, ROC
- Department of Urology, School of Medicine, National Yangming Chiao Tung University, Taipei, Taiwan, ROC
- General Education Center, University of Taipei, Taipei, Taiwan, ROC
- Corresponding authors at: Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei, Taiwan, ROC (J.-C Lin). Division of Urology, Taipei City Hospital Zhong Xiao Branch, Taipei, Taiwan, ROC (S.S.-S. Chen).
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Caenazzo L, Tozzo P. Microbiome Forensic Biobanking: A Step toward Microbial Profiling for Forensic Human Identification. Healthcare (Basel) 2021; 9:1371. [PMID: 34683051 PMCID: PMC8544459 DOI: 10.3390/healthcare9101371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
In recent years many studies have highlighted the great potential of microbial analysis in human identification for forensic purposes, with important differences in microbial community composition and function across different people and locations, showing a certain degree of uncertainty. Therefore, further studies are necessary to enable forensic scientists to evaluate the risk of microbial transfer and recovery from various items and to further critically evaluate the suitability of current human DNA recovery protocols for human microbial profiling for identification purposes. While the establishment and development of microbiome research biobanks for clinical applications is already very structured, the development of studies on the applicability of microbiome biobanks for forensic purposes is still in its infancy. The creation of large population microbiome biobanks, specifically dedicated to forensic human identification, could be worthwhile. This could also be useful to increase the practical applications of forensic microbiology for identification purposes, given that this type of evidence is currently absent from most real casework investigations and judicial proceedings in courts.
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Affiliation(s)
| | - Pamela Tozzo
- Laboratory of Forensic Genetics, Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
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