Transformation of the Taiwan Biobank 3.0: vertical and horizontal integration

The association between body mass index and osteoporosis in a Taiwanese population: a cross-sectional and longitudinal study

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.

Review of Indicators in the Context of Biobanking

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.

Navigating bottlenecks and trade-offs in genomic data analysis

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.

Challenges on the Development of Biodiversity Biobanks: The Living Archives of Biodiversity

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.

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

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.

Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing

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.

Perspectives and experiences of researchers regarding feedback of incidental genomic research findings: A qualitative study

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.

Precision Health in Taiwan: A Data-Driven Diagnostic Platform for the Future of Disease Prevention

“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.

Microbiome Forensic Biobanking: A Step toward Microbial Profiling for Forensic Human Identification

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.