Taiwan Biobank: A rich biomedical research database of the Taiwanese population.
Ontology highlight
ABSTRACT:
SUBMITTER: Feng YA
PROVIDER: S-EPMC9903657 | biostudies-literature | 2022 Nov
REPOSITORIES: biostudies-literature
Publications
Taiwan Biobank: A rich biomedical research database of the Taiwanese population.
Feng Yen-Chen Anne YA Chen Chia-Yen CY Chen Tzu-Ting TT Kuo Po-Hsiu PH Hsu Yi-Hsiang YH Yang Hwai-I HI Chen Wei J WJ Su Ming-Wei MW Chu Hou-Wei HW Shen Chen-Yang CY Ge Tian T Huang Hailiang H Lin Yen-Feng YF
Cell genomics 20221012 11
The Taiwan Biobank (TWB) is an ongoing prospective study of >150,000 individuals aged 20-70 in Taiwan. A comprehensive list of phenotypes was collected for each consented participant at recruitment and follow-up visits through structured interviews and physical measurements. Biomarkers and genetic data were generated from blood and urine samples. We present here an overview of TWB's genetic data quality, population structure, and familial relationship, which consists of predominantly Han Chinese ...[more]
Similar Datasets
Project description:The Taiwan Biobank (TWB) aims to build a nationwide research database that integrates genomic/epigenomic profiles, lifestyle patterns, dietary habits, environmental exposure history and long-term health outcomes of 300,000 residents of Taiwan. We describe here an investigation of the population structure of Han Chinese on this Pacific island using genotype data of 591,048 SNPs in an initial freeze of 10,801 unrelated TWB participants. In addition to the North-South cline reported in other Han Chinese populations, we find the Taiwanese Han Chinese clustered into three cline groups: 5% were of northern Han Chinese ancestry, 79.9% were of southern Han Chinese ancestry, and 14.5% belonged to a third (T) group. We also find that this T group is genetically distinct from neighbouring Southeast Asians and Austronesian tribes but similar to other southern Han Chinese. Interestingly, high degree of LD between HLA haplotype A*33:03-B*58:01, an MHC allele being of pathological relevance, and SNPs across the MHC region was observed in subjects with T origin, but not in other Han Chinese. This suggested the T group individuals may have experienced evolutionary events independent from the other southern Han Chinese. Based on the newly-discovered population structure, we detect different loci susceptible to type II diabetes in individuals with southern and northern Han Chinese ancestries. Finally, as one of the largest dataset currently available for the Chinese population, genome-wide statistics for the 10,810 subjects are made publicly accessible through Taiwan View (https://taiwanview.twbiobank.org.tw/index; date last accessed October 14, 2016) to encourage future genetic research and collaborations with the island Taiwan.
| S-EPMC6078601 | biostudies-literature
Project description:BackgroundBiobanks are highly organized infrastructures that allow the storage of human biological specimens associated with donors' personal and clinical data. These infrastructures play a key role in the development of translational medical research. In this context, we launched, in November 2015, the first biobank in Morocco (BRO Biobank) in order to promote biomedical research and provide opportunities to include Moroccan and North African ethnic groups in international biomedical studies. Here, we present the setup and the sample characteristics of BRO Biobank.MethodsPatients were recruited at several departments of two major health-care centers in the city of Oujda. Healthy donors were enrolled during blood donation campaigns all over Eastern Morocco. From each participant, personal, clinical, and biomedical data were collected, and several biospecimens were stored. Standard operating procedures have been established in accordance with international guidelines on human biobanks.ResultsBetween November 2015 and July 2020, 2446 participants were recruited into the BRO Biobank, of whom 2013 were healthy donors, and 433 were patients. For healthy donors, the median age was 35 years with a range between 18 and 65 years and the consanguinity rate was 28.96%. For patients, the median age was 11 years with a range between 1 day and 83 years. Among these patients, 55% had rare diseases (hemoglobinopathies, intellectual disabilities, disorders of sex differentiation, myopathies, etc.), 13% had lung cancer, 4% suffered from hematological neoplasms, 3% were from the kidney transplantation project, and 25% had unknown diagnoses. The BRO Biobank has collected 5092 biospecimens, including blood, white blood cells, plasma, serum, urine, frozen tissue, FFPE tissue, and nucleic acids. A sample quality control has been implemented and suggested that samples of the BRO Biobank are of high quality and therefore suitable for high-throughput nucleic acid analysis.ConclusionsThe BRO Biobank is the largest sample collection in Morocco, and it is ready to provide samples to national and international research projects. Therefore, the BRO Biobank is a valuable resource for advancing translational medical research.
| S-EPMC7738781 | biostudies-literature
Project description:The Taiwan Biobank (TWB) is a biomedical research database of biopsy data from 200 000 participants. Access to this database has been granted to research communities taking part in the development of precision medicines; however, this has raised issues surrounding TWB's access to electronic medical records (EMRs). The Personal Data Protection Act of Taiwan restricts access to EMRs for purposes not covered by patients' original consent. This commentary explores possible legal solutions to help ensure that the access TWB has to EMR abides with legal obligations, and with governance frameworks associated with ethical, legal, and social implications. We suggest utilizing "hash function" algorithms to create nonretrospective, anonymized data for the purpose of cross-transmission and/or linkage with EMR.
| S-EPMC5774504 | biostudies-literature
Project description:BackgroundGamma-aminobutyric acid type A (GABAA) receptors mainly mediate the effects of gamma-aminobutyric acid, which is the primary inhibitory neurotransmitter in the central nervous system. Abundant evidence suggests that GABAA receptors play a key role in sleep-regulating processes. No genetic association study has explored the relationships between GABAA receptor genes and sleep duration, sleep quality, and sleep timing in humans.MethodsWe determined the association between single-nucleotide polymorphisms (SNPs) in the GABAA receptor genes GABRA1, GABRA2, GABRB3, GABRA5, and GABRG3 and sleep duration, sleep quality, and sleep timing in the Taiwan Biobank with a sample of 10,127 Taiwanese subjects. There were 10,142 subjects in the original study cohort. We excluded 15 subjects with a medication history of sedative-hypnotics.ResultsOur data revealed an association of the GABRB3-GABRA5-GABRG3 gene cluster with sleep duration, which has not been previously identified: rs79333046 (beta = - 0.07; P = 1.21 × 10-3) in GABRB3, rs189790076 (beta = 0.92; P = 1.04 × 10-3) in GABRA5, and rs147619342 (beta = - 0.72; P = 3.97 × 10-3) in GABRG3. The association between rs189790076 in GABRA5 and sleep duration remained significant after Bonferroni correction. A variant (rs12438141) in GABRB3 was also found to act as a potential expression quantitative trait locus. Additionally, we discovered interactions between variants in the GABRB3-GABRA5-GABRG3 gene cluster and lifestyle factors, such as tea and coffee consumption, smoking, and physical activity, that influenced sleep duration, although some interactions became nonsignificant after Bonferroni correction. We also found interactions among GABRB3, GABRA5, and GABRG3 that affected sleep duration. Furthermore, we identified an association of rs7165524 (beta = - 0.06; P = 2.20 × 10-3) in GABRA5 with sleep quality and an association of rs79465949 (beta = - 0.12; P = 3.95 × 10-3) in GABRB3 with sleep timing, although these associations became nonsignificant after Bonferroni correction. However, we detected no evidence of an association of individual SNPs in GABRA1 and GABRA2.ConclusionsOur results indicate that rs189790076 in GABRA5 and gene-gene interactions among GABRB3, GABRA5, and GABRG3 may contribute to sleep duration in the Taiwanese population.
| S-EPMC8447520 | biostudies-literature
Project description:Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values of NPs in individual species facilitate the assessments and investigations of the therapeutic quality of herbs and phenotypes of microbes. Here, we describe an update of the NPASS natural product activity and species source database previously featured in NAR. This update includes: (i) new data of ∼95 000 records of the composition/concentration values of ∼1 490 NPs/NP clusters in ∼390 species, (ii) extended data of activity values of ∼43 200 NPs against ∼7 700 targets (∼40% and ∼32% increase, respectively), (iii) extended data of ∼31 600 species sources of ∼94 400 NPs (∼26% and ∼32% increase, respectively), (iv) new species types of ∼440 co-cultured microbes and ∼420 engineered microbes, (v) new data of ∼66 600 NPs without experimental activity values but with estimated activity profiles from the established chemical similarity tool Chemical Checker, (vi) new data of the computed drug-likeness properties and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties for all NPs. NPASS update version is freely accessible at http://bidd.group/NPASS.
| S-EPMC9825494 | biostudies-literature
Project description:Laboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m. domesticus-derived PGN2/Ms and BFM/Ms; M. m. castaneus-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M. m. musculus and M. m. castaneus. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the "Mishima Battery". These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.
| S-EPMC8913468 | biostudies-literature
Project description:A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium and a pilot for data integration between a Swedish clinical health registry and a biobank. We used the Sample avAILability (SAIL) method for data linking: first, created harmonised variables and then annotated and made searchable information on the number of specimens available in individual biobanks for various phenotypic categories. By operating on this categorised availability data we sidestep many obstacles related to privacy that arise when handling real values and show that harmonised and annotated records about data availability across disparate biomedical archives provide a key methodological advance in pre-analysis exchange of information between biobanks, that is, during the project planning phase.
| S-EPMC4929882 | biostudies-literature
Project description:Because stroke is the third leading disease that causes mortality in the world, the prevention of stroke from advanced carotid stenosis is an important issue. The carotid stent (CAS) is a less invasive to treat advanced carotid stenosis, but for high-risk patients it may cause some events after the procedure that reduces the benefit of stroke prevention. Because patients and their families have less information about risk of events after CAS and are easy concerned, this study calculates the individual probability of major adverse cardiovascular events including any stroke, myocardial infarction, or death after procedure.The analyzed dataset was composed of patients undergoing CAS from the longitudinal National Health Insurance claim database in Taiwan. The validation dataset was composed of patients undergoing CAS from the Tri-Service General Hospital. We excluded patients under 18 years of age. The prediction model was constructed with a multivariable Cox proportional hazard regression and performed with forward stepwise selection. The nomogram construction was based on the multivariable Cox model.The risk factors were determined as follows: age with a hazard ratio (HR) of 1.027 (95% confidence interval [CI]: 1.002-1.053) for every 1 year older, congestive heart failure with a HR of 2.196 (95% CI: 1.368-3.524), malignant disease with a HR of 1.724 (95% CI: 1.009-2.944), diabetes mellitus with a HR of 1.722 (95% CI: 1.109-2.674), and symptomatic status with a HR of 1.604 (95% CI: 1.027-2.507). The model showed good discrimination with a P < 0.001 (concordance index, 0.681; bootstrap corrected, 0.661) in the derivation data. The concordance index of external validation was 0.66 (P = 0.048), which indicates acceptable performance.We developed a nomogram with a visual scale method and prognostic information, and it is easy to use in clinical practice. The integer-base method may support communication between clinicians and patients before CAS to reduce the anxiety about making a treatment decision. However, insofar as older patients with multiple comorbidities are at high risk, the option of an alternative treatment strategy with medical therapy should be suggested. In the future, prospective tests should be performed to validate whether this model helps patients to prevent events.
| S-EPMC5008606 | biostudies-literature
Project description:Fecal occult blood test (FOBT) is a convenient tool for the screening of asymptomatic gastrointestinal (GI) bleeding while 「guaiac-based fecal occult test (G-FOBT) 」 is increasingly replaced by the use of an 「immunochemical-based test (I-FOBT) 」 that reacts with human globin, a protein that is digested by upper GI enzymes and is specific for detecting lower GI bleeding. However, in Taiwan, although the incidence of colorectal cancer is rapidly increasing, Helicobacter pylori-related upper GI pathologies remain highly prevalent, which may imply that mass screening solely based on I-FOBT could be insufficient as significant upper GI pathologies can be missed. Since I-FOBT dose not predict upper GI pathologies, the adjuncts of G-FOBT and H. pylori stool-antigen test (HpSA) may be a potential candidate to realize a pan-detecting assay based on stool samples in a population in which both lower and upper GI lesions are equally prevalent.
| 2105714 | ecrin-mdr-crc
Project description:BackgroundBiological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework.MethodsBy using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology. The first three models interpret database entries as individuals (IND), defined classes (SUBC), and classes with dispositions (DISP), respectively; the fourth model (HYBR) is a combination of SUBC and DISP. For the evaluation of these four models, we consider (i) database content retrieval, using ontologies as query vocabulary; (ii) information completeness; and, (iii) DL complexity and decidability. The models were tested under these criteria against four competency questions (CQs).ResultsIND does not raise any ontological claim, besides asserting the existence of sample individuals and relations among them. Modelling patterns have to be created for each type of annotation referent. SUBC is interpreted regarding maximally fine-grained defined subclasses under the classes referred to by the data. DISP attempts to extract truly ontological statements from the database records, claiming the existence of dispositions. HYBR is a hybrid of SUBC and DISP and is more parsimonious regarding expressiveness and query answering complexity. For each of the four models, the four CQs were submitted as DL queries. This shows the ability to retrieve individuals with IND, and classes in SUBC and HYBR. DISP does not retrieve anything because the axioms with disposition are embedded in General Class Inclusion (GCI) statements.ConclusionAmbiguity of biological database content is addressed by a method that identifies implicit knowledge behind semantic annotations in biological databases and grounds it in an expressive upper-level ontology. The result is a seamless representation of database structure, content and annotations as OWL models.
| S-EPMC5485580 | biostudies-literature