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Network configuration. The network configuration consists of three types of closed sub-networks; A) a network for identifiable data, B) a network for de-identified data, and C) a network for shared data. Only de-identification or anonymization actions can traverse between network A and network B or network B and network C, respectively. The two actions require off-line data transfers using portable devices with biometric authentication. VPN connections enable remote access from distant places of recruitment (community support centers and clinics) and data sharing (remote security rooms). An IP-VPN or wireless IP-VPN with a one-time password system meets the technological requirements of the security policy. The TMM biobank does not allow any remote access
Source publication
Background
With the goal of realizing genome-based personalized healthcare, we have developed a biobank that integrates personal health, genome, and omics data along with biospecimens donated by volunteers of 150,000. Such a large-scale of data integration involves obvious risks of privacy violation. The research use of personal genome and health i...
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Citations
... Concerning the HBs themselves, the establishment of their trustworthiness primarily centers on risk management. Risk management concerns primarily manifest in the safety and privacy issues of samples/data during collection, storage, access, and release, as well as the potential harm resulting from the collection and utilization of sample data (Takai-Igarashi et al., 2017). In addressing these issues, risks should be minimized to the greatest extent possible while also considering their necessity through comparative analysis. ...
Background: Human biobanks are an essential resource for contemporary medical research, crucial in treating and preventing human diseases and improving health. Public trust in human biobanks is a vital social prerequisite for their continued operation and related research.
Methods: Drawing on the “leap of faith” theory proposed by Georg Simmel and Guido Möllering, this paper first examines the relationship between public trust and human biobanks and the process through which such trust is established. Subsequently, based on the results of this analysis, targeted policy recommendations are put forward to consolidate or enhance public trust in human biobanks.
Results: Public trust in human biobanks stems from certain “good reasons,” through which uncertainty and vulnerability are “suspended” by faith, leading to a leap toward the “land of expectations.” In this progress, the critical factors in building and enhancing public trust in human biobanks are the public’s propensity to trust, the inherent trustworthiness of human biobanks, and the security and interactivity of the trust environment.
Conclusion: Public trust in human biobanks cannot be determined by any universal formula, as it is influenced by many factors, including intangible elements such as faith that defy empirical understanding. Nonetheless, public trust in human biobanks can be enhanced through measures such as fostering the public’s propensity to trust, enhancing the inherent trustworthiness of human biobanks, establishing structural safeguards for the trust environment through ethical norms, systems, and supervision, and promoting public participation.
... Biospecimens collected at the community support centers, including blood, saliva, urine, and oral plaque, as well as data collected during the physical and physiological examinations are anonymized and stored in the Biobank. Furthermore, these samples and information are stored in the database of the Tohoku Medical Megabank (dbTMM) for use in future studies (Takai-Igarashi et al. 2017) ) (Ogishima et al. 2021). ...
The Tohoku Medical Megabank Project (TMM) has been conducting a birth and three-generation cohort study (the BirThree Cohort Study). We recruited 73,529 pregnant women and their family members for this cohort study, which included 23,143 newborns and 9,459 of their siblings. We designed and are in the process of conducting three-step health assessments for each newborn at approximately ages of 5, 10 and 16. These health assessments are administered at seven community support centers. Trained genome medical research coordinators conduct physical examinations of and collect biological specimens from each participant. The Sendai Children’s Health Square has been established as the headquarters for these child health assessments and is utilized to accumulate knowledge that can facilitate the proper practice of child health assessments. We designed all the relevant health assessments facilities to allow parents and their children to participate in the health assessments concomitantly. Our centers serve as places where child participants and their parents can feel at ease as a result of the implementation of safety measures and child hospitality measures. The TMM BirThree Cohort Study is in the process of conducting strategically detailed health assessments and genome analysis, which can facilitate studies concerning the gene-environment interactions relevant to noncommunicable diseases. Through these operations, our study allows for a significant depth of data to be collected in terms of the number of biospecimens under study and the comprehensiveness of both basic and clinical data alongside relevant family information.
... If the documents are completed correctly, the sample can be registered and coded. 19 The coding process is an important element of sample preparation for biobanking. Typically, samples are pseudonymised, which makes it impossible for scientists to identify the donor and ensures the protection of donor data. ...
Resources from biobanks and biorepositories, such as human samples, are of increasing interest to specialists in various fields. However, whilst biobanks provide a crucial service, their efficient and effective management can prove challenging. When establishing a biobank many factors should be considered, such as the need for appropriate infrastructure, equipment, financial support, and highly specialised and suitably qualified personnel. The number and qualifications of the necessary personnel depend both on the biobank's size and type - i.e. a biobank that is large and diversified in terms of the stored material should be organised differently to a small biorepository. The core of the biobank should be composed of highly trained personnel that closely co-operate with the general and quality control manager. Due to the large amount of data related to the samples, an IT specialist might be needed. In the case of large population biobanks, personnel responsible for patient recruitment, documentation handling, sample collection and distribution to the biobank would be necessary. Furthermore, staff responsible for the infrastructure are also highly important, as they are the first responders to failures that may be critical for the biobank functioning. Depending on the type and size of the biobank/biorepository, some responsibilities and tasks could potentially be combined. Nevertheless, highly trained personnel with clear and precisely defined duties are the key to the proper functioning of a biobank.
... К таким банкам относятся биобанки ДНК для проектов изучения генома человека (PHG -Public Health Genomics, HuGenet ™, биобанк Genome в Эстонии, FarGen CARTaGENE и др.) [12][13][14]. Разработка критериев включения или исключения во время забора образцов привела к созданию эпидемиологических биобанков (заболеваний, включая редко встречающие заболевания) с целью определение рисков для здоровья человека [8][9][10][15][16][17][18][19][20][21][22]. ...
... Характеристики биобанков К общим характеристикам биобанков относятся [10,15]: -забор, обработка и хранение биологического материала в сочетании с медицинскими, эпидемиологическими данными, -динамичное развитие биобанков -постоянный забор биоматериала, -взаимосвязь с исследовательскими проектами, -конфиденциальность, анонимность данных образцов биологического материала доноров, -внедрение стандартов и процедур управления. ...
The features and problems of the development of biological banks are presented. Biological banks (Biobanks) play an important role in obtaining information and are a key link in diagnostics in the identification of new biomarkers of diseases, the development of prognostic tests and treatment – the creation of new targeted drugs for cancer and therapy. In the developing world, the role of biobanks is constantly increasing. The capabilities of biobanks make it possible to conduct a large-scale scientific analysis, to benefit the scientific community, the health of patients, and donors in the form of information about the diagnosis, prognosis, recommendations for the prevention and treatment of diseases. The continuous development of biobanks is supported by many years of experience and serves as a guide for the creation of new biobanks. Local government and the legal system must be ready for the development of biobanks. The interdisciplinary nature of biobanks contributes to the development of biomedical research and clinical practice.
... This is mainly because use of stored human materials may negatively impact the sample sources, in case of disclosure of genetic information about an individual or community. Potential dire consequences of such disclosure include stigma, psychological harm, discrimination or biosecurity [4,10,15]. ...
Background
Human biological materials are usually stored for possible future use in research because they preserve valuable biological information, save time and resources, which would have been spent on collection of fresh samples. However, use of these materials may pose ethical challenges such as unauthorized disclosure of genetic information, which can result in dire consequences for individuals or communities including discrimination, stigma, and psychological harm; has biosecurity implications; and loss of control or ownership of samples or data. To understand these problems better, we evaluated the extent to which tuberculosis (TB) clinical research protocols that were used to collect and store biological materials for future use conform to the requirements stated in the Uganda national guidelines for research involving humans as participants.
Methods
This was a retrospective review of TB clinical research projects approved by the Uganda National Council for Science and Technology (UNCST) from 2011 to 2015, to examine whether they fulfilled the requirements for ethical collection and use of human materials. Data were abstracted through review of the project protocols using a template developed based on the informed consent and the Materials Transfer Agreement (MTA) requirements in the national guidelines.
Results
Out of 55 research protocols reviewed, most of the protocols 83.6% had been used to collect the stored samples (sputum, blood and sometimes urine), 28% had a section on specimen collection and 24% mentioned ownership of the biological materials. With respect to review of the consent forms used in the studies that stored materials for future use, only 9% of the protocols had a separate consent form for storage of materials, 4.5% of the consent forms explained the risks, 11.4% explained the purpose of the study while 6.8% mentioned the place of storage for the collected materials.
Conclusion
Many of the studies reviewed did not meet the requirements for collection and storage of biological materials contained in the national guidelines, which indicates a need to additional training on this topic.
... dbTMM. During these processes, we took special notice of the sensitivity of the data, which met the criteria for strong protection according to our TMM data sharing policy 19 . ...
To reveal gene-environment interactions underlying common diseases and estimate the risk for common diseases, the Tohoku Medical Megabank (TMM) project has conducted prospective cohort studies and genomic and multiomics analyses. To establish an integrated biobank, we developed an integrated database called “dbTMM” that incorporates both the individual cohort/clinical data and the genome/multiomics data of 157,191 participants in the Tohoku Medical Megabank project. To our knowledge, dbTMM is the first database to store individual whole-genome data on a variant-by-variant basis as well as cohort/clinical data for over one hundred thousand participants in a prospective cohort study. dbTMM enables us to stratify our cohort by both genome-wide genetic factors and environmental factors, and it provides a research and development platform that enables prospective analysis of large-scale data from genome cohorts. A database integrating 1.3 trillion genome cohort data entries from 157,191 individuals in Japan will facilitate research into the gene-environment interactions underlying common diseases. The Tohoku Medical Megabank integrated database called dbTMM was developed by Soichi Ogishima, Masayuki Yamamoto and colleagues at Tohoku University in Japan. It incorporates the genome, metabolome, proteome, clinical, sociodemographic, lifestyle and environmental data from 84,073 adults, and 73,529 pregnant women and their families, including children. Blood and urine samples were collected from participants and analysed, then obtained genome/multiomics data were stored in dbTMM. Users can stratify the entire population into smaller populations based on multiple data variables, including whole genome variants, to search for statistically significant differences that might warrant further research. The dbTMM is expected to help clarify the genes and gene-environment interactions underlying common diseases and improve disease risk prediction.
... Developments in this important area are ongoing, and due to the complexity of the subject, providing further details is beyond the scope of this review article. However, we refer the interested reader to a number of excellent articles on this topic which highlight some of the key issues including the difficulties in balancing maximizing the benefit of organoid culture technology by making them widely available and providing detailed accompanying information whilst at the same time protecting donor identity 6,[67][68][69][70][71] . While close collaboration with pharmaceutical companies forms a vital step in the process of translating any academic discoveries from the bench to the bedside, the prospect of profit-making from human tissue donated for academic research is ethically contentious and likely to raise concern among the wider public 72 . ...
The development of human organoid culture models has led to unprecedented opportunities to generate self-organizing, three-dimensional miniature organs that closely mimic in vivo conditions. The ability to expand, culture, and bank such organoids now provide researchers with the opportunity to generate next-generation living biobanks, which will substantially contribute to translational research in a wide range of areas, including drug discovery and testing, regenerative medicine as well as the development of a personalized treatment approach. However, compared to traditional tissue repositories, the generation of a living organoid biobank requires a much higher level of coordination, additional resources, and scientific expertise. In this short review, we discuss the opportunities and challenges associated with the generation of a living organoid biobank. Focusing on human intestinal organoids, we highlight some of the key aspects that need to be considered and provide an outlook for future development in this exciting field.
... Once informed consent was obtained, we began analyzing the genomic data. Our cohort have used several types of IDs [36]. In brief, cohort IDs are personal identifiers that are directly linked with participants' names and personal information. ...
... Secure re-identification and results storage One of the major practical challenges was re-identification and storage of the genomic dataset. The genomic data were deidentified using two steps and stored in the TMM supercomputer [36]. In a research context, "re-identification" is a risk to data protection and management in biobanks and is generally prohibited. ...
Certain large genome cohort studies attempt to return the individual genomic results to the participants; however, the implementation process and psychosocial impacts remain largely unknown. The Tohoku Medical Megabank Project has conducted large genome cohort studies of general residents. To implement the disclosure of individual genomic results, we extracted the potential challenges and obstacles. Major challenges include the determination of genes/disorders based on the current medical system in Japan, the storage of results, prevention of misunderstanding, and collaboration of medical professionals. To overcome these challenges, we plan to conduct multilayer pilot studies, which deal with different disorders/genes. We finally chose familial hypercholesterolemia (FH) as a target disease for the first pilot study. Of the 665 eligible candidates, 33.5% were interested in the pilot study and provided consent after an educational “genetics workshop” on the basic genetics and medical facts of FH. The genetics professionals disclosed the results to the participants. All positive participants were referred to medical care, and a serial questionnaire revealed no significant psychosocial distress after the disclosure. Return of genomic results to research participants was implemented using a well-prepared protocol. To further elucidate the impact of different disorders, we will perform multilayer pilot studies with different disorders, including actionable pharmacogenomics and hereditary tumor syndromes.
... Specifically, in Europe, the General Data Protection Regulation (GDPR) provides a framework with which biobanks need to facilitate information transfer [36]. The in-depth analysis of the GDPR impact and recommendations on its practical implementation is achieved only in a minimal number of manuscripts [37,38] The general international consensus seems to be that for any transfer of data; three elements are needed: establishing informed consent; the material/data transfer agreements; and a code of conduct [39]. However, imposing such requirements on the safe handling of However, the concept of safe data handling goes beyond GDPR. ...
Infectious disease outbreaks, such as 'Coronavirus Disease 2019' (COVID-19), can constitute major global health threats with far-reaching consequences. As outbreaks develop, the international scientific community must provide high-quality scientific research-ready biological samples to solve the existing clinical and epidemiological questions to better combat the pandemic. Such examples are provided by dedicated biobank facilities, the latter collecting increasingly high volumes of biological samples.
However, the more significant concentrations of infectious or potentially infectious biological materials can create a safety risk. The current short report describes the first attempt to identify the published scientific works on biobanking and safety. Three broad thematic areas have been identified: the physical security relevant to staff and sample integrity, the data safety aspects, and the governance parameters relating to the previous two. While the current publications reflect a broad alignment with existing standards and best practices in the biobanking field, they also demonstrate an opportunity for further in-depth work on this field in the post-COVID-19 era.
... The final step is transporting the DNA plates and plate maps to the genotyping facility attached to the TMM Biobank, which is operated using LIMS by Group of Microarray-based Genotyping Analysis. For security control, different sample IDs were used for sample collection, storage and analysis (31). Capitalizing on this workflow, in May 2020, we obtained JPA data of 130,000 participants who met the criteria for QC analysis using control markers. ...
Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5–5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.
