Biobanks for life sciences and personalized medicine: importance of standardization, biosafety, biosecurity, and data management

Assessment of biobank awareness among medical students in Iran

BACKGROUND

Despite the rise of research biobanks in the Middle East, they continue to struggle with the limited number of donors. Although qualified healthcare professionals may address it, the awareness of biobanks among future physicians is low. This paper assesses the attitudes towards research biobanks among Iranian medical students.

METHODS

459 medical students completed an anonymous self-administered online questionnaire regarding the knowledge and attitudes of future physicians towards biobanking.

RESULTS

This study demonstrates that almost half of the students had not heard about biobanks, and one-third had mixed feelings about biobank research. The majority declared a willingness to share their biological material for biobank research and declared altruistic motivation. Students' willingness to donate was influenced by the type of tissues, the purpose of biobank research and trust in biobanks, which influenced their preference for a study-specific consent model. Students expressed concern over biospecimens' unethical or commercial use and data safety.

CONCLUSION

This research shows that promoting knowledge about biobank-based research among future physicians in Iran is crucial.

Evaluating Cryopreservation Methods in Biobanking: Impacts on Biomarker Integrity and Omics Data Reliability

Objectives: Personalized medicine emphasizes prevention and early diagnosis by developing genetic screening and biomarker assessment tools. Biobanks, including University of Piemonte Orientale (UPO) Biobank, support this effort by providing high-quality biological samples collected, processed, and stored using optimized standardized protocols. To determine the optimal long-term storage conditions for biospecimens used in biomedical research, we evaluated plasma and serum samples cryopreserved using two storage methods, cryovials and straws, across various analytical methodologies with differing sensitivity and robustness. Design and Methods: Plasma and serum samples cryopreserved in liquid nitrogen in vials and straw at the UPO Biobank were subjected to multiple analyses including standard biochemical laboratory analysis, targeted lipidomics, untargeted proteomics, and targeted metabolites quantification through mass spectrometry-based analytical techniques. Results: Our data demonstrate the robustness and applicability of both storage methods for standard laboratory analyses in evaluating clinically relevant markers in plasma and serum. Lipidomic analysis revealed slight disparities in lipid abundance, though these differences were mostly confined to specific lipid species, particularly fatty acids. Conversely, proteomic and metabolomic analyses uncovered variations in abundance in a significant, albeit limited, fraction of analytes between vials and straw-derived samples. Conclusions: By highlighting similarities and differences in samples stored in these conditions, this study provides significant insights into optimizing biobanking practices and understanding the factors that influence the integrity of cryopreserved biospecimens and the reliability of the data derived from them. Both straws and vials are convenient and efficient cryopreservation methods, essentially equivalent for samples dedicated to robust and relatively low-sensitive standardized analyses. However, our findings emphasize the need for caution when interpreting omics data from samples subjected to different cryopreservation methods, as subtle variations can arise even with different types of containers.

Quality management, ethical considerations, and emerging challenges in genomics and biobanking: A comprehensive review

The integration of genomics into personalized medicine has the potential to transform healthcare by customizing treatments according to individual genetic profiles. This paper examines the diverse applications of genomics, including the identification of disease susceptibility, improvement of diagnostic methods, optimization of drug therapies, and monitoring of treatment responses. It also explores the expanding global market for genetic testing and the increasing implementation of whole-genome sequencing in clinical practice, with a focus on pilot programs that are advancing comprehensive genomic analysis. Despite challenges such as high costs, data interpretation complexities, and ethical concerns, significant efforts are being made to address these issues. Additionally, the creation of biobanks as vital resources for preserving high-quality biosamples and supporting research highlights the critical need for infrastructure development in genomics. By fostering interdisciplinary collaboration and establishing robust ethical and regulatory frameworks, personalized medicine can ensure equitable access to tailored therapies and enhance health outcomes for everyone. This abstract provides an overview of the transformative potential of genomics and personalized medicine in ushering in a new era of precision healthcare.

A data management system for precision medicine

Precision, or personalised medicine has advanced requirements for medical data management systems (MedDMSs). MedDMS for precision medicine should be able to process hundreds of parameters from multiple sites, be adaptable while remaining in sync at multiple locations, real-time syncing to analytics and be compliant with international privacy legislation. This paper describes the LogiqSuite software solution, aimed to support a precision medicine solution at the patient care (LogiqCare), research (LogiqScience) and data science (LogiqAnalytics) level. LogiqSuite is certified and compliant with international medical data and privacy legislations. This paper evaluates a MedDMS in five types of use cases for precision medicine, ranging from data collection to algorithm development and from implementation to integration with real-world data. The MedDMS is evaluated in seven precision medicine data science projects in prehospital triage, cardiovascular disease, pulmonology, and oncology. The P4O2 consortium uses the MedDMS as an electronic case report form (eCRF) that allows real-time data management and analytics in long covid and pulmonary diseases. In an acute myeloid leukaemia, study data from different sources were integrated to facilitate easy descriptive analytics for various research questions. In the AIDPATH project, LogiqCare is used to process patient data, while LogiqScience is used for pseudonymous CAR-T cell production for cancer treatment. In both these oncological projects the data in LogiqAnalytics is also used to facilitate machine learning to develop new prediction models for clinical-decision support (CDS). The MedDMS is also evaluated for real-time recording of CDS data from U-Prevent for cardiovascular risk management and from the Stroke Triage App for prehospital triage. The MedDMS is discussed in relation to other solutions for privacy-by-design, integrated data stewardship and real-time data analytics in precision medicine. LogiqSuite is used for multi-centre research study data registrations and monitoring, data analytics in interdisciplinary consortia, design of new machine learning / artificial intelligence (AI) algorithms, development of new or updated prediction models, integration of care with advanced therapy production, and real-world data monitoring in using CDS tools. The integrated MedDMS application supports data management for care and research in precision medicine.

Biobanks and data interoperability in Latin America: engendering high-quality evidence for the global research ecosystem

Currently, each biobank in Latin America operates with its own set of standards for database creation and management, resulting in a lack of regional and international interoperability. Furthermore, regulations concerning data protection, curation, and the transfer of biological samples and associated data vary significantly from country to country, by complicating efforts to create a unified data-sharing platform. To address these challenges, Latin America should promote the development of an integrated regional network of biobanks to generate high-quality evidence within the global research ecosystem. This initiative will combine regulatory science—focused on interoperability standards across semantic, technical, legal, and organizational dimensions—and meta-science, which assesses the quality of scientific practice. Evidence indicates that harmonized standards in biobanks lead to higher-quality, more reliable data, thereby facilitating the reproducibility of scientific studies. This paper aims to identify and address existing regulatory, policy, and infrastructure gaps in Latin America to establish harmonized interoperability criteria essential for reproducing biomedical studies. Additionally, it seeks to propose minimum standards for regulating biobank networks, which will promote the development of medical products on a global scale, thereby engendering high quality evidence for the global research ecosystem and enhancing Latin America’s integration into it.

Data Governance and Distribution of Biobank: A Case from a Chinese Cancer Hospital

Objectives: To facilitate the regionalization, specialization, and digitization of biobanks, three issues regarding data collection and application must be addressed (1) integration and distribution of data governance, (2) efficiency and efficacy of data governance, and (3) sustainability of data governance. Methods: We collaborated with stakeholders to identify priorities and assess infrastructure needs through the continuous evaluation and analysis of projects. We developed data management solutions, catalogs, and data models to optimize and support data collection, distribution, and application. Furthermore, ontologies were used to facilitate data integration from multiple sources, and Minimum Information About BIobank Data Sharing (MIABIS) was defined as accessible to all patients. To enhance data integrity, we conducted retrospective and prospective follow-up studies. Results: We completed infrastructure upgrades to match technical solutions and research demands. An information management software with six primary functional divisions was developed for data governance. We optimized the database structure and changed the biospecimen accumulation model from biospecimen-based to patient-centered and service-oriented. Subsequently, we specified 85 attributes of MIABIS to describe the biobank contents. A dual-pillar approach was adopted to expand the biobank's data in collaboration with other institutions, and MIABIS served as a bridge for both vertical and horizontal networks. From 2003 to 2021, we collected a total of 156,997 patient biospecimens/data from 20 cancer types, matching 53,113 cases from follow-up surveys. In addition, we supplied more than 40,000 biospecimens/data points for above 300 scientific research projects. Conclusions: An appropriate information platform for a biobank is fundamental to data collection, distribution, and application, particularly in the context of data-intensive research. We implemented a standardized scientific data structure to fulfill the research requirements. The sustainable development of a biobank depends on a scientific, standardized, and service-oriented data governance approach, along with the efficient utilization of emerging technologies.

Closing Editorial: Colorectal Cancer-A Molecular Genetics Perspective

Colorectal cancer (CRC) remains a significant global health challenge, ranking third in incidence and second in mortality among all cancers [...].

Data Management in Biobanking: Strategies, Challenges, and Future Directions

Biobanking plays a pivotal role in biomedical research by providing standardized processing, precise storing, and management of biological sample collections along with the associated data. Effective data management is a prerequisite to ensure the integrity, quality, and accessibility of these resources. This review provides a current landscape of data management in biobanking, discussing key challenges, existing strategies, and potential future directions. We explore multiple aspects of data management, including data collection, storage, curation, sharing, and ethical considerations. By examining the evolving technologies and methodologies in biobanking, we aim to provide insights into addressing the complexities and maximizing the utility of biobank data for research and clinical applications.

A systematic review of mobile brain/body imaging studies using the P300 event-related potentials to investigate cognition beyond the laboratory

The P300 ERP component, related to the onset of task-relevant or infrequent stimuli, has been widely used in the Mobile Brain/Body Imaging (MoBI) literature. This systematic review evaluates the quality and breadth of P300 MoBI studies, revealing a maturing field with well-designed research yet grappling with standardization and global representation challenges. While affirming the reliability of measuring P300 ERP components in mobile settings, the review identifies significant hurdles in standardizing data cleaning and processing techniques, impacting comparability and reproducibility. Geographical disparities emerge, with studies predominantly in the Global North and a dearth of research from the Global South, emphasizing the need for broader inclusivity to counter the WEIRD bias in psychology. Collaborative projects and mobile EEG systems showcase the feasibility of reaching diverse populations, which is essential to advance precision psychiatry and to integrate varied data streams. Methodologically, a trend toward ecological validity is noted, shifting from lab-based to real-world settings with portable EEG system advancements. Future hardware developments are expected to balance signal quality and sensor intrusiveness, enriching data collection in everyday contexts. Innovative methodologies reflect a move toward more natural experimental settings, prompting critical questions about the applicability of traditional ERP markers, such as the P300 outside structured paradigms. The review concludes by highlighting the crucial role of integrating mobile technologies, physiological sensors, and machine learning to advance cognitive neuroscience. It advocates for an operational definition of ecological validity to bridge the gap between controlled experiments and the complexity of embodied cognitive experiences, enhancing both theoretical understanding and practical application in study design.

Impact of the delay in cryopreservation timing during biobanking procedures on human liver tissue metabolomics

The liver is a highly specialized organ involved in regulating systemic metabolism. Understanding metabolic reprogramming of liver disease is key in discovering clinical biomarkers, which relies on robust tissue biobanks. However, sample collection and storage procedures pose a threat to obtaining reliable results, as metabolic alterations may occur during sample handling. This study aimed to elucidate the impact of pre-analytical delay during liver resection surgery on liver tissue metabolomics. Patients were enrolled for liver resection during which normal tissue was collected and snap-frozen at three timepoints: before transection, after transection, and after analysis in Pathology. Metabolomics analyses were performed using 1H Nuclear Magnetic Resonance (NMR) and Liquid Chromatography-Mass Spectrometry (LC-MS). Time at cryopreservation was the principal variable contributing to differences between liver specimen metabolomes, which superseded even interindividual variability. NMR revealed global changes in the abundance of an array of metabolites, namely a decrease in most metabolites and an increase in β-glucose and lactate. LC-MS revealed that succinate, alanine, glutamine, arginine, leucine, glycerol-3-phosphate, lactate, AMP, glutathione, and NADP were enhanced during cryopreservation delay (all p<0.05), whereas aspartate, iso(citrate), ADP, and ATP, decreased (all p<0.05). Cryopreservation delays occurring during liver tissue biobanking significantly alter an array of metabolites. Indeed, such alterations compromise the integrity of metabolomic data from liver specimens, underlining the importance of standardized protocols for tissue biobanking in hepatology.

Protective effects of different lyoprotectants on survival of clinical bacterial isolates in a hospital biobank

Nowadays the significant role of biobanks in medical, diagnostic, industrial, and environmental research is well known. Bacterial biobanks could be used as a good resource for designing new treatments, biomedical and industrial researches, and laboratory diagnostics. To have a collection of bacteria from clinical samples and maintain their long-term viability, their preservation needs appropriate protective agents, like cryoprotectants and lyoprotectants. In this study, we collected and characterized Gram-negative and Gram-positive bacteria carrying important antibiotic resistance markers from different clinical samples of hospitalized children. Sucrose (10%), skimmed milk (10%), skimmed milk plus sodium glutamate (10% + 1%), and bovine serum albumin (BSA, 10%) were used as lyoprotectants during the freeze-drying procedure. The survival rate of the lyophilized samples was calculated by dilution plating and measuring the colony forming unit (CFU) after 3 months of storage. The culture analysis results indicated that 25 of the 27 studied bacterial genera (Dilutions 10-3 to 10-6), including Shigella, Methicillin-resistant S. aureus, Acinetobacter spp., Escherichia spp., Pseudomonas spp., Klebsiella spp., Enterococcus spp., were recovered in cultured fractions from all preservation conditions, while 2 genera were only detected in a single preservation condition (2/27, 7.4%). Based on the results, sucrose (10%) and skimmed milk (10%) presented the most protective features. The survival rates varied significantly according to types of the bacteria. Collectively, our results showed a diversity in the recovery of different bacterial genera after lyophilization. While statistically no significant difference was detected among the studied protective agents, sucrose (10%) and skimmed milk (10%) exhibited more effective lyoprotective properties for both Gram-positive and Gram-negative bacteria among the clinical isolates in our study.

ALISTER - Application for lipid stability evaluation and research

BACKGROUND AND AIMS

In lipidomic and metabolomic studies, pre-analytical pitfalls enhance the risk of misusing resources such as time and money, as samples that are analyzed may not yield accurate or reliable data due to poor sample handling. Guidance and pre-analytic know-how are necessary for translation of omics technologies into routine clinical testing. The present work aims to enable decision making regarding sample stability in every phase of lipidomics- and metabolomics-centered studies.

MATERIALS AND METHODS

Data of multiple pre-analytic studies were aggregated into a database. Flexible approaches for evaluating these data were implemented in an RShiny-based web-application, tailored towards broad applicability in clinical and bioanalytic research.

RESULTS

Our "Application for lipid stability evaluation & research" - ALISTER facilitates decision making on blood sample stability during lipidomic and metabolomic studies, such as biomarker research, analysis of biobank samples and clinical testing. The interactive tool gives sampling recommendations when planning sample collection or aids in the assessment of sample quality of experiments retrospectively.

CONCLUSION

ALISTER is available for use under https://itmp.shinyapps.io/alister/. The application enables and simplifies data-driven decision making concerning pre-analytic blood sample handling and fits the needs of clinical investigations from multiple perspectives.

Standardizing digital biobanks: integrating imaging, genomic, and clinical data for precision medicine

Advancements in data acquisition and computational methods are generating a large amount of heterogeneous biomedical data from diagnostic domains such as clinical imaging, pathology, and next-generation sequencing (NGS), which help characterize individual differences in patients. However, this information needs to be available and suitable to promote and support scientific research and technological development, supporting the effective adoption of the precision medicine approach in clinical practice. Digital biobanks can catalyze this process, facilitating the sharing of curated and standardized imaging data, clinical, pathological and molecular data, crucial to enable the development of a comprehensive and personalized data-driven diagnostic approach in disease management and fostering the development of computational predictive models. This work aims to frame this perspective, first by evaluating the state of standardization of individual diagnostic domains and then by identifying challenges and proposing a possible solution towards an integrative approach that can guarantee the suitability of information that can be shared through a digital biobank. Our analysis of the state of the art shows the presence and use of reference standards in biobanks and, generally, digital repositories for each specific domain. Despite this, standardization to guarantee the integration and reproducibility of the numerical descriptors generated by each domain, e.g. radiomic, pathomic and -omic features, is still an open challenge. Based on specific use cases and scenarios, an integration model, based on the JSON format, is proposed that can help address this problem. Ultimately, this work shows how, with specific standardization and promotion efforts, the digital biobank model can become an enabling technology for the comprehensive study of diseases and the effective development of data-driven technologies at the service of precision medicine.

Pharmacogenomics Beyond Single Common Genetic Variants: The Way Forward

Interindividual variability in genes encoding drug-metabolizing enzymes, transporters, receptors, and human leukocyte antigens has a major impact on a patient's response to drugs with regard to efficacy and safety. Enabled by both technological and conceptual advances, the field of pharmacogenomics is developing rapidly. Major progress in omics profiling methods has enabled novel genotypic and phenotypic characterization of patients and biobanks. These developments are paralleled by advances in machine learning, which have allowed us to parse the immense wealth of data and establish novel genetic markers and polygenic models for drug selection and dosing. Pharmacogenomics has recently become more widespread in clinical practice to personalize treatment and to develop new drugs tailored to specific patient populations. In this review, we provide an overview of the latest developments in the field and discuss the way forward, including how to address the missing heritability, develop novel polygenic models, and further improve the clinical implementation of pharmacogenomics.

UPO Biobank: The Challenge of Integrating Biobanking into the Academic Environment to Support Translational Research

Biobanks are driving motors of precision and personalized medicine by providing high-quality biological material/data through the standardization and harmonization of their collection, preservation, and distribution. UPO Biobank was established in 2020 as an institutional, disease, and population biobank within the University of Piemonte Orientale (UPO) for the promotion and support of high-quality, multidisciplinary studies. UPO Biobank collaborates with UPO researchers, sustaining academic translational research, and supports the Novara Cohort Study, a longitudinal cohort study involving the population in the Novara area that will collect data and biological specimens that will be available for epidemiological, public health, and biological studies on aging. UPO Biobank has been developed by implementing the quality standards for the field and the ethical and legal issues and normative about privacy protection, data collection, and sharing. As a member of the "Biobanking and Biomolecular Resources Research Infrastructure" (BBMRI) network, UPO Biobank aims to expand its activity worldwide and launch cooperation with new national and international partners and researchers. The objective of this manuscript is to report an institutional and operational experience through the description of the technical and procedural solutions and ethical and scientific implications associated with the establishment of this university research biobank.

Metabolomics of infectious diseases in the era of personalized medicine

Infectious diseases continue to be a major cause of morbidity and mortality worldwide. Diseases cause perturbation of the host's immune system provoking a response that involves genes, proteins and metabolites. While genes are regulated by epigenetic or other host factors, proteins can undergo post-translational modification to enable/modify function. As a result, it is difficult to correlate the disease phenotype based solely on genetic and proteomic information only. Metabolites, however, can provide direct information on the biochemical activity during diseased state. Therefore, metabolites may, potentially, represent a phenotypic signature of a diseased state. Measuring and assessing metabolites in large scale falls under the omics technology known as "metabolomics". Comprehensive and/or specific metabolic profiling in biological fluids can be used as biomarkers of disease diagnosis. In addition, metabolomics together with genomics can be used to differentiate patients with differential treatment response and development of host targeted therapy instead of pathogen targeted therapy where pathogens are more prone to mutation and lead to antimicrobial resistance. Thus, metabolomics can be used for patient stratification, personalized drug formulation and disease control and management. Currently, several therapeutics and in vitro diagnostics kits have been approved by US Food and Drug Administration (FDA) for personalized treatment and diagnosis of infectious diseases. However, the actual number of therapeutics or diagnostics kits required for tailored treatment is limited as metabolomics and personalized medicine require the involvement of personnel from multidisciplinary fields ranging from technological development, bioscience, bioinformatics, biostatistics, clinicians, and biotechnology companies. Given the significance of metabolomics, in this review, we discussed different aspects of metabolomics particularly potentials of metabolomics as diagnostic biomarkers and use of small molecules for host targeted treatment for infectious diseases, and their scopes and challenges in personalized medicine.

Banking on a new understanding: translational opportunities from veterinary biobanks

Current advances in geroscience are due in part to the discovery of biomarkers with high predictive ability in short-lived laboratory animals such as flies and mice. These model species, however, do not always adequately reflect human physiology and disease, highlighting the need for a more comprehensive and relevant model of human aging. Domestic dogs offer a solution to this obstacle, as they share many aspects not only of the physiological and pathological trajectories of their human counterpart, but also of their environment. Furthermore, they age at a considerably faster rate. Studying aging in the companion dog provides an opportunity to better understand the biological and environmental determinants of healthy lifespan in our pets, and to translate those findings to human aging. Biobanking, the systematic collection, processing, storage, and distribution of biological material and associated data has contributed to basic, clinical, and translational research by streamlining the management of high-quality biospecimens for biomarker discovery and validation. In this review, we discuss how veterinary biobanks can support research on aging, particularly when integrated into large-scale longitudinal studies. As an example of this concept, we introduce the Dog Aging Project Biobank.

Data platforms for open life sciences-A systematic analysis of management instruments

Open data platforms are interfaces between data demand of and supply from their users. Yet, data platform providers frequently struggle to aggregate data to suit their users' needs and to establish a high intensity of data exchange in a collaborative environment. Here, using open life science data platforms as an example for a diverse data structure, we systematically categorize these platforms based on their technology intermediation and the range of domains they cover to derive general and specific success factors for their management instruments. Our qualitative content analysis is based on 39 in-depth interviews with experts employed by data platforms and external stakeholders. We thus complement peer initiatives which focus solely on data quality, by additionally highlighting the data platforms' role to enable data utilization for innovative output. Based on our analysis, we propose a clearly structured and detailed guideline for seven management instruments. This guideline helps to establish and operationalize data platforms and to best exploit the data provided. Our findings support further exploitation of the open innovation potential in the life sciences and beyond.

Quality matters: International standards for biobanking

Human biospecimens provide the basis for research, leading to a better understanding of human disease biology and discovery of new treatments that are tailored to individual patients with cancer or other common complex diseases. The collection, processing, preservation, storage and providing access to these resources are key activities of biobanks. Biobanks must ensure proper quality of samples and data, ethical and legal compliance as well as transparent and efficient access procedures. The standards for biobanking outlined herein are intended to be implemented in biobanks and to supply researchers with high‐quality samples fitted for an intended use.

MOSS: multi-omic integration with sparse value decomposition

SUMMARY

This article presents multi-omic integration with sparse value decomposition (MOSS), a free and open-source R package for integration and feature selection in multiple large omics datasets. This package is computationally efficient and offers biological insight through capabilities, such as cluster analysis and identification of informative omic features.

AVAILABILITY AND IMPLEMENTATION

https://CRAN.R-project.org/package=MOSS.

SUPPLEMENTARY INFORMATION

Supplementary information can be found at https://github.com/agugonrey/GonzalezReymundez2021.

Quality Management in Polish Biobanking Network-Current Status Before the Implementation of Unified and Harmonized Integrated Quality Management System

In 2017, Polish Biobanking Network was established in Poland, within BBMRI.pl project titled "Organization of Polish Biobanking Network within the Biobanking and Biomolecular Resources Research Infrastructure BBMRI-ERIC" as a strategic scientific infrastructure concept. One of the key elements of the project was the verification of the current status of QMS in the Polish biobanking institutions and the implementation of common solutions. The main goal was to indicate the current QMS level and determine the starting points for QMS development for each biobank of the Polish Biobanking Network (PBN). Within 3 years, 35 audit visits were performed. The current status and the level of QMS implementation in each biobank were assessed. Five hundred and seventy recommendations were prepared. The data was analyzed using Fischer Exact test to determine whether or not a significant association was observed. Three areas of analysis were covered: (1) BBMRI.pl status, (2) QMS implementation level and (3) private/public party, respectively. The results were discussed within 15 areas. Concluding remarks showed that some differences were observed in the case of subgroups analysis. There is convergence in QMS within the biobanks where Tissue Banks are located. Moreover, some discrepancies between the QMS implementation level in BBMRI.pl Consortium biobanks and PBN biobanks are observed. Nevertheless, the consortium members are obliged to prepare other biobanks willing to enter the PBN as Members/Observers or which already are in the PBN, so that they can meet the requirements of the quality management system that will enable efficient management of biobanking processes in these units. That is why some actions within BBMRI.pl projects are organized to help the whole biobanking community in Poland implement the harmonized solution.

Impact of the pre-examination phase on multicenter metabolomic studies

The development of metabolomics in clinical applications has been limited by the lack of validation in large multicenter studies. Large population cohorts and their biobanks are a valuable resource for acquiring insights into molecular disease mechanisms. Nevertheless, most of their collections are not tailored for metabolomics and have been created without specific attention to the pre-analytical requirements for high-quality metabolome assessment. Thus, comparing samples obtained by different pre-analytical procedures remains a major challenge. Here, ¹H NMR-based analyses are used to demonstrate how human serum and plasma samples collected with different operating procedures within several large European cohort studies from the Biobanking and Biomolecular Resources Infrastructure - Large Prospective Cohorts (BBMRI-LPC) consortium can be easily revealed by supervised multivariate statistical analyses at the initial stages of the process, to avoid biases in the downstream analysis. The inter-biobank differences are discussed in terms of deviations from the validated CEN/TS 16945:2016 / ISO 23118:2021 norms. It clearly emerges that biobanks must adhere to the evidence-based guidelines in order to support wider-scale application of metabolomics in biomedicine, and that NMR spectroscopy is informative in comparing the quality of different sample sources in multi cohort/center studies.

Population-nosological research biobank of the National Medical Research Center for Therapy and Preventive Medicine: analysis of biosamples, principles of collecting and storing information

Aim. To analyze the structure of clinical data, as well as the principles of collecting and storing related data of the biobank of the National Medical Research Center for Therapy and Preventive Medicine (hereinafter Biobank).

Material and methods. The analysis was carried out using the documentation available in the Biobank, as well as the databases used in its work. The paper presents clinical data on biosamples available in the Biobank as of August 18, 2021.

Results. At the time of analysis, the Biobank had 373547 samples collected from 54192 patients within 37 research projects. The article presents the analysis of data representation and quantitative assessment of the presence/absence of common diagnoses in clinical projects. Approaches to documenting clinical information associated with biological samples stored in the Biobank were assessed. The methods and tools used for standardization and automation of processes used in the Biobank were substantiated.

Conclusion. The Biobank of the National Medical Research Center for Therapy and Preventive Medicine is the largest research biobank in Russia, which meets all modern international requirements and is one of the key structures that improve the research quality and intensify their conduct both within the one center and in cooperation with other biobanks and scientific institutions. The collection and systematic storage of clinical abstracts of biological samples is an integral and most important part of the Biobank’s work.

Biobank as a key component of supporting research in phthisiology and infectious diseases

Conducting fundamental and clinical research in the field of tuberculosis is an important step towards reducing related morbidity and mortality, but access to a sufficient number of high-quality samples required for research is an unsolved problem in Russia. This review is devoted to biobanking as a key component of modern research in personalized medicine, as well as to the status and prospects for developing this area in phthisiology and infectious diseases combined with tuberculosis.

Human exposome assessment platform

The Human Exposome Assessment Platform (HEAP) is a research resource for the integrated and efficient management and analysis of human exposome data. The project will provide the complete workflow for obtaining exposome actionable knowledge from population-based cohorts. HEAP is a state-of-the-science service composed of computational resources from partner institutions, accessed through a software framework that provides the world's fastest Hadoop platform for data warehousing and applied artificial intelligence (AI). The software, will provide a decision support system for researchers and policymakers. All the data managed and processed by HEAP, together with the analysis pipelines, will be available for future research. In addition, the platform enables adding new data and analysis pipelines. HEAP's final product can be deployed in multiple instances to create a network of shareable and reusable knowledge on the impact of exposures on public health.

Small extracellular vesicles from menstrual blood-derived mesenchymal stem cells (MenSCs) as a novel therapeutic impetus in regenerative medicine

Menstrual blood-derived mesenchymal stem cells (MenSCs) have great potential in regenerative medicine. MenSC has received increasing attention owing to its impressive therapeutic effects in both preclinical and clinical trials. However, the study of MenSC-derived small extracellular vesicles (EVs) is still in its initial stages, in contrast to some common MSC sources (e.g., bone marrow, umbilical cord, and adipose tissue). We describe the basic characteristics and biological functions of MenSC-derived small EVs. We also demonstrate the therapeutic potential of small EVs in fulminant hepatic failure, myocardial infarction, pulmonary fibrosis, prostate cancer, cutaneous wound, type-1 diabetes mellitus, aged fertility, and potential diseases. Subsequently, novel hotspots with respect to MenSC EV-based therapy are proposed to overcome current challenges. While complexities regarding the therapeutic potential of MenSC EVs continue to be unraveled, advances are rapidly emerging in both basic science and clinical medicine. MenSC EV-based treatment has great potential for treating a series of diseases as a novel therapeutic strategy in regenerative medicine.

Basic principles of biobanking: from biological samples to precision medicine for patients

The term "biobanking" is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.

Data quality for federated medical data lakes

Purpose

Medical research requires biological material and data collected through biobanks in reliable processes with quality assurance. Medical studies based on data with unknown or questionable quality are useless or even dangerous, as evidenced by recent examples of withdrawn studies. Medical data sets consist of highly sensitive personal data, which has to be protected carefully and is available for research only after the approval of ethics committees. The purpose of this research is to propose an architecture to support researchers to efficiently and effectively identify relevant collections of material and data with documented quality for their research projects while observing strict privacy rules.

Design/methodology/approach

Following a design science approach, this paper develops a conceptual model for capturing and relating metadata of medical data in biobanks to support medical research.

Findings

This study describes the landscape of biobanks as federated medical data lakes such as the collections of samples and their annotations in the European federation of biobanks (Biobanking and Biomolecular Resources Research Infrastructure – European Research Infrastructure Consortium, BBMRI-ERIC) and develops a conceptual model capturing schema information with quality annotation. This paper discusses the quality dimensions for data sets for medical research in-depth and proposes representations of both the metadata and data quality documentation with the aim to support researchers to effectively and efficiently identify suitable data sets for medical studies.

Originality/value

This novel conceptual model for metadata for medical data lakes has a unique focus on the high privacy requirements of the data sets contained in medical data lakes and also stands out in the detailed representation of data quality and metadata quality of medical data sets.

BBMRI-ERIC Negotiator: Implementing Efficient Access to Biobanks

Various biological resources, such as biobanks and disease-specific registries, have become indispensable resources to better understand the epidemiology and biological mechanisms of disease and are fundamental for advancing medical research. Nevertheless, biobanks and similar resources still face significant challenges to become more findable and accessible by users on both national and global scales. One of the main challenges for users is to find relevant resources using cataloging and search services such as the BBMRI-ERIC Directory, operated by European Research Infrastructure on Biobanking and Biomolecular Resources (BBMRI-ERIC), as these often do not contain the information needed by the researchers to decide if the resource has relevant material/data; these resources are only weakly characterized. Hence, the researcher is typically left with too many resources to explore and investigate. In addition, resources often have complex procedures for accessing holdings, particularly for depletable biological materials. This article focuses on designing a system for effective negotiation of access to holdings, in which a researcher can approach many resources simultaneously, while giving each resource team the ability to implement their own mechanisms to check if the material/data are available and to decide if access should be provided. The BBMRI-ERIC has developed and implemented an access and negotiation tool called the BBMRI-ERIC Negotiator. The Negotiator enables access negotiation to more than 600 biobanks from the BBMRI-ERIC Directory and other discovery services such as GBA/BBMRI-ERIC Locator or RD-Connect Finder. This article summarizes the principles that guided the design of the tool, the terminology used and underlying data model, request workflows, authentication and authorization mechanism(s), and the mechanisms and monitoring processes to stimulate the desired behavior of the resources: to effectively deliver access to biological material and data.

Vignettes to Illustrate the Value of Tumor Biobanks in Cancer Research in Canada

Background: Tumor biobanks are a common research infrastructure. As a collection of biospecimens and annotated data collected to support a multitude of research projects, biobanks facilitate access to materials that are the critical fuel for the generation of data in up to 40% of cancer research publications. However, quantifying how to measure biobanks' impact and their value on the field of cancer research discoveries and findings, has not been well elucidated. Methods: We have used a qualitative case study approach to illustrate the impact of tumor biobanks. We assessed the impact of three research studies published between 2010 and 2012 that required easily accessible "classic" biobanks. Each study utilized preassembled collections of tumor biospecimens with associated patient outcomes data at the outset of the research project. We compared the resulting journal impact factor, altmetric and field-weighted citation impact factor scores for each article to a set of six "benchmark" articles that represent cancer research and treatment discoveries from the same time period and two sentinel scientific discovery articles. Results: We developed a value model using a literature search and design-thinking methodologies to illustrate the contributions of these "classic" model biobanks to these research studies. Assessment of the three example articles supported by biobanks demonstrates that the output can have impact that is comparable to the impact of a set of benchmark articles describing milestones in the field of cancer research and cancer care. Conclusions: These case studies illustrate the value of the sustained investment of funds, planning, time, and effort on the part of the biobanks before the conduct of the research study to be able to ultimately support high-value research. The "value" model will enable further discussion around impact and may be useful in better delineating qualitative metrics of biobank value in the future.

Anticipatory Governance in Biobanking: Security and Risk Management in Digital Health

Although big-data research has met with multiple controversies in diverse fields, political and security implications of big data in life sciences have received less attention. This paper explores how threats and risks are anticipated and acted on in biobanking, which builds research repositories for biomedical samples and data. Focusing on the biggest harmonisation cluster of biomedical research in Europe, BBMRI-ERIC, the paper analyses different logics of risk in the anticipatory discourse on biobanking. Based on document analysis, interviews with ELSI experts, and field research, three types of framing of risk are reconstructed: data security, privacy, and data misuse. The paper finds that these logics downplay the broader social and political context and reflects on the limits of the practices of anticipatory governance in biobanking. It argues that this regime of governance can make it difficult for biobanks to address possible future challenges, such as access to biomedical data by authorities, pressures for integrating biobank data with other type of personal data, or their use for profiling beyond medical purposes. To address potential controversies and societal implications related to the use of big data in health research and medicine, the paper suggests to expand the vocabulary and practices of anticipatory governance, in the biobanking community and beyond.

In situ Adipogenesis in Biomaterials Without Cell Seeds: Current Status and Perspectives

For cosmetic and reconstructive purposes in the setting of small-volume adipose tissue damage due to aging, traumatic defects, oncological resections, and degenerative diseases, the current strategies for soft tissue replacement involve autologous fat grafts and tissue fillers with synthetic, bioactive, or tissue-engineered materials. However, they all have drawbacks such as volume shrinkage and foreign-body responses. Aiming to regenerate bioactive vascularized adipose tissue on biomaterial scaffolds, adipose tissue engineering (ATE) has emerged as a suitable substitute for soft tissue repair. The essential components of ATE include scaffolds as support, cells as raw materials for fat formation, and a tolerant local environment to allow regeneration to occur. The commonly loaded seeding cells are adipose-derived stem cells (ASCs), which are expected to induce stable and predictable adipose tissue formation. However, defects in stem cell enrichment, such as donor-site sacrifice, limit their wide application. As a promising alternative approach, cell-free bioactive scaffolds recruit endogenous cells for adipogenesis. In biomaterials without cell seeds, the key to sufficient adipogenesis relies on the recruitment of endogenous host cells and continuous induction of cell homing to scaffolds. Regeneration, rather than repair, is the fundamental dominance of an optimal mature product. To induce in situ adipogenesis, many researchers have focused on the mechanical and biochemical properties of scaffolds. In addition, efforts to regulate an angiogenic and adipogenic microenvironment in cell-free settings involve integrating growth factors or extracellular matrix (ECM) proteins onto bioactive scaffolds. Despite the theoretical feasibility and encouraging results in animal models, few of the reported cell-free biomaterials have been tested in humans, and failures of decellularized adipose tissues in adipogenesis have also been reported. In these cases, the most likely reason was the lack of supporting vasculature. This review summarizes the current status of biomaterials without cell seeds. Related mechanisms and influencing factors of in situ adipogenesis in cell-free biomaterials, dilemma in the development of biomaterials, and future perspectives are also addressed.

Guidelines for Biobanking of Bone Marrow Adipose Tissue and Related Cell Types: Report of the Biobanking Working Group of the International Bone Marrow Adiposity Society

Over the last two decades, increased interest of scientists to study bone marrow adiposity (BMA) in relation to bone and adipose tissue physiology has expanded the number of publications using different sources of bone marrow adipose tissue (BMAT). However, each source of BMAT has its limitations in the number of downstream analyses for which it can be used. Based on this increased scientific demand, the International Bone Marrow Adiposity Society (BMAS) established a Biobanking Working Group to identify the challenges of biobanking for human BMA-related samples and to develop guidelines to advance establishment of biobanks for BMA research. BMA is a young, growing field with increased interest among many diverse scientific communities. These bring new perspectives and important biological questions on how to improve and build an international community with biobank databases that can be used and shared all over the world. However, to create internationally accessible biobanks, several practical and legislative issues must be addressed to create a general ethical protocol used in all institutes, to allow for exchange of biological material internationally. In this position paper, the BMAS Biobanking Working Group describes similarities and differences of patient information (PIF) and consent forms from different institutes and addresses a possibility to create uniform documents for BMA biobanking purposes. Further, based on discussion among Working Group members, we report an overview of the current isolation protocols for human bone marrow adipocytes (BMAds) and bone marrow stromal cells (BMSCs, formerly mesenchymal), highlighting the specific points crucial for effective isolation. Although we remain far from a unified BMAd isolation protocol and PIF, we have summarized all of these important aspects, which are needed to build a BMA biobank. In conclusion, we believe that harmonizing isolation protocols and PIF globally will help to build international collaborations and improve the quality and interpretation of BMA research outcomes.

Biosafety Requirements for Autopsies of Patients with COVID-19: Example of a BSL-3 Autopsy Facility Designed for Highly Pathogenic Agents

Information obtained from autopsies of patients infected with high-risk pathogens is an important pillar in managing a proper response to pandemics, particular in the early phase. This is due to the fact that autopsy allows efficient evaluation of comorbidities for risk assessment, as well as identification of key pathophysiological and molecular mechanisms in organs driving the severity of disease which might be important targets for therapeutic interventions. In the case of patients who have died of infection with unknown pathogens, isolation and culture of pathogens from the affected organs is another important opportunity for a proper response to (re)emerging infectious diseases. However, the situation of COVID-19 demonstrated that there were concerns about performing autopsies because of biosafety risks. In this review we compare requirements for biosafety level 3 (BSL-3) laboratories from the European Commission and the World Health Organization and summarize specific recommendations for postmortem analysis of COVID-19-deceased patients from the Centers for Disease Control and Prevention. Furthermore, we describe in detail a BSL-3 facility with enhanced protection of personnel and an environment that has been designed for performing autopsies, biobanking of collected tissue specimens, and culture of pathogens in cases of high-risk pathogen infections and report on the experience obtained in operating this facility in the context of COVID-19.

Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19

All of humans and other mammalian species are colonized by some types of microorganisms such as bacteria, archaea, unicellular eukaryotes like fungi and protozoa, multicellular eukaryotes like helminths, and viruses, which in whole are called microbiota. These microorganisms have multiple different types of interaction with each other. A plethora of evidence suggests that they can regulate immune and digestive systems and also play roles in various diseases, such as mental, cardiovascular, metabolic and some skin diseases. In addition, they take-part in some current health problems like diabetes mellitus, obesity, cancers and infections. Viral infection is one of the most common and problematic health care issues, particularly in recent years that pandemics like SARS and COVID-19 caused a lot of financial and physical damage to the world. There are plenty of articles investigating the interaction between microbiota and infectious diseases. We focused on stimulatory to suppressive effects of microbiota on viral infections, hoping to find a solution to overcome this current pandemic. Then we reviewed mechanistically the effects of both microbiota and probiotics on most of the viruses. But unlike previous studies which concentrated on intestinal microbiota and infection, our focus is on respiratory system's microbiota and respiratory viral infection, bearing in mind that respiratory system is a proper entry site and residence for viruses, and whereby infection, can lead to asymptomatic, mild, self-limiting, severe or even fatal infection. Finally, we overgeneralize the effects of microbiota on COVID-19 infection. In addition, we reviewed the articles about effects of the microbiota on coronaviruses and suggest some new therapeutic measures.

Biobanking for Cancer Biomarker Research: Issues and Solutions

Biomarkers are critical tools that underpin precision medicine. However there has been slow progress and frequent failure of biomarker development. The root causes are multifactorial. Here, we focus on the need for fast, efficient, and reliable access to quality biospecimens as a critical area that impacts biomarker development. We discuss the past history of biobanking and the evolution of biobanking processes relevant to the specific area of cancer biomarker development as an example, and describe some solutions that can improve this area, thus potentially accelerating biomarker research.

Study of laboratory staff' knowledge of biobanking in Côte d'Ivoire

Background

A biobank is a structure which collects and manages biological samples and their associated data. The collected samples will then be made available for various uses. The sharing of those samples raised ethical questions which have been answered through specific rules. Thus, a Biobank functioning under tight ethical rules would be immensely valuable from a scientific and an economic view point. In 2009, Côte d’Ivoire established a biobank, which has been chosen to house the regional biobank of Economic Community of West African States (ECOWAS) countries in 2018. To ensure optimal and efficient use of this biobank, the scientific community must be aware of its existence and its role. It was therefore necessary to evaluate the knowledge of laboratories staff on the role and activities of a biobank.

Methods

This descriptive study was done by questioning staff from laboratories working on human’s health, animals or plants. The laboratories were located in southern Côte d’Ivoire.

Results

A total of 205 people completed the questionnaire. Of these 205 people, 34.63% were biologists, 7.32% engineers, 48.78% technicians and 9.27% PhD students. The average length of work experience was 10.11 ± 7.83 years. In this study, 43.41% of the participants had never heard of biobanking. Only 48.78% of participants had a good understanding of the role of a biobank. Technicians and PhD students were less educated on the notion of biobank (p < 0.000001). Although biologists were more educated on this issue, 21.13% of them had a misconception of biobank. Good knowledge of the role of a biobank was not significantly related to the work experience’s length (p > 0.88).

Conclusion

The level of knowledge of laboratory staff about biobanking needs to be improved. Training on the role, activities and interests of the biobank is important.