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

Pediatric biobanks to enhance clinical and translational research for children

Including children in biomedical research is an argument for continual reflection and practice refinement from an ethical and legal standpoint. Indeed, as children reach adulthood, a reconsent method should be used, and data connected with samples should ideally be updated based on the children's growth and long-term results. Furthermore, because most pediatric disorders are uncommon, children's research initiatives should conform to standard operating procedures (SOPs) set by worldwide scientific organizations for successfully sharing data and samples. Here, we examine how pediatric biobanks can help address some challenges to improve biomedical research for children. Indeed, modern biobanks are evolving as complex research platforms with specialized employees, dedicated spaces, information technologies services (ITS), and ethical and legal expertise. In the case of research for children, biobanks can collaborate with scientific networks (i.e., BBMRI-ERIC) and provide the collection, storage, and distribution of biosamples in agreement with international standard procedures (ISO-20387). Close collaboration among biobanks provides shared avenues for maximizing scarce biological samples, which is required to promote the translation of scientific breakthroughs for developing clinical care and health policies tailored to the pediatric population. Moreover, biobanks, through their science communication and dissemination activities (i.e., European Biobank Week), may be helpful for children to understand what it means to be engaged in a research study, allowing them to see it as a pleasant, useful, and empowering experience. Additionally, biobanks can notify each participant about which projects have been accomplished (i.e., through their websites, social media networks, etc.); they can facilitate future reconsent procedures and update sample-associated data based on the children's growth. Finally, because of the increasing interest from public and commercial organizations in research efforts that include the sharing and reuse of health data, pediatric biobanks have a crucial role in this context. Consequently, they could benefit from funding opportunities for sustaining research activities even regarding rare pediatric disorders.  Conclusion: Pediatric biobanks are helpful for providing biological material for research purposes, addressing ethical and legal issues (i.e. data protection, consent, etc.), and providing control samples from healthy children of various ages and from different geographical regions and ethnicities. Therefore, it is vital to encourage and maintain children's engagement in medical research programs and biobanking activities, especially as children become adults, and reconsent procedures must be applied. What is Known: • Biobanks are critical research infrastructures for medical research, especially in the era of "omic" science. However, in light of their fragility and rights children's participation in biobanking and medical research programs is a complex argument of continuous debate in scientific literature. What is New: • We propose a review of the literature on pediatric biobanks with a particular focus on oncological biobanks. The main current limitations and challenges for pediatric biobanks are presented and possible solutions are discussed.

Evolution of biobanks and ethical governance for the emerging applications in biomedical research

The establishment of a biobank and effective utilization of the biological resources comes with lot of challenges which require operating processes and effective governance structure with public awareness. As biobank is an evolving field of data driven health-care research, guided strategies in line with the national and international statutory body regulations is important. A trustworthy governance is paramount in developing a sustainable way of establishing, maintaining and successful functioning of a biobank. This paper highlights the structure of biobank governance, challenges and processes of effective integration of governance strategies.

The prevention of falls in patients with Parkinson's disease with in-home monitoring using a wearable system: a pilot study protocol

BACKGROUND

Parkinson's disease (PD) is a chronic, progressive neurodegenerative condition that gradually worsens motor function and leads to postural instability and, eventually, falls. Several factors may influence the frequency of future falls, such as slowness, freezing of gait, loss of balance, and mobility problems, cognitive impairments, and the number of previous falls. The TED bracelet is an advanced technological wearable device able to predict falls.

AIMS

This principal aim is to investigate the feasibility of a full-scale research project that uses the TED bracelet to identify whether individuals with PD are at risk of falling.

METHODS

This study will involve a pilot prospective observational study design; the subjects will include 26 patients suffering from mild PD and 26 others with no PD and no gait problems. Data will be collected from the TED bracelet and then compared to a paper-based fall diary. The enrolled participants will have a scheduled outpatient evaluation to collect both clinical and instrumental data as well as biological samples.

DISCUSSION

This pilot study could then be implemented in a larger form to further evaluate the effectiveness of the TED device. Finally, it will help further develop gait monitoring systems for people with Parkinson's disease and other neurodegenerative diseases that can affect physical function and mobility, such as dementia and Alzheimer's.

CONCLUSIONS

Preventing falls and their complications could lead to major advancements in the quality of home care for patients with PD, which would significantly impact the quality of life of both these patients and their caregivers.

Identification and Assessment of Risks in Biobanking: The Case of the Cancer Institute of Bari

Simple Summary

Risk assessment is one of the requirements for all activities involving the management of human biological samples within the framework of the new ISO 20387:2018. Although some theoretical approaches are available for preparing risk assessments in general, there is no evidence in the literature of examples of listed insurable risks for cancer biobanks. To fill this gap and to provide an overview of the survey performed in our cancer Biobank, we have assessed potential exposures to insurable risks. After an analysis of the Biobank structure and focusing on natural catastrophe risks, we produced a summary map of risk scenarios. In addition to implementing security awareness, this also lays the foundation for transferring the residual risk arising from Biobank activities to the insurance market.

Abstract

Although research biobanks are among the most promising tools to fight disease and improve public health, there are a range of risks biobanks may face that mainly need to be assessed in an attempt to be relieved. We conducted a strategic insurance review of an institutional cancer biobank with the aim of both identifying the insurable risks of our own Biobank and gathering useful evidence of primary exposure to insurable risks. In this practical scenario, risks have been outlined and categorized into inherent and residual risks, along with their possible impact on biobank maintenance. Results at the Biobank of the Cancer Institute of Bari showed evidence of potentially significant and intrinsic risk due to highly relevant threats, along with already implemented improvements that significantly reduce risks to a range of relative acceptability.

Integrative multi-omics approach to targeted therapy for glioblastoma

This review describes recent technological advances applied to glioblastoma (GBM), a brain tumor with dismal prognosis. International consortial efforts suggest the presence of molecular subtypes within histologically identical GBM tumors. This emphasizes that future treatment decisions should no longer be made based solely on morphological analyses, but must now take into consideration such molecular and cellular heterogeneity. The use of single-cell technologies has advanced our understanding and assignation of functional subtypes revealing therapeutic vulnerabilities. Our team has developed stratification approaches in the past few years, and we have been able to identify patient cohorts enriched for various signaling pathways. Importantly, our Glioportal brain tumor resource has been established under the National Neuroscience Institute Tissue Bank in 2021. This resource offers preclinical capability to validate working hypotheses established from patient clinical datasets. This review highlights recent developments with the ultimate goal of assigning functional meaning to molecular subtypes, revealing therapeutic vulnerabilities.

A Survey on the Role of Artificial Intelligence in Biobanking Studies: A Systematic Review

Introduction: In biobanks, participants' biological samples are stored for future research. The application of artificial intelligence (AI) involves the analysis of data and the prediction of any pathological outcomes. In AI, models are used to diagnose diseases as well as classify and predict disease risks. Our research analyzed AI's role in the development of biobanks in the healthcare industry, systematically. Methods: The literature search was conducted using three digital reference databases, namely PubMed, CINAHL, and WoS. Guidelines for preferred reporting elements for systematic reviews and meta-analyses (PRISMA)-2020 in conducting the systematic review were followed. The search terms included "biobanks", "AI", "machine learning", and "deep learning", as well as combinations such as "biobanks with AI", "deep learning in the biobanking field", and "recent advances in biobanking". Only English-language papers were included in the study, and to assess the quality of selected works, the Newcastle-Ottawa scale (NOS) was used. The good quality range (NOS ≥ 7) is only considered for further review. Results: A literature analysis of the above entries resulted in 239 studies. Based on their relevance to the study's goal, research characteristics, and NOS criteria, we included 18 articles for reviewing. In the last decade, biobanks and artificial intelligence have had a relatively large impact on the medical system. Interestingly, UK biobanks account for the highest percentage of high-quality works, followed by Qatar, South Korea, Singapore, Japan, and Denmark. Conclusions: Translational bioinformatics probably represent a future leader in precision medicine. AI and machine learning applications to biobanking research may contribute to the development of biobanks for the utility of health services and citizens.

Prospective Real-World Gynaecological Cancer Clinical Registry with Associated Biospecimens: A Collaborative Model to Promote Translational Research between GEICO and the Spanish Biobank Network

Patient registries linked to biorepositories constitute a valuable asset for clinical and translational research in oncology. The Spanish Group of Ovarian Cancer Research (GEICO), in collaboration with the Spanish Biobank Network (RNBB), has developed a multicentre, multistakeholder, prospective virtual clinical registry (VCR) associated with biobanks for the collection of real-world data and biological samples of gynaecological cancer patients. This collaborative project aims to promote research by providing broad access to high-quality clinical data and biospecimens for future research according to the needs of investigators and to increase diagnostic and therapeutic opportunities for gynaecological cancer patients in Spain. The VCR will include the participation of more than 60 Spanish hospitals entering relevant clinical information in harmonised electronic case report forms (eCRFs) in four different cohorts: ovarian, endometrial, cervical, and rare gynaecological cancers (gestational trophoblastic disease). Initial data for the cases included till December 2021 are presented. The model described herein establishes a real-world win-win collaboration between multicentre structures, promoted and supported by GEICO, that will contribute to the success of translational research in gynaecological cancer.

A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies

Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein–Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic 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.

Management of biobanking for medical genetics research

Biobanking is one of the most important elements of the modern infrastructure for biomedical research. Organization of a biobank on the basis of the N. P. Bochkov Medical Genetics Research Center provides a centralized infrastructure for preparing biomaterial for research. Biobank has the format of a research equipment sharing center and works with two types of unique biomaterials from patients with genetic diseases: blood/blood components and vital cells of various tissue origin. The storage facility of the Biobank is equipped with low-temperature (-80° C) and cryostorage (-196° C) systems. Identification and search of samples is carried out using a bar-coding system and is implemented through the information interface of the biobank, which is integrated into the general database of patients at the Medical Genetics Research Center. Information on biomaterial samples is presented in periodically updated catalogs on the page of equipment sharing center “Biobank”. Biobank collection is available to internal and external users.

Role of Biobanks for Cancer Research and Precision Medicine in Hepatocellular Carcinoma

INTRODUCTION

Hepatocellular carcinoma (HCC) is a highly complex and deadly cancer. There is an urgent need for new and effective treatment modalities. Since the primary goal in the management of cancer is to cure and improve survival, personalized therapy can increase survival, reduce mortality rates, and improve quality of life. Biobanks hold potential in leading to breakthroughs in biomedical research and precision medicine (PM). They serve as a biorepository, collecting, processing, storing, and supplying specimens and relevant data for basic, translational, and clinical research.

OBJECTIVE

We aimed to highlight the fundamental role of biobanks, harboring high quality, sustainable collections of patient samples in adequate size and variability, for developing diagnostic, prognostic, and predictive biomarkers to develop and PM approaches in the management of HCC.

METHOD

We obtained information from previously published articles and BBMRI directory.

RESULTS AND CONCLUSION

Biobanking of high-quality biospecimens along with patient clinical information provides a fundamental scientific infrastructure for basic, translational, and clinical research. Biobanks that control and eliminate pre-analytical variability of biospecimens, provide a platform to identify reliable biomarkers for the application of PM. We believe, establishing HCC biobanks will empower to underpin molecular mechanisms of HCC and generate strategies for PM. Thus, first, we will review current therapy approaches in HCC care. Then, we will summarize challenges in HCC management. Lastly, we will focus on the best practices for establishing HCC biobanking to support research, translational medicine in the light of new experimental research conducted with the aim of delivering PM for HCC patients.

Molecular Characterization of Prostate Cancers in the Precision Medicine Era

Prostate cancer (PCa) therapy has been recently revolutionized by the approval of new therapeutic agents in the metastatic setting. However, the optimal therapeutic strategy in such patients should be individualized in the light of prognostic and predictive molecular factors, which have been recently studied: androgen receptor (AR) alterations, PTEN-PI3K-AKT pathway deregulation, homologous recombination deficiency (HRD), mismatch repair deficiency (MMRd), and tumor microenvironment (TME) modifications. In this review, we highlighted the clinical impact of prognostic and predictive molecular factors in PCa patients' outcomes, identifying biologically distinct subtypes. We further analyzed the relevant methods to detect these factors, both on tissue, i.e., immunohistochemistry (IHC) and molecular tests, and blood, i.e., analysis of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). Moreover, we discussed the main pros and cons of such techniques, depicting their present and future roles in PCa management, throughout the precision medicine era.