Ensuring sample quality for biomarker discovery studies - Use of ict tools to trace biosample life-cycle

The growing demand of personalized medicine marked the transition from an empirical medicine to a molecular one, aimed at predicting safer and more effective medical treatment for every patient, while minimizing adverse effects. This passage has emphasized the importance of biomarker discovery studies, and has led sample availability to assume a crucial role in biomedical research. Accordingly, a great interest in Biological Bank science has grown concomitantly. In biobanks, biological material and its accompanying data are collected, handled and stored in accordance with standard operating procedures (SOPs) and existing legislation. Sample quality is ensured by adherence to SOPs and sample whole life-cycle can be recorded by innovative tracking systems employing information technology (IT) tools for monitoring storage conditions and characterization of vast amount of data. All the above will ensure proper sample exchangeability among research facilities and will represent the starting point of all future personalized medicine-based clinical trials

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.11Ysciescopu

Baobab LIMS: An open source biobank laboratory information management system for resource-limited settings

Philosophiae Doctor - PhDA laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open source LIMS are available. The decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. However, to find a LIMS that incorporates all possible requirements of a biobank may often be a complicated endeavour. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the development of Baobab LIMS, an open source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. Baobab LIMS is based on the Plone web-content management framework, a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines. The Baobab LIMS components were tested and evaluated in three human biobanks. The testing of the LIMS modules aided in the mapping of the biobanks requirements to the LIMS functionalities, and furthermore, it helped to reveal new user suggestions, such as the enhancement of the online documentation. The user suggestions are demonstrated to be important for both LIMS strengthen and biobank sustainability. Ultimately, the practical LIMS evaluations showed the ability of Boabab LIMS to be used in the management of human biobanks operations of relatively different biobanking workflows

Towards norms for accreditation of biobanks for human health and medical research:Compilation of existing guidelines into an ISO certification/accreditation norm-compatible format

In recent years, biobanks have evolved into professional infrastructures that acquire, validate, process, store, manage and distribute biological material of human origin to public or private end-users/researchers. This article (a) highlights the importance of quality assurance for both the biobank basic processes and sample annotation in order to ensure reliable results of research based on these samples, (b) suggests that certification according to international standards can contribute to the organization of the biobanking processes while accreditation can contribute to the organization of sample characterization/validation, and (c) provides a compilation of all existing guidelines against an International Organization for Standardization (ISO) format.</p

Preservation of DNA Privacy During the Large Scale Detection of COVID-19

As humanity struggles to contain the global COVID-19 pandemic, privacy concerns are emerging regarding confinement, tracing and testing. The scientific debate concerning privacy of the COVID-19 tracing efforts has been intense, especially focusing on the choice between centralised and decentralised tracing apps. The privacy concerns regarding COVID-19 testing, however, have not received as much attention even though the privacy at stake is arguably even higher. COVID-19 tests require the collection of samples. Those samples possibly contain viral material but inevitably also human DNA. Patient DNA is not necessary for the test but it is technically impossible to avoid collecting it. The unlawful preservation, or misuse, of such samples at a massive scale may hence disclose patient DNA information with far-reaching privacy consequences. Inspired by the cryptographic concept of "Indistinguishability under Chosen Plaintext Attack", this paper poses the blueprint of novel types of tests allowing to detect viral presence without leaving persisting traces of the patient's DNA. Authors are listed in alphabetical order.Comment: 10 pages, 1 figur

Stem cell banking: between traceability and identifiability

Stem cell banks are increasingly seen as an essential resource of biological materials for both basic and translational research. Stem cell banks support transnational access to quality-controlled and ethically sourced stem cell lines from different origins and of varying grades. According to the Organisation for Economic Co-operation and Development, advances in regenerative medicine are leading to the development of a bioeconomy, 'a world where biotechnology contributes to a significant share of economic output'. Consequently, stem cell banks are destined to constitute a pillar of the bioeconomy in many countries. While certain ethical and legal concerns are specific to the nature of stem cells, stem cell banking could do well to examine the approaches fostered by tissue banking generally. Indeed, the past decade has seen a move to simplify and harmonize biological tissue and data banking so as to foster international interoperability. In particular, the issues of consent and of traceability illustrate not only commonalities but the opportunity for stem cell banking to appreciate the lessons learned in biobanking generally. This paper analyzes convergence and divergence in issues surrounding policy harmonization, transnational sharing, informed consent, traceability and return of results in the context of stem cell banks