Biopreservation and Biobanking最新文献

Introduction: Advancements in biomedical research depend on the quality and availability of biological samples. Despite their sophisticated storage capabilities, biobanks face significant challenges in sample management, with stored specimens often remaining unused and researchers struggling to access the required samples.

Objectives: To analyze the challenges in biospecimen access and traceability, evaluate existing solutions, and propose a framework for integrated sample management in global research collaboration.

Methods: A scoping review was conducted across PubMed, Scopus, and Web of Science databases, supplemented by grey literature (2004-2024). The analysis included an examination of Biobank Information Management Systems and an evaluation of sample management systems, tracking technologies, and governance frameworks.

Results: The analysis revealed fragmented management systems, with at least 38 different biobanking software solutions offering limited interoperability. Proprietary systems and vendor lock-ins create significant barriers to data sharing. Sample tracking shows the evolution from manual to digital systems; however, cross-institutional tracking remains challenging. Reproducibility issues account for significant challenges in research, whereas inefficient resource utilization persists, with 67% of biobanks citing underutilization as a major concern.

Conclusions: Addressing biobank sample access and traceability requires a shift from an institution-centric to an ecosystem-wide approach. Its success depends on integrating technological solutions such as Blockchain, the Internet of Things, and artificial intelligence with governance frameworks while ensuring alignment with stakeholder needs. Future developments should focus on implementing integrated traceability systems that support transparent and accountable sample management across the global research ecosystem.

The Canadian Partnership for Tomorrow's Health (CanPath) reflects upon its original decisions around sample aliquoting strategies for its specimen inventory based on what is now commonly released to researchers. We propose an updated aliquoting strategy for new collections that balances upfront resources with volumes sought for downstream analysis. This updated aliquoting strategy will help inform teams establishing new biobanks or managing existing biobanks that are considering new collections.

Background: To systematically evaluate the long-term stability of cryopreserved RNA, we extended RNA quality monitoring in our renal biobank from 7 to 11 years for samples stored in PAXgene® Blood RNA tubes at -80°C.

Materials and methods: We assessed the suitability of archived PAXgene® RNA tubes for RNA sequencing by performing quality control on 217 chronic kidney disease samples, stratified by storage duration 7 (n = 62), 9 (n = 98), and 11 (n = 57) years. RNA was extracted from 2.5 mL whole blood using the PAXgene® Blood RNA Kit, with quality assessed based on concentration (Qubit™ Fluorometer, yield), purity (NanoDrop™ 2000 spectrophotometer, A_260/A280 and A_260/230 ratios), and integrity (Agilent 2100 Bioanalyzer, RNA integrity number, RIN). Sequencing eligibility required ≥500 ng total RNA and RIN ≥6.0.

Results: Median RNA yields were comparable across storage durations (7-year 7.00 µg, 9-year: 7.11 µg, and 11-year: 6.79 µg, p = 0.870). The median A_260/280 ratios were 2.03 (7-year), 2.08 (9-year), and 2.07 (11-year) (p < 0.001, all ≥1.8), while median A_260/230 ratios were 1.72, 1.77, and 1.87, respectively (p = 0.550). RNA integrity, as measured by RIN, showed median values of 8.90 (7-year), 9.00 (9-year), and 8.80 (11-year). While no significant differences were observed between the 7- and 9-year (p = 0.537) or 7- and 11-year groups (p = 0.052), the 9-year group had slightly higher RIN values than the 11-year group (p < 0.05). Sequencing suitability remained consistently high (7-year: 97%, 9-year: 98%, and 11-year: 98%, p = 0.750), with 98% (212/217) of samples meeting the standards. Even under stricter RIN thresholds, pass rates remained robust (RIN ≥ 7.0: 94%, RIN ≥ 8.0: 88%).

Conclusion: PAXgene® Blood RNA tubes stored at -80°C for up to 11 years provide high-quality RNA suitable for total RNA sequencing.

Background: The efficient management of consent information is essential for the ethical and legal handling of biobank resources in accordance with participant consent. However, many traditional biobanks rely on paper-based consent forms, which are often illegible and unsuitable for processing at scale. This study aims to automate the reading and quality control of paper-based consent forms.

Methods: We optimized a proprietary optical character recognition (OCR) model to recognize handwritten Korean characters in a standard paper-based consent template. We generated 1000 synthetic consent documents for training. The test dataset, comprising synthetic standard consent forms (n = 192), was used to estimate recognition accuracy. Then, this model was further trained with synthetic nonstandard consent forms (n = 1000) to optimize for the unstructured consent forms. The final model was then applied to the routine consent management process of the biobank using 3,790 pages of consent forms for the performance evaluation.

Results: This optimized OCR model showed an accuracy of 88.94% and 91.88% when tested on the 192-page standard and 1000-page nonstandard test datasets of paper-based consent forms, respectively. Moreover, when this OCR model was applied to consent forms in a routine of biobanking processes, it showed an accuracy of 91.25% and an F1-score of 0.91, indicating the model's high overall performance and excellent generalization capability for data.

Conclusions: We optimized a proprietary artificial intelligence-based OCR tool to develop a highly efficient and reliable OCR-based consent management model for paper-based consent documents. This approach could contribute to the digital transformation of traditional biobanking processes of paper-based consent forms.

The "fitness-for-purpose" of biospecimens is paramount for reproducible genomic and proteomic research, yet is frequently compromised by preanalytical variability. To identify key determinants of sample quality in prostate cancer (PCa), a disease characterized by challenging tissue procurement, we conducted a retrospective quality audit of 300 radical prostatectomy specimens. Biospecimens were stratified based on Tumor Nuclei Percentage (TNP) against established thresholds for proteomic (TNP ≥ 20%) and genomic (TNP ≥ 50%) applications, revealing significant heterogeneity in the cohort's overall quality. Subsequent analysis of preanalytical data revealed that the tissue procurement method-conventional macroscopic inspection, preoperative magnetic resonance imaging (MRI)-guidance, or biopsy-guidance-was the single most significant factor associated with achieving high-quality strata. For the stringent genomics-grade threshold (TNP ≥ 50%), guided procurement methods (MRI: 60.00%; Biopsy: 56.00%) more than doubled the yield of qualifying samples compared with conventional inspection (28.00%; p < 0.0001). This work establishes guided procurement not merely as a superior technique, but as an essential quality assurance standard for modern PCa biobanking, ensuring the collection of biospecimens that are truly "fit-for-purpose" in the era of precision medicine.

Introduction: Biobanking is a crucial foundation for biomedical research, allowing for the collection, storage, and study of biological samples and related data. In Africa, expanding biobanks offers a chance to investigate the continent's rich genetic diversity and tackle local health challenges. Yet, infrastructure shortcomings, inconsistent regulations, and varied ethical standards continue to hinder the sustainable growth of biobanking efforts across Africa. The Pan-African Biobanking Network (PABNet) is an initiative of African biobankers that provides information and services for the African biobanking community. The study was aimed at evaluating the current status of biobanking in Africa.

Methods: From February 2024 to January 2025, a structured online survey questionnaire was dispatched to African biobanks through such networks as Biobank and Cohort Building Network and Medical Biorepositories of South Africa. The three main areas were general biobank characteristics, systems of ethics and regulation, and Strengths, Weaknesses, Opportunities and Threats assessment. The questionnaires were scrutinized by top African biobanking experts to be properly contextualized. The questionnaires were then interpreted as a tool for establishing maturity in operation, resources available, and engagement in professional networks.

Results: A total of 22 biobanks from 11 countries took part. Most were fairly new, with a median staff size of six and a wide range of sample types. Although 77% had quality management systems and 91% used unique specimen identifiers, only 43% had formal accreditation. Main strengths included diverse sample collections (77%) and participation in professional networks (68%). However, major obstacles included weak legal frameworks (82%), regulatory delays (73%), funding shortages (91%), and gaps in consent procedures.

Conclusion: This preliminary survey reports significant results of African biobanking showing willingness to cconductand urgent needs for harmonized ethics, explicit procedures for accreditation, and aligned policies. The PABNet is well-positioned to fill these gaps through promoting local use of international standards, launching training programs, and facilitating improved governance. These measures will help build a robust, internationally integrated biobanking system fitting Africa's research setting.

Microorganisms play a crucial role in the stability and functioning of ecosystems, responsible for essential processes such as soil nutrient cycling, plant growth, marine biogeochemical cycles, and human health. The conservation of microorganisms and microbiomes has become a priority in biotechnology and ecosystem sustainability. The preservation of these organisms is crucial not only to maintain biodiversity but also to ensure they continue to fulfill their vital roles in the ecosystem. Their role in maintaining ecosystem stability is urgent and underscores the importance of their conservation. Current conservation techniques, such as cryopreservation, freeze-drying, and storage in dry media, are essential to preserve their viability, genetic stability, and functionality. However, effective conservation goes beyond merely preserving survival; it is crucial to maintain their functionality and genetic diversity intact. Emerging methods, such as the use of nanoparticles, vitrification, and biofilms, have shown great potential to improve the protection of microorganisms from extreme environmental conditions, allowing for more effective and long-term conservation. The development of new conservation technologies is vital to overcoming the limitations of traditional methods. These innovations not only improve the viability and functionality of microorganisms but also facilitate the restoration of degraded ecosystems and foster progress in fields such as medicine, agriculture, and industry. Ensuring the conservation of these organisms is critical to ensuring the health and sustainability of our ecosystems and humanity in the future.

Introduction: A major roadblock to the investigation of emerging "omic" technologies is the availability of clinically derived tumor tissue. This problem is compounded by tissue being processed in labs using formalin-fixation, paraffin-embedding. A novel approach that circumvents these barriers was developed and tested. This approach represents an opportunity for biobanks to generate hard-to-obtain specimens from clinical tumor specimens for emerging "omic" research studies.

Objectives: This study demonstrates a specimen processing method capable of creating new samples dedicated for multi-omic studies from clinical tissues, all without detracting from the current formalin-fixed, paraffin-embedded process.

Methods: Using this new method, aliquots for the study of exosomes and metabolites can be generated from primary bladder cancers excised via transurethral resections. Once procured, the nature of tumor-derived exosomes can be examined using an exosome protein microRNA one-stop biosensor and metabolites via liquid-chromatography tandem mass spectrometry. Intact cells are also recovered and can be prepared for examination by either Thin-Prep cytology methods or the creation of cell blocks. The latter methods are used to confirm the phenotype of the cells present in these aliquots.

Results: Populations of diagnostic tumor cells were confirmed to be recovered and morphologically consistent with the originating parent tissue. Isolation and characterization of exosomes from these dedicated samples confirmed the presence of tumor-specific signal molecules. The untargeted profiling of other dedicated aliquots found identifiable metabolites of multiple different classes that had been extracted from these tumor cells.

Conclusion: The fight against cancer will involve understanding its complexities. Developing technologies to under-studied analytes of cancer will be integral to this process. The adoption of the described tumor specimen processing approach in primary bladder cancer in this study represents a novel means for biobanks to generate and collect dedicated aliquots for research into these analytes of increasing importance.