Introduction

The era of precision medicine necessitates the large-scale collection and storage of high-quality human biospecimens linked with comprehensive clinical data. Biobanks are critical infrastructures that provide essential materials such as tissues, blood, urine, and novel sample types to fuel research in healthcare, disease mechanisms, and fundamental biology [1]. Recognizing the growing importance of the microbiome in health and disease, specialized biobanking efforts are required [2].

In South Korea, the government-funded Korea Biobank Network supports these initiatives and has been instrumental in advancing precision medicine through the systematic collection and storage of biospecimens [3]. As part of this national initiative, the Female Breast and Genital Disease with Microbiome Biobank Network (FDMNet) was established in 2021. This specialized network comprises five university hospital biobanks (Inje University Busan Paik Hospital, Dong-A University Hospital, Inha University Hospital, Kyungpook National University Hospital, and Pusan National University Hospital) working collaboratively to support research on female breast and genital diseases, with a crucial emphasis on supporting microbiome research. The FDMNet aims to distribute high-quality bioresources, including traditional biospecimens, microbiome-related samples, and associated imaging data, using standardized protocols and ethical governance structures.

Despite significant investments in the biobank infrastructure worldwide, several studies have identified challenges in maximizing the utilization of these resources. International assessments have revealed barriers, including complex access procedures, inadequate awareness among researchers, and governance challenges [1,4]. However, limited research has evaluated these factors in specialized biobank networks, particularly in the Asian context. The effectiveness of biobank networks depends not only on the quality of stored specimens, but also on how well these resources meet researcher needs and expectations, a critical aspect that requires systematic assessment.

To address this knowledge gap and document the user experiences of our biobank operations, we conducted an annual descriptive survey from 2022 to 2024. This study aimed to characterize researcher awareness and utilization patterns of biobank resources, identify specific barriers faced by researchers, describe evolving research requirements for specialized samples and clinical/imaging data, understand the need for advanced resources such as digital pathology and -omics data, and gauge interest in emerging areas such as microbiome research. As a descriptive needs assessment, this study did not test formal hypotheses but rather sought to capture longitudinal patterns in user-reported experiences and requirements. These findings are expected to guide improvements in biobank operations, help develop targeted strategies to address user-identified challenges, inform resource allocation, support educational program development, and enhance the alignment between biobank services and researcher needs within the broader context of precision medicine advancement in Korea.

Methods

Ethics statement: This study was exempt from full review by the Institutional Review Board, as the research involved an anonymous survey with no collection of personally identifiable information and minimal risk to participants.

1. Survey design and distribution

Anonymous annual surveys were conducted between 2022 and 2024 using an online questionnaire platform (Naver Forms). The survey instrument, including questions and response options, is presented in Supplementary Material 1. The survey link was distributed via email to the staff members of five network hospitals: Inje University Busan Paik Hospital, Dong-A University Hospital, Inha University Hospital, Kyungpook National University Hospital, and Pusan National University Hospital. The survey covered various aspects of biobank utilization, including sample donation patterns and experiences, resource usage and research planning, challenges in accessing biobank resources, specific research interests, requirements for biospecimen types and clinical data, and awareness of microbiome research. Personal information was not collected.

2. Data collection and analysis

Survey responses were collected annually with participation rates ranging from 27 respondents/year to 68 respondents/year. The five network university hospitals collectively employed approximately 1,527 tenure-track staff members, with 68 participants responding in 2022, representing a maximum response rate of 4.5%. The actual eligible population was larger as non-tenure-track staff, such as clinical professors and clinical fellows, were also invited. The data were analyzed to identify trends in utilization patterns, track changes in researcher needs, and document user-reported experiences with current biobank services. Descriptive statistics were used to analyze the quantitative data, and open-ended responses were reviewed to identify recurring themes and suggestions for improvement.

3. Thematic analysis of qualitative user feedback

To gain a deeper insight into the qualitative data collected from the annual surveys conducted between 2022 and 2024, we utilized Uniform Manifold Approximation and Projection (UMAP), a technique for visualizing complex, high-dimensional data. Open-ended survey responses were first cleaned to ensure relevance, and the text was converted into numerical vectors using OpenAI’s text-embedding-3-large model (OpenAI, San Francisco, CA, USA), which effectively captured semantic relationships. UMAP was applied to reduce these high-dimensional embeddings to two dimensions, enabling visualization through scatter plots. This method helped identify recurring themes in user concerns, offering a clearer understanding of the inconveniences experienced by users.

4. Artificial intelligence usage in manuscript writing

The artificial intelligence chatbot Claude 3.7 Sonnet (Anthropic, San Francisco, CA, USA) was employed to enhance the readability and language accuracy of manuscript writing.

Results

1. Participation and sample donation trends

The survey data show a concerning trend in participation rates over the 3 years, with numbers declining from 68 participants in 2022 to 27 participants in 2024 (Table 1). Despite this decline in overall participation, the willingness to donate samples to the biobank remained relatively high in 2022 (69.1%) and 2023 (75.0%), although it dropped significantly to 37.0% in 2024 (Table 2). This sharp decline in both participation and donation rates in 2024 coincided with the nationwide healthcare crisis that began in February 2024, when mass resignations of resident doctors disrupted hospital operations across South Korea [5].

2. Resource utilization and research planning

The survey revealed an active engagement with biobank resources (Table 3). A significant majority (approximately three-quarters) of the respondents were involved with the biobank in some capacity, planning future usage (28.7%), having previously conducted research (28.7%), or currently conducting research (21.8%) using its resources. This high level of involvement may reflect a response bias toward researchers who are already interested in or utilizing the biobank. Nonetheless, approximately one-quarter of the respondents (24.1%) expressed no interest in using the resources, indicating an opportunity for enhanced outreach and education regarding the benefits and services offered by the biobank.

3. Challenges and access barriers

The survey identified several significant challenges in the utilization of biobank resources (Table 4). Based on the combined results, the three major challenges reported by users were sample acquisition (23.0%), collection of health/medical data (21.8%), and financial issues (14.9%). These findings suggest that there are ongoing opportunities to improve sample access procedures, streamline health data collection processes, and address the financial barriers researchers face when utilizing biobank resources.

Further analysis of the free-text responses using natural language techniques identified three distinct thematic groups reflecting the key areas of inconvenience reported by biobank users (Fig. 1). The first group highlights sample collection and consent-related issues, including difficulties in obtaining informed consent, challenges in sample collection procedures, and problems with clearly conveying sample-specific information. The second cluster focuses on data management and anonymization challenges, including issues with anonymizing patient data, managing stored resources, identifying existing data, and complications encountered during additional research proposals or execution. The third group pertains to administrative and procedural barriers, including inconveniences related to document preparation, procedural clarity, system mismatches, and broader administrative hurdles. These themes provide a comprehensive overview of the recurring challenges faced by biobank users and offer valuable insights into targeted operational improvements.

4. Research sample sources and usage patterns

The institutional biobank remained the predominant source of research samples across all years, maintaining >85% usage (Table 5). However, there was a notable decline in collaboration with other institutions, dropping from 63.2% in 2022 to 0% in 2024. This trend may also be due to the healthcare crisis that has been ongoing in South Korea since 2024.

The reasons for the reluctance to use biobank samples (Table 6) revealed several persistent barriers. Based on the combined results, complex access procedures (31.0%) represent the most significant challenge, followed by lack of knowledge about the process (23.9%), and concerns about the stringent Institutional Review Board (IRB) approval process (11.6%). Usage fees were cited as an issue by a small proportion of respondents (3.9%). These findings highlight the importance of simplifying access procedures and improving education regarding biobank utilization.

5. Research focus areas and specimen types

Regarding specialized research areas (Table 7), breast neoplasms (12.3%) and female genital neoplasms (11.0%) emerged as primary areas of interest across the survey period. Nonneoplastic female genital conditions (7.7%) and placental and perinatal diseases (4.5%) were also consistent research interests. These findings help identify the “steady sellers” in terms of research focus areas, which can guide future biospecimen collection and resource allocation strategies.

The demand for various biospecimen types (Table 8) showed a clear preference for blood (24.5%) and tissue (23.9%) samples across all survey years. Notably, there was also significant interest in advanced resources such as next generation sequencing (NGS) and omics data (8.4%) and in-depth resources such as digital pathology and medical imaging (6.5%). The interest in these advanced and in-depth resources likely reflects the growing awareness that biobanks can provide more than physical samples, thus challenging the traditional perception that biobanks store only conventional biospecimens. Other body fluids (7.1%), feces (2.6%), and urine (1.9%) were requested, although less frequently.

6. Clinical information requirements and microbiome research

The survey revealed an evolving need for clinical information (Table 9), with a marked increase in requests for diagnostic codes and names (19.1%–59.3% from 2022 to 2024), tumor-node-metastasis (TNM) staging information, and basic demographic data. This trend suggests growing sophistication in research requirements and the need for more comprehensive clinical data integration.

Regarding microbiome research awareness (Table 10), although there was significant interest, most respondents (66.5%) indicated a lack of sufficient knowledge. This suggests opportunities for educational initiatives and support programs to facilitate microbiome research using biobank resources.

Discussion

Our findings reveal a concerning decline in researcher participation and sample donations to the biobank in 2024, with respondents falling from 60 to 27 and donation rates from 75% to 37% (Tables 1, 2). This decline coincided with South Korea’s healthcare crisis beginning in February 2024, when >90% of resident doctors resigned to protest government policies [5]. Clinical staff, who also collected samples and collaborated on research, were overwhelmed with patient care, leading to suspended research and disrupted sample collection. Although not proving causation, this correlation underscores how healthcare system disruptions can threaten biobank sustainability, a factor often overlooked in planning. Despite these challenges, the relatively high level of engagement among respondents who are aware of the biobank’s services reflects findings from other studies showing that biobank users often report higher satisfaction with sample acquisition than nonusers [4]. However, as Critchley et al. [6] demonstrated, trust remains the cornerstone of successful biobank operations, accounting for >40% of the variance in participation intention. The decline in interinstitutional collaborations from 63.2% in 2022 to 0% in 2024 is particularly concerning because such partnerships are vital for comprehensive biospecimen collection and research advancement.

As a descriptive needs assessment rather than a hypothesis-driven study, our study provides valuable longitudinal documentation of real-world biobank utilization patterns in a specialized Asian biobank network. While we acknowledge the limitations of self-reported survey data and relatively small sample sizes, such descriptive assessments are rare in disease-focused and microbiome-oriented networks and can inform operational improvements by highlighting persistent barriers and evolving researcher needs.

The barriers to biobank utilization identified in our study, complex access procedures (31.0%), lack of knowledge about the process (23.9%), and concerns about IRB approval (11.6%), mirror challenges reported in other biobanking environments. While we did not measure metrics of formal service efficiency, these user-reported barriers aligned with our thematic analysis clusters, particularly administrative and data management challenges, suggesting specific areas of operational focus. Van Draanen et al. [7] found that researchers primarily expressed concerns regarding governance, collaboration, and costs when considering participation in a virtual biobank. Similarly, in Germany, Klingler et al. [4] reported that the unavailability of specific biosamples, high costs, limited information accessibility, and time-consuming access processes were the key barriers to biobank collaboration. Our thematic analysis of user inconvenience revealed clusters around sample collection/consent issues, data management challenges, and administrative barriers, suggesting areas for targeted operational improvements. However, longitudinal interpretation of clustering patterns should be made cautiously, given the small number of free-text responses analyzed (5–7 per year). As Hirtzlin et al. [8] observed in their European Union survey, the harmonization of ethical and legal standards is crucial for facilitating collaboration while ensuring participant rights and quality standards. The lack of awareness of biobank services among potential users, highlighted in our study, aligns with the findings of Bossert et al. [9], where only 30.8% of the public reported awareness of biobanks, despite generally positive attitudes toward biobank research.

The research interests identified in our survey, particularly in breast (12.3%) and female genital (11.0%) neoplasms, demonstrate the importance of disease-focused biobanking initiatives. Lee’s 20-year analysis of biomarker-related publications [10] shows that cancer-related biomarkers represented over 27% of all biomarker publications in 2017, highlighting the critical role of oncology-focused biobanks in supporting precision medicine. Our findings regarding specimen preferences, predominantly blood (24.5%) and tissue (23.9%) samples, align with Lee’s observation [10] that blood-derived biosamples appeared in 50% of biomarker-related publications. The growing interest in advanced resources, such as NGS and -omics data (8.4%), reflects the evolution of biobanking beyond physical sample storage. Moreover, while 66.5% of our respondents indicated interest in, but insufficient knowledge of microbiome research, this represents an opportunity for educational initiatives to bridge this gap. The increasing demand for comprehensive clinical information, particularly diagnostic codes and TNM staging, emphasizes the need for integrated data management systems that support the growing sophistication of biomedical research.

For FDMNet to address these challenges and enhance its service to the research community, several strategies should be implemented. First, streamlining access procedures and providing clear information on biobank processes would address the most significant barriers identified in our study. This could include the development of a unified online application portal with standardized forms across all network sites. Second, improving communication with both contributors and users, a factor emphasized by Mester et al. [11] who found that 97% of biobank participants desired regular research updates, could enhance engagement and trust. Practical steps include quarterly email updates and a dedicated intranet page summarizing the available resources. Third, expanding educational initiatives in microbiome research would capitalize on existing interests and potentially increase the utilization of these specialized resources. Short, on-demand video modules and annual workshops can be implemented within existing budgets. Finally, strengthening governance structures to ensure equitable access, ethical oversight, and quality control would build trust, a factor that Critchley et al. [6] identified as the strongest predictor of participation intention. These improvements, guided by our survey findings and supported by international best practices, will position FDMNet to better serve the evolving needs of the research community, despite the challenges posed by the recent healthcare crisis and the changing research landscape.

Supplementary materials

Article information

Conflicts of interest

No potential conflict of interest relevant to this article was reported.

Acknowledgments

Hye In Lee, Jimin Yu, Ji Eun Lee, and Jin Hui Kim (Inje Biobank, Inje University Busan Paik Hospital, Busan, Korea) provided support for conducting the survey and organizing the results.

Funding

This study was supported by the Korea National Institute of Health (KNIH) Research Project (Project No. 2024ER050900).

Author contributions

Conceptualization: all authors; Data curation, Methodology, Visualization: SA; Formal analysis: SA, ANS, LK, KUC, MSR, EYK; Funding acquisition: EYK; Investigation: SA, HJC, MSK; Project administration: EYK; Resources, Supervision: ANS, LK, KUC, MSR, EYK; Writing-original draft: SA; Writing-review & editing: all authors.

Fig. 1.

Uniform Manifold Approximation and Projection (UMAP) visualization of biobank usage inconveniences. UMAP is used to cluster embeddings of user responses regarding inconvenience while using the biobank. The bottom-left cluster reflects challenges related to the practical aspects of sample collection and obtaining informed consent. The center-right cluster highlights difficulties in managing anonymized data and accessing sufficient information for research. The top cluster represents barriers tied to administrative procedures and documentation processes. Data points are color-coded by year.

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References

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