Biobanks are essential in modern biomedical research, enabling the systematic collection, storage, and distribution of biospecimens and associated clinical data to advance precision medicine [1]. Collaborative biobank networks are valuable in large-scale or rare-disease research [2], because they enhance data interconnectivity, standardization, and quality assurance [3].
Female breast and genital diseases, including breast, ovarian, and cervical cancers, remain a major global health burden [4], of which breast cancer is the most common malignancy, with increasing incidence in younger populations and marked molecular heterogeneity [5]. Ovarian cancer is often diagnosed at advanced stages and has the poorest prognosis [6]. Although cervical cancer is largely prevented through human papillomavirus vaccination and screening, it still causes significant morbidity and mortality worldwide [7]. However, the molecular mechanisms, tumor microenvironments, and microbiome interactions involved in these diseases remain unclear.
Therefore, the Female Breast and Genital Diseases with Microbiome Biobank Network (FDMNet) was established in 2021 as a multi-institutional collaborative biobank network to collect and share high-quality biospecimens and harmonized clinical datasets, including microbiome resources for female-specific diseases. Additionally, a recent repeated cross-sectional survey of FDMNet highlighted usage patterns, barriers, and opportunities, underscoring the importance of streamlined governance and researcher support [8].
FDMNet comprises five hospital-based biobanks, Inje University Busan Paik Hospital (hub), Dong-A University Hospital, Inha University Hospital, Kyungpook National University Hospital, and Pusan National University Hospital, and is supported by the Korea Biobank Network (KBN). FDMNet aims to systematically collect, process, manage, and distribute high-quality biospecimens, including microbiome- related specimens, such as stool, vaginal discharge, and cervical discharge, along with linked clinical data for research on female breast and genital diseases. The network is governed by operations, standardization, quality management, and technology support committees to ensure operational efficiency and standardization and three researcher- centered working groups that promote studies on breast diseases, obstetric and gynecological diseases, and microbiome research, actively driving innovative research and maximizing the scientific value of the collected resources.
The overall operational framework of FDMNet is illustrated in Fig. 1. Eligible participants were women aged ≥19 years diagnosed with or treated for breast or female genital diseases who provided written consent for biospecimen donation. Patients with incomplete data, unrelated systemic diseases, or declining donation were excluded.
Each participating hospital collects and manages high-quality biospecimens, along with related clinical and epidemiological information. These resources were subsequently consolidated at Inje University Busan Paik Hospital, enabling standardized data integration and facilitating data sharing for research in academia and industry.
Participating hospitals collected biospecimens and related clinical data, which were transferred to Inje University Busan Paik Hospital. The hub operates an electronic medical record (EMR)-based clinical data warehouse (CDW) with an automated extract, transform, and load (ETL) process to convert deidentified data into the KBN common data model (CDM) format for standardized sharing.
Based on the KBN CDM [9], FDMNet developed and collected >100 supplementary clinical and epidemiological variables, besides 88 core variables, focusing on breast and genital diseases. These included data on cancers, pregnancy, delivery, and postpartum conditions, such as pathology, obstetric information, chemotherapy history, and ultrasonography findings.
These extended variables were integrated into the KBN portal to improve data quality and support disease-specific precision medicine research.
The participating hospitals developed CDM and ETL systems based on their institutional infrastructure. To promote research use, Inje University Busan Paik Hospital provides analysis cost support to investigators. Next-generation sequencing (NGS) and other analytical data generated through this support were deposited in the biobank. For the breast disease cohort, microbiome NGS data generated from stool samples stored at different temperatures were provided to researchers in the FASTQ format.
All datasets underwent standardized quality-control procedures, and data distribution was permitted only to researchers approved by the Institutional Review Board (IRB) approval and completed a data-use agreement.
This reciprocal process eliminates the need for researchers to reproduce the same datasets, reduces unnecessary costs, and enriches resource diversity, thereby strengthening its value as a collaborative research network.
All sites were operated under IRB-approved protocols with informed consent. Biospecimen and data management complied with the human biospecimen management guidelines of the National Biobank of Korea (NBK) and relevant international standards. Nine standard operating procedures covered the entire biospecimen lifecycle. Key quality metrics, DNA purity (A260/280) ≥1.8 and RNA integrity number (RIN) ≥7.0, were consistently met across sites. Participation in NBK external proficiency testing ensures benchmarking and continuous improvement in resource quality.
Between 2021 and 2023, the FDMNet enrolled 7,421 participants (Table 1), including 3,297 with breast cancer, 2,832 with female genital cancer, and 1,292 with placenta-related diseases. The collected biospecimens included 1,041 tumor tissues and 767 normal tissues (often as matched pairs), 4,192 whole blood samples, 6,472 plasma samples, 5,920 serum samples, 5,893 buffy coat samples, and 2,492 urine samples. Microbiome-related specimens totaled 1,711 (vaginal discharge, cervical discharge, and stool). Additional resources included 4,297 imaging datasets (digital pathology, magnetic resonance imaging, computed tomography, mammography, ultrasonography, and positron emission therapy), 405 omics datasets (including NGS), and 307 tissue microarrays (TMAs) for gynecologic and breast cancers.
Between 2021 and 2023, FDMNet distributed 40 disease-specific biospecimens and datasets, including 32 academic and eight industry projects. These resources support studies on biomarker discovery, microbiome-based diagnostics, and precision medicine.
A joint academic-industry study published in The Breast Journal demonstrated that multi-microRNA analysis improved mammography-based breast cancer risk assessment [10]. These outcomes highlight the scientific and translational value of FDMNet resources.
Overall, the FDMNet integrates standardized biospecimens with clinical, epidemiological, imaging, and microbiome data to build a sustainable infrastructure for women’s precision medicine. Its disease-specific focus on female breast and genital diseases enables the efficient integration of tailored data and biospecimens, serving as a scalable model for disease-focused biobank networks.
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