MUB Biobank, as an entity dedicated to Total Quality Management, is cooperating with multiple entities oriented on genomics, transcriptomics, metabolomics, and proteomics assays to develop best practices in omics research. As a Multidisciplinary Team, we have developed an integrated system for quality control of biospecimens at every single step to minimize the impact of pre-analytical variables on the final results of high-throughput studies.
Our study addresses the challenges posed by the rapid development of novel molecular techniques in omics assays and their impact on traditional biobanking practices. We collaborated with the Indivumed Group and utilized biospecimens from oncological patients in Polish clinics. Our focus was on serum and plasma samples along with fresh-frozen tissue samples.
For serum and plasma samples, we implemented a range of quality control measures, including monitoring hemolysis, ensuring RNA extraction efficiency, assessing cDNA library quality and quantity, and verifying NGS raw data. Tissue samples underwent pathologic evaluation to confirm histology and determine tumor content.
To ensure the suitability of biospecimens for advanced research applications, we introduced molecular-based quality control methods aligned with the demands of high-throughput assays. We developed distinct workflows for conducting preanalytical quality control of serum/plasma and fresh-frozen tissue samples.
Overall, our work contributes to the advancement of biobanking practices by providing novel workflows and quality control methods that enhance the integrity and suitability of biospecimens for cutting-edge molecular research.
In our DATA REPOSITORY, we have included resources crucial for the implementation and replication of our methods that are customizable to accommodate the capabilities of different biobanking entities oriented on the development of a Quality Management System for high-throughput research.
- Workflows: Detailed step-by-step procedures outlining the preanalytical quality control measures for serum/plasma and fresh-frozen tissue samples. These workflows provide guidance on monitoring hemolysis, assessing RNA extraction efficiency, evaluating cDNA library quality and quantity, and verifying NGS raw data.
I. Workflows for quality control of biospecimens dedicated to high-throughput assays
- Algorithm of QC for plasma and serum samples based on visual assessment of hemolysis, spectrophotometric analysis, and quantification RT-PCR method based on hsa-miR-451a and hsa-miR-23a-3p expression levels,
- Decision Tree for Identification of Outlier Samples presenting a quality control model for RNA extracted from plasma and serum samples,
- Visual Presentation of OMICS-QC Model for Plasma and Serum,
- Algorithm of QC for Plasma and Serum Biobanking presenting essential pre-analytical and analytical QC processes,
- Algorithm of QC for Fresh Frozen Tissue Biobanking to ensure the reliability and integrity of the collected samples for high-throughput assays,
- NGS Liquid Biopsy Flowchart for miRNA Assay presenting the collection and processing the liquid biopsy samples to extract total RNA, specifically targeting miRNAs. The extracted RNA is then converted into miRNA libraries, which are sequenced using NGS platforms, followed by data analysis to identify miRNA expression patterns and potential biomarkers.
II. Workflows dedicated to the process of biobanking as an essential part of the research
- MUB Biobank - The process of Biospecimens and Data Collection - schema presenting the overview of the Quality Management System implemented on every step of samples and data collection in MUB Biobank,
- MUB Biobank - Collection of Tissue Samples - schema presenting the detailoed workflow of tissue sample collection by Clinical Team at MUB Biobank.
III. Workflows illustrating the Data Management process between MUB Biobank and Multi-omics Research Groups
- SmartBioBase Overview presenting the SmartBioBase, which has been implemented as a warehouse for different types of data collected within MUB Biobank,
- SmartBioBase Architecture along with the functionalities of ONCOSup Service,
- MUB Biobank - Data and Sample Flow between Biobank IT Platform SmartBioBase and Multi-omics Research Groups,
- NGS Panel Tests for Driver Mutations
NGS panel tests for driver mutations were developed using samples from MUB Biobank, enabling the detection of specific genetic alterations associated with cancer. These tests utilize NGS technology to analyze multiple genes simultaneously, providing valuable information for personalized treatment and targeted therapies.
- NGS Panel Test - Liquid Biopsy - NGS Panel test for driver mutations in liquid biopsy samples from Patients with non-small cell lung cancer (NSCLC) implemented in ONCOSup Service,
- NGS Panel Test - FFPE Tissue - NGS Panel test for driver mutations in FFPE samples from Patients with NSCLC implemented in ONCOSup Service,
- Certification Process of ONCOSup Service including Technical and Analytical Certification with International Schemes of External Quality Assessment (EQA)
- Datasets: Raw and processed data generated from the various assays and analyses conducted in our study. This includes data from spectrophotometric hemolysis analysis, RNA integrity assessment, cDNA library quality assessment, and NGS raw data. The datasets provide researchers with a valuable resource for benchmarking, validation, and comparison purposes.
- Fresh Frozen Tissue - Quality Points for NGS - the comprehensive set of data presenting the quality control points evaluated for the purpose of Next Generation Sequencing (NGS): concentration of nucleic acids on DNA and RNA levels, RNA Integrity Number, PreSeq QC RT-PCR assay on DNA and RNA levels, and KAPA Library Quantification,
- Results of Quality Control for Plasma and Serum presenting the data on the quality of plasma and serum samples prior to the NGS assays, including visual assessment of hemolysis, spectrophotometric analysis, and, in selected samples, quantification RT-PCR method based on hsa-miR-451a and hsa-miR-23a-3p expression levels,
- Quality Control for Libraries and NGS Raw Data presenting the evaluation of analytical parameters of cDNA libraries and NGS raw data derived from NSCLC and control serum samples,
- Quality Control for RNA Extraction The parameters obtained in the quality control process for RNA extracted from serum blood samples using the ExiSEQ NGS sample QC kit – small RNA/microRNA (Exiqon, Denmark),
- RNA Integrity Number Assessment presenting the electropherograms obtained from the intact RNA, RIN = 9.0 and partially degraded RNA, RIN = 3.8,
- List of up-regulated miRNAs - NSCLC vs. control that were developed by Differential Expression analysis,
- Heatmap NGS NSCLC vs. Control presenting the results of Differential Expression analysis of miRNA,
Data generated by Functional analysis - Enrichment analysis for the differentially expressed miRNA - NSCLC vs. control:
- MUB Biobank - Clinical and sample data - a comprehensive set of data collected from every Patient by Study Nurses from MUB Biobank. Please, be aware of multiple sheets combined into one file.
- Legal and Ethical Documents: MUB Biobank Informed Consent Form
In the MUB Biobank, an Informed Consent Form is an essential component of the sample and data collection process. The Informed Consent Form provides detailed information to potential donors about the purpose, procedures, risks, and benefits of participating in the biobanking procedure. The Form was reviewed and approved by the Ethics Committee of The Medical University of Bialystok: protocol codes: R-I-002/357/2014, date of approval: 11.09.2014; R-I-002/600/2019, date of approval: 19.12.2019 and APK.002.171.2021, date of approval: 25.03.2021.
By including these resources in the data repository, we aim to facilitate the implementation of our methods by providing researchers with comprehensive documentation, software tools, and access to relevant datasets. This ensures transparency, reproducibility, and the ability to build upon our work in the scientific community.
Please, find below the schemas presenting the organizational aspects of MUB Biobank:
- The Organization of MUB Biobank Oncological Collection schema presenting the process of primary collection of biospecimens and data along with a follow-up,
- MUB Biobank Pathways of Lung Cancer Patients that was implemented during the MOBIT Project funded by the National Center of Research and Development,
- MUB Biobank - Types of Biospecimens preserved within the Oncological Collection at MUB Biobank,
- MUB Biobank - Types of Data collected and shared within the Oncological Collection at MUB Biobank.