Introduction - Concept of Biobanks
Definition and Genesis of Biobanks
Types of Biobanks
Basic Components of Biobank
Samples Analysis and Preservation Methods
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pre-clinical SOPs: Assessment of the Research Participant, Safety Guidelines, Specimen Identification and Labeling,
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clinical SOPs: Blood Collection – Venipuncture, Saliva Collection, Urine Collection, Faeces Collection, Buccal Collection, Bronchoalveolar Lavage Collection using Bronchoscopy,
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laboratory SOPs: Personal Protective Equipment, Specimen Receipt, Preparation of Serum and Plasma from Blood, DNA Extraction from Blood, RNA Extraction from Blood, Protein Extraction from Blood, Peripheral Blood Mononuclear Cell isolation from Blood, Processing of Urine, Processing of Buccal Swabs for DNA Extraction, Processing of Faeces for DNA extraction, Processing of Tissue Samples, Processing of Cultured Cells, Processing of Bronchoalveolar Lavage [26].
Tissue | Target | Preservation methods (e.g. medium/buffer/vial type/kit) | Short term storage/transport conditions | Long term storage conditions | Special notes | Literature |
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Blood | DNA | EDTA, whole blood or serum | 4 °C or on wet ice, within 24 h | −80 °C for years | – | |
RNA | Paxgene®/Tempus™ tubes | 4 °C or on wet ice, within 24 h | −80 °C for years | Blood in Tempus™ tubes may be stored up to 6 years in −80 °C. | ||
Proteomics | Plasma separating tube with heparin and serum separation tube with heparin and Plain tube | 4 °C or on wet ice, within 24 h | Plasma and RBCs in −80 °C | Storage of RBCs is recommended at −80 °C for cell membrane proteomics research. | ||
Biochemistry | Plasma separating tube with heparin and serum separation tub and Plain tube with heparin | 4 °C or on wet ice, within 24 h | Plasma, immediate analysis or − 80 °C for years | – | [26] | |
PBMC (Peripheral Blood Mononuclear Cells) | acid citrate dextrose, BD CPT™, LeukoSep™ | RT, within 24 h | −80 °C or preferred LN2 with a cryopreservative | – | ||
Circulating Tumor Cells | Cell-Free DNA™ BCT® tube | for at least 4 days at RT | −80 °C or preferred LN2 with a cryopreservative | – | ||
Cell-free DNA | Streck® Cell-Free DNA™ Blood Collection Tubes | up to 7 days at ambient temperature, avoid shipping/storage in 4 °C | immediate extraction or − 80 °C for years | Plasma is preferable to serum, cell lysis should be avoided to prevent increase of unspecific cfDNA level. Spike-in should be considered. | ||
Circulating non-coding RNA | Plasma or plasma separating tube | 4 °C or on wet ice, within 24 h | Plasma samples should be frozen immediately at −80 °C (stability) up to 1 year | Archival samples may be used | ||
Exosomes | Plasma or plasma separating tube | 4 °C or on wet ice, within 24 h | −80 °C for years | Special equipment needed for exosomes isolation: ultracentrifuge/chromatographs/filters. | ||
Platelets (e.g. tumor-educated platelets) | EDTA | 4 °C or on wet ice, within 48 h | Obtain the platelet-rich plasma with series of centrifugation, process within 48 h | The platelet pellet collected on RNAlater® and frozen at −80 °C; plasma stored directly at −80 °C. | [45] | |
Metabolomics | Plasma separating tube with heparin and serum separation tube and Plain tube | 4 °C or on wet ice, within 24 h | −80 °C for years | – | [26] CEN/TS 16945:2016 | |
Tumor | DNA | Tumor parts: snap freeze in cooled isopentane | Preserve within an hour from excision/biopsy; transport in closed, sterile container on ice at 4 °C before preservation | −80 °C or liquid nitrogen | – | |
formalin-fixed, paraffin-embedded (FFPE) | Store at RT, embed within 72 h | RT in dry conditions for years | In case of DNA extracted from FFPE samples - special NGS library preparation needed due to degraded and shredded template). | |||
RNA | RNAlater™ - RNA preservation | Preserve within an hour from excision/biopsy; if RNA preservative added – transport within 72 h when stored at 4 °C | Discard preservation medium and store at −80 °C | May be also retrieved from FFPE samples and analyzed with NGS. | ||
Protein | Tumor part snap freeze in cooled isopentane | Preserve within an hour from excision/biopsy; transport in closed, sterile container on ice at 4 °C before preservation | store at −80 °C | – | [26] | |
Microscopic morphology | FFPE – 10% buffered formalin | Store at RT, embed within 72 h | RT in dry conditions for years | Samples preserved in RNALater may also serve for microscopic morphology analysis purposes | ||
OCT (Optimal Cutting Temperature medium)-embedded -snap frozen | Preserve within an hour from excision/biopsy; transport in closed, sterile container on ice at 4 °C before preservation | −80 °C for years | ||||
Cancer cells for culture | Before cells isolation – culture medium with or without fetal bovine serum (FBS) | 4 °C or on wet ice, within 24 h | LN2 with a cryopreservative or implant in immunodeficient mouse. | |||
Cervical cytology | DNA, RNA, protein, cells | Liquid biopsies in Thinprep (TP) containing 20 ml PreservCyt | 1–4 weeks RT | −25 °C | – | [54] |
Urine | Metabolic products, DNA, RNA, protein | e.g. 9 ml in the vacutainer system | 4 °C or on wet ice, within 24 h | Direct storage in −80 °C or immediate analysis | – | |
Semen | Semen analysis, DNA, RNA, protein | Sterile container | Immediate analysis: heating chamber 37 °C; for storage - 4 °C or on wet ice, within 24 h | −80 °C or preferred LN2 with a cryopreservative | Semen analysis - within few hours after acquisition | |
Stool | DNA, RNA, Proteome, Microbiome | Sterile container or Genotek tubes for DNA analyses | RT, within 24 h | Direct storage in −80 °C or immediate extraction | – | |
Saliva | DNA, biomarkers | Sterile container or collection kit | RT, within 24 h | −80 °C for years | Exceptionally increased value of specimen if provided full record of oral diseases. | |
Breast milk | Trace of organic pollutants (POP), biochemical composition analysis | Sterile, clean bottles, e.g. with Teflon coating | 4 °C, for no longer than 72 h | at −20 °C, for longer periods. Freezing expressed human milk is safe for at least 3 months. | If the sample cannot be refrigerated, you can add a small tablet of potassium dichromate (POP analysis, document available at: http://www.ccbasilea-crestocolmo.org.uy/wp-content/uploads/2010/11/ing1.final_.SOP-POP-Regional-Sampling-Breast-Milk-1.pdf date of access: 27.07.2017). | |
Nail and hair | Metal trace, DNA, brominated and organophosphate flame retardants exposure, effects of cosmetic products | Nails should be clipped after a few weeks after recent clipping Clean, labeled envelope | room temperature in the driest condition possible | Like short term, may be stored frozen at −20 °C for long term | Limited usefulness, questionable value, noninvasive collection, status of medium/long term exposure. |
IT Systems
Institution | Document | Content | Year | Source (date of access: 27.07.2017) |
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National Cancer Institute | NCI Best Practices for Biospecimen Resources | A. Scope, applicability, and implementation B. Technical and operational best practices C. Ethical, legal, and policy best practices | 2016 | |
International Society for Biological and Environmental Repositories | Best Practices for Repositories: Collection, Storage, Retrieval and Distribution of Biological Materials for Research | Repository planning considerations, facilities, storage equipment and environments, quality management, safety, training, records management, cost management, biological material tracking, packaging and shipping, specimen collection, processing and retrieval, legal and ethical issues for biospecimens, specimen access, utilization and destruction | 2012 | |
Molecular Medicine Ireland (MMI) | MMI Guidelines for Standardised Biobanking | Part I: Pre-clinical standard operating procedures Part II: Clinical standard operating procedures Part III: Laboratory standard operating procedures | 2010 | |
Organization for Economic Cooperation & Development | OECD Guidelines on Human Biobanks and Genetic Research Databases | Part I. Guidelines on Human Biobanks and Genetic Research Databases Part II. Annotations | 2009 |
Record Constitution
Workflow and Online Tools for Biobanking
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BioMedBridges Legal Assessment Tool (LAT)
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Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) legal WIKI
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Human Sample Exchange Regulation Navigator (hSERN)
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International Policy interoperability and data Access Clearinghouse’ (IPAC) provided by the Public Population Project in Genomics and Society (P3G) [76].
Ethical and Legal Issues
The Role of Biobanks in Personalized Medicine
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Prediction - patient response to the treatment on the basis of the genetic profile – KIT mutation (N505I) and sensitivity to imatinib [100]