Best Practices In Biobanking

Best Practices In Biobanking By Kiara W. Biagioni Biobanks or biorepositories are facilities that collect, process, store and distribute biospecimens and associated data, mainly for biological and medical research. They constitute a crucial resource, supporting cutting-edge investigation in fields such as oncology, genomics and personalised medicine, and the development of diagnostics and therapeutics. Agencies, such as the National Cancer Institute and the biomedical scientific community at large, recognise that standardised, high-quality biorepositories are critical for progress in areas such as post-genomics cancer research, and for this reason have established formal best practices for the handling, storage and shipping of these biospecimens. The first biorepositories consisted of collections, usually held at academic institutions, where samples were manually loaded and retrieved from -20°C/-80°C freezers or liquid nitrogen (LN2) tanks without any uniform standard for the management of samples. In the last decade, however, second-generation biobanks have been designed with the implementation of standardised protocols in mind, covering sample processing and storage, as well as annotation and tracking. They have also increasingly incorporated automated liquid handling technologies for some tasks, and can accommodate a large number of sophisticated samples. The amount and type of data associated with the biospecimens has increased in complexity over the years, going from basic information such as date of collection and disease diagnosis, to large data sets that include information about the disease state of the donor, as well as phenotypic, genetic, metabolic or biochemical parameters. The repositories held at modern biobanks are professionally and systematically maintained to ensure both preservation of sample properties, and the integrity of the associated clinical or genetic data. This is because the reliability of molecular, biochemical and clinical data generated by modern day biospecimens is dependent on the quality and consistency of sampling and processing. In addition, biobanks are faced with the challenge of stabilising a growing diversity of complex specimens such as living cells and tissues that are often unique and irreplaceable. Therefore, high standards of quality in sample preparation, monitoring and security are of the utmost importance to biobank managers. These standards ensure the accuracy and reproducibility of the research based on these repositories. This article will focus on five key considerations in the preparation and storage of biospecimen samples. Sample preparation More biobanks are adopting state-of-the-art systems to meet higher industry standards, stringent regulatory requirements and an escalating volume of samples and data analysis. These systems can incorporate sample processing assisted by robotic liquid handling and automated container handling, storage and retrieval. The biobanking workflow starts with sample collection and processing, both crucial when setting up and expanding a biorepository. Workspace design has an impact on sample preparation, especially when high throughput is required, or when efficiency in processing time is of critical importance to maintain sample quality. Optimal use of facility space can be enhanced by choosing equipment that offers high capacity while reducing footprint, to support the need for rapid expansion. For the selection of critical equipment such as biological safety cabinets, it is important take into account reliability, ergonomics and energy efficiency, in addition to sample protection features. When collecting and processing samples, rigorous adherence to best practices will avert problems that could jeopardise valuable specimens and compromise years of research. The use of advanced technologies, integrated informatics solutions and the adoption of standardised, validated protocols are critical to ensure the viability and reliability of samples. Attention to specimen handling should not be overlooked. By employing appropriate equipment and materials, biobanks can handle increasing demand and optimise downstream processes. Elements to consider include: -High quality disposable products, free of contaminants, in order to maintain the integrity and purity of the collected samples. -Sample collection containers that are secure, traceable and designed for streamlined downstream processing. -Consumables and equipment designed for high throughput when required. -Liquid handling technology appropriate to the need for speed and reproducibility. It is also beneficial to employ the latest technology advances to prevent sample loss and degradation. -Controlled rate cooling and freezing procedures, tools and equipment to appropriately get biospecimen into a frozen state for maximum viability for downstream use. -Automated data management, electronic sample records and secure chain of custody Sample organisation throughout the biobank workflow greatly contributes to the maintenance of operational efficiency and sample traceability. It is now possible to use traceable and standardised containers and processes to ensure uniformity across collection sites, supporting a robust chain of sample identification and custody. This can be combined with the use of specially designed transportation containers, or ‘shippers’, manufactured for organised and secure transfer of biospecimens from collection site to processing location, ensuring the highest quality once these samples are removed from storage. Managing all this data and archiving it for regulatory purposes, patient or donor privacy, or researcher’s access is reliant on state-of-the-art informatics solutions that integrate instrumentation across the lab and across the extended biobanking facility, sometimes across multiple research locations. With a laboratory information management system (LIMS) the biobank can more easily respond to sample requests and chain of custody reports when all sample life cycle data is centrally archived and available to anyone needing it. Temperature control is one of the most critical parameters during the processing cycle of the biospecimens, and is crucial for sample quality and viability. Even small variations in specimen temperature during handling or transportation can affect the recovery of samples after storage, or the reproducibility of subsequent clinical or molecular analysis. The quality of prepared samples can be dramatically enhanced by using holding technologies that deliver reliable, ice-free sample cooling or freezing. For example, when freezers are integrated with the LIMS, a constant record of temperature is available related to any sample, and alerts can be automated so that anomalies in temperature can be addressed before loss of sample integrity becomes an issue. Many biobank samples not only have to be processed quickly under controlled temperatures, but must also be preserved at cryogenic temperatures to help ensure that their properties are maintained for as long as possible. Cryogenic storage is accomplished by using LN2, which provides storage temperatures below the glass transition phase. At these temperatures, the biochemical activities that cause degradation stop as the samples take on the properties of glass. Cells and living organisms need to be prepared for storage using specific freezing protocols which have been developed to optimise sample viability after thawing. Typically, these protocols combine the use of a cryoprotective agent (CPA) that helps prevent ice crystallisation in a biological sample, and a freezing system that can mitigate the impact of the physical and chemical properties of the freezing process. There are two types of sample preparation systems available to address the freezing needs of biological samples. Programmable, controlled-rate freezers use LN2 as a coolant and are designed to safely usher samples through nucleation and provide a constant rate of cooling that can be programmed by the end user to meet the need of specific sample types. Programmable freezers are designed to provide a high level of control and customisation as well as allow for preparation of many samples at one time. Programmable freezers also allow for freezing of samples below the glass transition phase, meaning sample preparation can match the need of sample storage when LN2 storage is required. A less costly alternative is a passive cooling system, consisting of specially-designed containers that provide insulation and controlled cooling when placed within a -80°C freezer. The use of passive cooling systems introduces the need for an extra handling step when the specimens are transferred from the -80°C freezer to a LN2 environment. To maintain strict temperature control during this step, and to avoid transient warming that would compromise the viability and efficacy of the frozen biospecimens, transportation units designed for cold chain management must be used. These devices can also be used for sorting, loading or packing cryopreserved samples. Options range from compact, portable chambers to full-sized, mobile workstations. The different technologies available can deliver stable temperatures at specific ranges for prolonged lengths of time. Some technology options include a power supply or rechargeable batteries, and others can accommodate data monitoring features. The workflow from sample collection to storage in a biobank should accommodate the possibility that the sample will likely be used downstream in an assay that is currently not even imagined. Consider the Framingham Study, which began collecting blood samples before Watson and Crick defined the structure of DNA! Researchers building a collection should consider processing samples before freezing and storage to minimise freeze-thaw cycles. Aliquoting samples into very small volumes (70μl) for one-time use both eliminates freeze-thaw cycles and makes samples easier to share in collaborative research. Extracting and aliquoting DNA prior to freezing and storage will ensure the highest quality of genomic material for downstream assays. Sample record keeping and monitoring While some of the newer biobank facilities have been extensively designed from the outset around automation capabilities to facilitate the intended retrieval rates and storage capacity, many others are based on smaller collections of samples that still rely on manual loading and retrieval methods. In both cases, growing consideration is being given to adequate monitoring of the storage condition of samples and of the repository stock as critical functions in biobank management. In addition, if the use of biospecimens falls under regulatory compliance, the ability to monitor quality parameters of the samples and to keep accurate records is paramount. The recent introduction of tracking technology greatly facilitates this task. Tracking technology can be automated through the use of tubes with permanent traceable features that enable scanning and tracking through data management software (for example, containers with linear and 2D barcodes that are part of the permanent construction of the tube, used in combination with barcode readers). In facilities without barcode reading equipment, the use of human readable identification elements are also valuable features to support tracking. Biobanks are increasingly adopting the use of integrated software systems to store all clinical and biological information associated with their samples, and the use of technology such as Laboratory Information Management Systems (LIMS). The LIMS acts as the repository for all sample lifecycle data, which is critical to scientists utilising those samples. The LIMS can be fully integrated with all instruments in the lab so that workflow is improved and more efficient, and all test data is electronically and securely compiled and stored with each sample. A centralised LIMS enables the organisation to scale up as demand increases because it can manage all biospecimen locations, online request management, data compliance and security, chain of custody and patient demographics as well as client billing. When samples are managed electronically, with seamless transmission of data between multiple laboratories, an integrated research network is possible. Standardising on a LIMS solution across a group of collaborative organisations is a means of achieving necessary data sharing and improved public access to findings. Today’s purpose-built LIMS for biobanks and biorepositories offer security, interconnectivity, instrument integration and data management capabilities necessary to manage increasingly complex research requirements and large-scale sample collections. Sample storage and security A comprehensive protection plan for biospecimen storage addresses all elements involved in this key function of biobanks. One of the most critical factors in storage of biosamples is temperature. The type of specimen, anticipated duration of storage, biologic properties of interest and viability must all be taken into consideration when selecting the appropriate storage temperature. Tissues and other samples embedded in paraffin blocks need to be stored at temperatures below 27°C, in humidity and pest-controlled environments. Fluids such as blood or urine are separated into their respective components before storage, to ensure that each fraction can be maintained under optimal conditions. Whole blood cryopreservation is considered a cost-effective and efficient way for storage of viable blood cells for large scale studies. When the future uses of samples are unknown or not specified, tissues are commonly maintained in the vapour phase of LN2, just as with viable cell lines that have a determined future path. Biospecimen containers are chosen with both storage and analytical goals in mind. They must be of high quality, with materials and design properties compatible with storage conditions, and that prevent sample loss. The size, type and number of containers must also be planned according to anticipated use and expected number of users. It is also useful to choose containers of a volume and design that minimise the cost of collection and storage. Storage equipment must meet the required needs of the type of specimen held, delivering reliable temperature uniformity, and with recovery and back-up systems to minimise sample loss. As previously mentioned, many biobanks store long term in the vapour phase of LN2, but they will also have needs for storage temperatures warmer than those afforded by LN2, based on what is being stored. Many biobank freezers are specially designed for storage at -80°C. Ideally, after opening the door, each shelf may be opened separately, thus maximising temperature conservation. The insulation of storage equipment helps to maintain temperatures dependably. Large biobank facilities for biospecimens maintained at -80°C use specialised freezer systems that can hold up to 10 million samples and are equipped with robotic systems to move samples between loading and dispensing hatches and interior racks. These systems can be integrated with the LIMS, to allow the search and location of samples with specific profile of biological or donor characteristics and to process retrieval requests. The use of remote monitoring systems enables biobanks to survey vital storage equipment in realtime throughout the facility. Wireless temperature sensors can simultaneously monitor the temperatures of different sections inside the storage systems, or even the interior of transportation units necessary for the preservation of the cold chain. These systems monitor equipment parameters 24/7, and can also send out instant, customisable notifications of power or mechanical failures. Some remote monitoring systems can also assist in determining when equipment is aged and needs maintenance or replacement. Many also feature multiple reporting options available to meet a diversity of needs. Biobank facilities must have back-up equipment, such as an alternative power source that is automatically activated when needed. Biobank systems should also establish back-up storage of rare and particularly valuable samples, and have procedures in place to respond to equipment failure, weather emergencies and other critical situations. Finally, human biobanks hold biospecimens that were donated by research participants, whose rights must be protected through appropriate practices, like those ensuring privacy. Some important biobank practices, in addition to the use of data security systems, include coding of biospecimens, data encryption and establishment of restricted levels of access by biobank staff. Maintaining cold chain in handling and shipping specimens Samples typically spend nearly all of their ‘lifetime’ in storage. However, it is those brief moments when samples must be handled and transferred when they are most at risk. Depending on the type of sample, even a transient temperature excursion can result in some deterioration in molecular integrity, and potentially skew the results of an assay. Biobanking best practices thus extend to shipping and handling, with the focus on maintaining correct temperature of the samples as they move from the patient to the lab to the biobank and so on, a process called ‘cold chain’. Cold chain is an especially critical issue when the biological materials in question are therapies or active bio-pharmacological ingredient. Food and Drug Administration (FDA) requirements for maintaining cold chain are becoming more and more stringent, and the criteria for the data needed to show conformance to cold chain are becoming more stringent as well. This is an issue key to biobanking that is often overlooked at the bench research level, when sample storage is the main focus. Outsourcing your sample management Installing the infrastructure needed to ensure the safety and integrity of research materials can be challenging as well as expensive. The cost of temperature monitoring systems, electrical infrastructure, liquid nitrogen supply tanks, redundant HVAC and the other facility systems needed to ensure sample integrity can quickly overwhelm a research budget. When the expertise needed is also added in (trained technicians, including after-hours on-call staff; proven Standard Operating Procedures to implement best practices and ensure cold chain compliance; and other expertise), outsourcing sample management to a professionally operated biobank is very often the most cost-effective solution. Conclusion - Best Practices In Biobanking Biobanks are becoming an essential and increasingly sophisticated resource in biology and medical research. Technological advances such as automation and computerisation are transforming the management of biobanks and enabling the implementation of integrated systems to manage samples, data, personnel, policies and procedures for the distribution of biological specimens and other services. The trend is towards larger and more centralised biobanks, which improves the economics of sample processing, storage, distribution and data analysis. The development of evidence-based standard operation procedures and the adoption of technical best practices, in combination with the use of technological innovations in materials and equipment, can support the generation of biorepositories holding high quality samples associated with well-characterised, reliable data. DDW --- This article originally featured in the DDW Summer 2014 Issue --- Kiara Biagioni is Global Product Manager for Storage Tracking products at Thermo Fisher Scientific. She holds a BS in Biology and an MBA. Kiara’s career originally started in structural biology, where she had the opportunity to automate many traditionally manual laboratory operations to increase throughput, efficiency and consistency. Since 2011 Kiara has been particularly focused on the exciting and growing area of Biobanking with a rapidly expanding portfolio of 2D barcoded storage tubes and equipment.