June 1, 2017 (Vol. 37, No. 11)
Biobanks play a crucial role in biomedical research by optimizing the storage, tracking, utilization, and distribution of a broad range of biospecimens together with the clinical information and patient consent linked to each sample. The size and diversity of biobanks continue to increase, as do the needs of researchers for high quality, richly annotated biospecimens for their research studies, and the pressures placed on biobanks to meet regulatory requirements and comply with privacy and ethics policies.
These factors are all contributing to the growing design and operational challenges biobanks are facing across their operational workflow. Advances in process design, automation, and informatics can all help improve the efficiency of biobanking. This tutorial focuses on how a centralized informatics solution can optimize sample collection and storage procedures, and ensure accurate tracking of samples, and consent and compliance with regulatory and privacy requirements.
The ability to use a single laboratory information management system (LIMS) to manage and integrate all aspects of a biorepository—even one that spans multiple physical biobanks—can minimize the inherent complexity and improve the security of sample and data storage. Ultimately, by overcoming these informatics challenges associated with sample collection, tracking, and storage, biobanks can enhance their sample distribution capabilities to both internal and external researchers. Finding and sharing biospecimens with greater ease and speed will help support collaboration among researchers.
Streamlining Sample Handling and Storage
The typical biorepository workflow for collection, storage, and distribution of biospecimens encompasses the following key steps:
• Patient consent—patient provides consent to participate in a research study
• Sample collection—patient sample collected at collection site
• Sample accessioning—demographics and clinical and quality annotations collected and linked to sample
• Storage—samples securely stored under appropriate conditions
• Distribution—send samples to approved researchers for use in studies
These steps, and the operations they entail, introduce several challenges. One is the need to determine the most efficient way to store and track biospecimens and the accompanying clinical data for each sample. Another critical aspect of this process involves detailed tracking of the chain of custody—everything that happens to a sample once it enters the biorepository—and the patient consent, which indicates how a sample can be used for research purposes. Securely managing patient privacy data adds yet another level of complexity. An additional hurdle is the need for easy access by researchers to the samples to maximize their utilization. Finally, inefficiency in the current biorepository process that is due to either paper-based data management or use of Excel-based systems represents a further challenge.
LabVantage Biobanking, based on the LabVantage 8 platform, is a purpose-built configurable off-the-shelf (COTS) LIMS with standard features targeted to meet the needs of the biobanking community. It provides a single, centralized informatics system capable of managing the storage and maintenance of annotated sample data across multiple banks. The system can follow the chain of custody to determine where a particular sample is stored at all times, quickly and accurately.
Built-in workflows aim to improve data accuracy, increase process efficiency, and facilitate compliance with regulatory requirements. They include software tools to facilitate electronic data capture, storage visualization, consent management tools, and harmonized specimen accessioning. The preconfigured workflows guide laboratory personnel through their daily tasks, covering a full range of functions from checking custody to sample accessioning, shipping samples, unpacking packages, creating child samples, and filing samples.
Visualization of Storage. This tool provides an onscreen hierarchal view of the specimen flow showing the various freezers in a biobank and the boxes and plates that each freezer contains (Figure 1). This visualization tool gives a quick and easy overview of the full storage capacity and allows the user to zoom in on specific freezers to assess utilization and identify available space. It is particularly valuable for optimizing storage.
Consent Management. Patient consent is essential for researchers to be able to access and utilize patient samples in their research projects. A biobank must have ready access to digitized consent forms that are linked to and track through the system with the associated samples. The consent management function tracks patient consent documentation to ensure that biological specimen handling follows both regulatory requirements and any special preferences stated by the donor. Visual icons reflect consent status on participant and sample list pages, making it easier to search for a sample based on answers to consent questions.
Specimen Accessioning. This refers to the process of recording specimens and subject information. The importance of using a controlled vocabulary for sample accessioning cannot be overemphasized. This standardization of terminology ensures that all involved parties are using the same language to record the sample and clinical information, including clinical diagnosis, microscopic diagnosis, tissue types, organs, metastasis, and species, for example.
Request Management. When researchers need a specimen with specific traits for their research, they will place a request with a biobank. The challenge then lies in efficiently and quickly identifying the best match between a researcher’s needs and the samples in the biorepository. A centralized LIMS solution can facilitate and expedite sample sharing by providing an interface that researchers can use to search specimen collections and associated clinical information, submit requests, and track all related correspondence. The LIMS can also help biobanks manage specimen requests and prioritize them for processing.
Genealogy Viewer. This tool facilitates protocol-driven specimen collection, handling, storage, aliquoting, and testing, along with the ability to track complete “cradle to grave” genealogy of aliquots, derivatives, and pooled samples. Within the genealogy viewer function, users can record information under the following categories: sample family, pooled samples, discrepancies, procedures, comments, treatments, aliases, auxiliary studies, and services (Figure 2).
Removing Data Silos in Biobanking
The use of a single, centralized LIMS for biobank management can help eliminate many of the current informatics-related challenges that are at least in part due to sample and data management approaches that have led to data silos, which can inhibit data integration and access. LabVantage Biobanking integrates all aspects of biorepository management to facilitate storage, tracking, and distribution of well-annotated biospecimens with accompanying consent, while still enforcing necessary security and privacy oversights. The system restricts unauthorized access to patient data. A LIMS system enables compliance with 21 CFR Part 11 and HIPAA by providing the ability to capture electronic signatures along with audit trails and to maintain patient privacy while ensuring chain of custody.
Further easing data handling, the LabVantage system eliminates the need for manual collection and cross-referencing of information from different sources. Existing methods for managing this data that rely on paper- or Excel-based recordkeeping systems are inefficient and introduce bottlenecks into the biobanking workflow.
A quick shipment dialog added to LabVantage 8 distinguishes between internal packages versus external shipments to researchers. The system now handles internal delivery differently than custodial department transfers (CDTs), with a new “take custody” dialog intended to improve the transfer of custody. Upon receipt of a requisition, the appropriate samples are retrieved from storage and packaged for distribution. Each biospecimen is accompanying by annotation with clinical and quality information.
A single, unified COTS LIMS for managing a biorepository offers numerous advantages. From a broad perspective, such a system can oversee and simplify sample receipt, storage, and allocation. On a day-to-day scale, it can easily and reliably manage inventory of sample collection kits, for example. With a centralized LIMS, biobanks benefit from the elimination of data silos that can obstruct efficient data integration, allowing for more efficient workflows, harmonized processes, and quicker, easier access to research samples.