Biobanking Informatics: The Key to Standardization

As the use of biobanks increases in clinical settings, more informatics tools are coming available to ensure the quality of biospecimens and data

Justin G. Mychek-Londer, PhD

Dr. Justin G. Mychek-Londer is a freelance scientist and founder of J. Londer Laboratories with an interest in how emergent technology can help better the world.

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Published:Jan 29, 2021
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Biobanks were identified as a top-ten technology set to change the world in a 2009 Time Magazine article. Since then, biobanks have become increasingly prominent in clinical settings and have grown concomitantly with technologies such as next-generation high-throughput sequencing and big data. As the numbers, interconnectedness, scales, and complexities of biobanks have grown, several informatics tools have become available to help ensure biospecimens and data are of high quality. 

Guidelines for biobanking standardization

An early effort to raise the quality in biobanking through standardization was initiated with the founding of the International Society for Biological and Environmental Repositories (ISBER) in 2000. In 2005, 2012, and 2018, ISBER published their best practices for biobanking. In 2012, the USA National Cancer Human Biobank published their first biobank standard operating procedures and best practices

Generally, these and other similar guidelines contain suggestions for what donor information to record (e.g., age, sex, nutritional status, exercise habits, smoking, and alcohol consumption) and for how to track, procure, handle, store, and prepare human biospecimens to help ensure high quality, accuracy, and reproducibility. In addition, minimum suggested requirements and methods for standardizing medical and scientific terminology, units, data formatting, file naming, and computer code used in biobanking have similarly emerged. 

Ultimately, guidelines for best practices for a biobank often vary or get adapted based on factors such as individual biobank goals, needs, scale, membership in larger biobanking networks, resources, already-established collections, and the ability to implement informatics.

Informatics-based tools that facilitate standardization, quality, and tracking

A good example of an informatics-based approach and toolset that has been used to help standardize and track data is the Standard Preanalytical Coding for Biospecimens (SPREC). SPREC defines easy to use annotations that help document in vitro preanalytical biospecimen details (e.g., type of sample, collection method, primary sample container, sample processing, method of fixation, warm/cold ischemia time, and storage) and includes criteria that may influence downstream biospecimen analyses. An associated biobank information management system, called SPRECware, can be used in working environments where biospecimens are procured. Entry of SPREC into the system produces physical barcodes corresponding to entries for each biospecimen that link to standardized long form information all kept on localized networks and databases. 

Similarly, the Biospecimen Reporting for Improved Study Quality (BRISQ) guidelines classify suggested biospecimen parameters to be reported into tiers where tier one items are the most important, tier two items are reported if available, and tier three items are less frequently recorded or reported. 

Additional informatics tools to help standardize biospecimen management and tracking include freezer inventory technologies and freezer mapping systems, RFID tagging, pre-packaged commercialized endeavors for PC software, and low-cost and scalable open-source platforms. Commercial systems can be costly to implement and difficult to adapt to specific user needs, whereas open-source platforms may lack functionality but can be adapted to user needs. Prominently emerging cloud-based platforms offer advantages including real-time, sharable, and easy-to-access biospecimen data, and could help improve the efficiency of obtaining approvals from and informing associated regulatory committees. 

Tools are generally implemented at the levels of collections and individual biobanks. The choice of which tool to use ultimately comes down to factors like user needs, organizational structure and goals, resources, and the ability to implement potentially diverse informatics requirements. 

A searchable framework for standardized biospecimens 

 A directory containing one of the largest catalogs of searchable biobanks and human biospecimens is available through the Biobanking and Biomolecular Resources Research Infrastructure and the European Research Infrastructure Consortium (BBMRI-ERIC). The BBMRI-ERIC has developed informatics to facilitate standardized and user-friendly searches from a directory of 515 biobanks in European member states. The catalog contains more than 60 million samples, although only subsets of these are standardized and results are aggregated in searches to some degree. At least 136 of the biobanks included are clinical or disease-specific, and 189 are population-based biobanks. The BBMRI-ERIC has become a useful tool for analyses of disease, novel biomarkers, and new drugs. 

Information about relative measures of standardized sample sizes in the BBRMI-ERIC biobanks is aggregated to a degree. Contact details for requesting information about and access to the biospecimens at biobanks in search directory results are provided. Access is controlled by individual biobank administrators who retain autonomy over decisions about access. A census of BBMRI-ERIC biobanks in the directory indicates that at minimum, 23 percent require a monetary fee as part of the access request and 28 percent offer access based on expected project collaboration with the requestor. Yet without the developments of informatics and standardizations from BBMRI-ERIC, exposure for these biobanks would be reduced—a problem for smaller biobanks wishing to provide better information and exposure about their available inventories. 

Standardization can help improve health care

Biobanks are diverse and numerous; therefore, gaps in standardizations are inevitable. However, based upon the progress made thus far, today’s medical professionals should be optimistic that standardization through biobanking informatics will continue to help improve health-related issues previously proven to be challenging to understand, assess, and address. 

Justin G. Mychek-Londer, PhD

Dr. Justin G. Mychek-Londer is a freelance scientist and founder of J. Londer Laboratories with an interest in how emergent technology can help better the world.