November 15, 2006 (Vol. 26, No. 20)

More Unified and Large-Scale Software Systems to Track Biological Materials

Today’s drug discovery and development is critically dependent on biospecimens. In development of a drug or new procedure, a company may collect hundreds of thousands of these specimens from both humans and animals, beginning with basic research and continuing all the way to post-approval Phase IV trials.

Traditionally, methods for collecting and storing biospecimens have been highly regimented and specific. The growth of biomarker research and personalized medicine has brought a radical shift in the way companies collect and store specimens for R&D, calling for more unified and large-scale software systems to track their biological materials.

Past Models

In past models, samples were either collected during discovery for the purpose of exploring a biological pathway that could lead to a drug or during development to prove the safety and efficacy of a drug candidate. Having two different drivers for biospecimen collection led to fragmented approaches.

Discovery was limited to specific assays on small populations of specimens that were banked in a local freezer for the limited duration of that particular research. On the development side, most clinical protocols applied a fairly fixed process of collecting materials from patients enrolled in a trial, testing those samples, and then banking them only for a FDA-mandated holding period.

Hence, many firms have applied painfully ad hoc and informal systems to track, store, and process these materials. The records for these materials proliferated in spreadsheets, access databases, and laboratory notebooks on a lab-by-lab basis, even homegrown Microsoft Access databases written by research assistants in their spare time or laboratory technicians flipping through a notebook placed next to a freezer.

The recent focus on molecular medicine, genomics, and biomarker research have changed this landscape considerably. The promise of genomic and personalized medicine lies in the ability to forge a connection between phenotypic clinical data and scientific measurements on collected specimens, such as the results of an SNP, transcriptional profile, or sequencing assay.

Research is shifting toward molecular profiling, where specific assays are conducted on large populations of diseased and normal specimens to aid the search for genetic, protein, and transcriptional clues to the origin and pathways of disease. With this trend, the need for the en masse integration of clinical data with scientific results has become critical to identify the criteria for subpopulations that may best benefit from a new drug or treatment.

Long-term longitudinal studies, such as government-managed biobanks, where populations are followed for a long period of time to uncover population trends, now require the ability to operationally track millions of specimens. Many pharmaceutical companies are also creating patient registries, which are prospective banks of a large number of samples from particular patient populations, in the hope of examining genetic or transcriptional trends that may yield clues to potential treatments or drug response profiles. Together, these trends have increased the number of discovery samples that are collected.


Such industry changes have generated interest in maintaining organized centralized databases of biospecimens across an organization’s entire drug discovery and development enterprise. This centralization is further driven by the need to better manage multifaceted patient consent and regulatory issues related to sample collection and in recognition of the scale, expense, and longevity of biospecimen collection.

Given that molecular profiling requires consented human samples, each material is governed by a complex intersection of a patient consent agreement, the collection site’s institutional review board (IRB) requirements, and HIPAA or other privacy concerns. Materials may often only be used for certain purposes or held for a certain amount of time. An organization thus requires to effectively monitor acceptable uses for its samples, track consent agreements, and process consent revocations when needed.

Consent management is nearly impossible if a single sample is tracked within several different disconnected databases. Moreover, the aggregation of consented clinical and nonclinical samples requires greater regulatory scrutiny both from a privacy and FDA GLP/GCP compliance perspective, which is better assisted by a centralized database.

Especially in pharmacogenomics, samples collected prospectively for preclinical discovery may later need to be assayed for FDA submissions, meaning that discovery organizations must retain the capacity to maintain materials for subsequent GLP research. This often leads to a desire to maintain segregation within a database between GLP and non-GLP materials. Given the large scale of collection and expense of rare samples, companies need cross-organization, accurate operational support during sample handling.

In addition, the significant number of experiments that are duplicated from laboratory to laboratory, across various departments and throughout their global organizations would be eliminated by an enterprise approach to biospecimen management and results tracking.

Enterprise Biobanking

Such a need for centralization necessitates a new class of enterprise biobanking software systems, such as the Sapphire™ BioBanking Solution available from LabVantage Solutions (

These systems maintain centralized records of an entire organization’s biological material assets, as well as the by-products of the experimental process, such as aliquots and derivatives. Sapphire thus serves as a consistent platform for their storage and handling, allowing an organization to take advantage of sophisticated chain of custody features, such as electronic signatures and shipping and receiving functionality. Company can also centralize their consent and study management records.

By providing a standard infrastructure for the storage, data capture, retrieval, and processing of samples throughout an organization, each individual lab can leverage a robust infrastructure to manage workflow and maintain accurate sample records. Moreover, these solutions are able to be validated to manage both GLP/GCP and non-GLP materials, allowing for the consistent production of regulatory filings, scientific experimental reports, and validated clinical development records.

The toolset for sample storage, handling, and shipping is only the first part of the solution. An important aspect of enterprise-grade systems is the ability to address the needs of multiple laboratories around the world, so that it can truly serve as a single operational and logistical point of record for an organization’s samples.

Sapphire has broad and robust features for integrating with existing laboratory information management systems (LIMS) and clinical trial management systems (CTMS). Integration is essential to avoid re-entry of data. It is also capable of global deployment and management, so that it can be accessed throughout the enterprise.

Additionally, the system is flexible enough to allow for a variety of different business processes to be configured and deployed to assimilate with the procedures and business practices already in place. For example, Sapphire’s thin-client technology enables enterprise-wide access and visibility to the solution simply through an Internet Explorer browser. Flexibility in turn reduces total cost of ownership and enables rapid deployment with little end user training.

It offers robust features for intricate data capture, compliance, chain of custody, and location-management functionality on a global basis across virtually unlimited repositories.

Through Sapphire’s Evergreen configuration tool, the solution is extensively meta-data configurable and easily adapted to a customer’s particular biobanking processes, while maintaining the ability to upgrade the configuration to future versions of the software.

Sapphire’s open architecture allows for easy integration with internal systems, public and private databases, and instrumentation. The module is part of LabVantage’s Sapphire platform, so it is seamlessly integrated with its laboratory information management solution for life sciences R&D as well, providing an advantage to companies that want to standardize their sample and data collection software across laboratories.

Jeremy Gilbert, a software architect and life sciences industry consultant at Springboard Informatics, has also consulted for LabVantage Solutions. Web: E-mail: [email protected].

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