Introduction
In the era of big data, the pharmaceutical industry has been inundated with vast amounts of nucleic acid sequence information, a byproduct of the next generation sequencing (NGS) revolution. With this explosive growth in data volume, researchers and regulatory institutions face significant challenges in processing, understanding, and applying this information effectively. The transformation of raw data into meaningful insights is no simple task, particularly when complex computational workflows are involved. This is further compounded when it comes to communicating these findings within a regulatory environment that demands both transparency and rigor.
A recently published journal article in Drug Discovery Today (DOI: 10.1016/j.drudis.2024.103884) introduced a structured response to this challenge by advocating for the use of BioCompute Objects (BCOs). Authored by an interdisciplinary team led by Dr. Jonathon G. Keeney from the Department of Biochemistry and Molecular Medicine at The George Washington University, the paper discusses the application of BCOs as a robust mechanism for clearly conveying computational analyses.
BioCompute Objects: Streamlining Computational Communication
BioCompute Objects are instances of pipeline documentation that adhere to the IEEE 2791-2020 standard. This standardization lends itself to ensuring consistency and reproducibility of computational workflows, which is especially relevant in the high-stakes context of regulatory environments. In the realm of drug discovery, the ability to clearly articulate and repeat analyses is crucial for regulatory approval processes and scientific advancement.
The Drug Discovery Today article provides a compelling suite of BCO examples. These BCOs pertain to computational workflows designed to identify viral contaminants in biological manufacturing—a concern of particular importance for vaccine production. The use of BCOs in this context demonstrates how complex data analytics can be documented and shared transparently to support regulatory submissions.
As Dr. Keeney and his colleagues elaborate, the presented BCOs are modeled after real examples one might find in a regulatory submission. However, these have the benefit of being publicly shared, allowing for broader dissemination and vetting by the scientific community. The BCO ecosystem represents an interconnected set of elements that comprise a complete computational narrative, from data acquisition to analysis and interpretation.
Impact on Regulatory Processes
The Drug Discovery Today article underscores the potential that standardized computational documentation has in streamlining regulatory communications. Regulatory authorities, such as the U.S. Food and Drug Administration (FDA), often require detailed descriptions of computational workflows as part of their evaluation process. By using a BCO framework, companies can provide a clear, auditable trail that not only satisfies regulatory requirements but also promotes transparency and trust.
Additionally, BCOs hold the promise of accelerating the approval process by reducing ambiguity and misinterpretation of computational methodologies. The precision and clarity offered by BCOs can lead to more efficient regulatory reviews and faster time-to-market for life-saving treatments.
Real-World Applications and Future Directions
The article highlights the relevance of BCOs through a real-world example: the detection of adventitious viruses in vaccine manufacturing. This timely case study demonstrates how BCOs support high-throughput screening (HTS) and metagenomics approaches in ensuring vaccine safety and efficacy.
Moreover, the authors anticipate that the adoption of BCOs will not be limited to regulatory environments. It is expected that the framework will permeate various facets of bioinformatics, from clinical research collaborations to academic institutions. By fostering a common language around computational workflows, BCOs can facilitate international cooperation and data sharing, necessary elements for advancing global health initiatives.
References
1. Keeney, J. G., Gulzar, N., Baker, J. B., Klempir, O., Hannigan, G. D., Bitton, D. A., Maritz, J. M., King, C. H. S., Patel, J. A., Duncan, P., & Mazumder, R. (2024). Communicating computational workflows in a regulatory environment. Drug Discovery Today, 103884. https://doi.org/10.1016/j.drudis.2024.103884
2. The IEEE Standards Association. (2020). IEEE 2791-2020 – IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication. https://standards.ieee.org/standard/2791-2020.html
3. U.S. Food and Drug Administration (FDA). (2020). Regulatory Framework for Bioinformatics Tools. https://www.fda.gov/medical-devices/digital-health/regulatory-framework-bioinformatics-tools
4. Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18
5. Hatzis, C., Bedard, P. L., Birkbak, N. J., et al. (2015). Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward? Cancer Research, 75(15), 3067-3074. https://doi.org/10.1158/0008-5472.CAN-15-0652
Keywords
1. BioCompute Objects
2. Computational workflows
3. Regulatory environment
4. High-throughput sequencing
5. Drug discovery bioinformatics
Conclusion
Through the lens of this recent publication in Drug Discovery Today, the use of BCOs emerges as an innovative and necessary advancement in the communication of bioinformatics in regulatory environments. By standardizing computational workflow documentation, BCOs remove barriers to understanding complex data analyses, enhancing reproducibility, regulatory compliance and ultimately, patient safety.
The article by Dr. Keeney and his team serves as a benchmark for future developments in the field of drug discovery. As the industry continues to embrace technological advances in bioinformatics, BCOs stand out as crucial tools for bridging the gap between complex data science and the stringent requirements of regulatory submissions. The positive implications for pharmaceutical development processes and global health are manifold, indicating a bright future for standardized computational communication within the scientific community.