Difference between revisions of "Journal:Bridging the collaboration gap: Real-time identification of clinical specimens for biomedical research"
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==Introduction== | ==Introduction== | ||
In the era of precision medicine, human biospecimens are an important resource for basic, [[Translational research|translational]], and clinical research and are increasingly needed to advance our understanding of human physiology, disease, treatment response, and outcomes. The field of [[Biobank|biobanking]] has undergone significant optimization efforts by national and international communities to improve and harmonize biospecimen curation to support this need.<ref name="vanOmmenBBMRI15">{{cite journal |title=BBMRI-ERIC as a Resource for Pharmaceutical and Life Science Industries: The Development of Biobank-Based Expert Centres |journal=European Journal of Human Genetics |author=van Ommen, G.-J.B.; Törnwall, O.; Bréchot, C. et al. |volume=23 |issue=7 |pages=893-900 |year=2015 |doi=10.1038/ejhg.2014.235 |pmid=25407005 |pmc=PMC4463510}}</ref><ref name="LanghofCurrent18">{{cite journal |title=Current Practices for Access, Compensation, and Prioritization in Biobanks. Results From an Interview Study |journal=European Journal of Human Genetics |author=Langhof, H.; Kahrass, H.; Illig, T. et al. |volume=26 |issue=11 |pages=1572–1581 |year=2018 |doi=10.1038/s41431-018-0228-x |pmid=30089824 |pmc=PMC6189200}}</ref> However, the operationalization and maintenance of biobanks is resource-intensive and often cost prohibitive for many institutions. In addition, long-term biobanking may be suboptimal for some types of testing, such as for studies that rely on [[Lability|labile]] analytes.<ref name="ShabhikhaniTheProc14">{{cite journal |title=The Procurement, Storage, and Quality Assurance of Frozen Blood and Tissue Biospecimens in Pathology, Biorepository, and Biobank Settings |journal=Clinical Biochemistry |author=Shabihkhani, M.; Lucey, G.M.; Wei, B. et al. |volume=47 |issue=4–5 |pages=258-66 |year=2014 |doi=10.1016/j.clinbiochem.2014.01.002 |pmid=24424103 |pmc=PMC3982909}}</ref><ref name="EllervikPreanal15">{{cite journal |title=Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking |journal=Clinical Chemistry |author=Ellervik, C.; Vaught, J. |volume=61 |issue=7 |pages=914-34 |year=2015 |doi=10.1373/clinchem.2014.228783 |pmid=25979952}}</ref> As a result, comprehensive access to human biospecimens remains limited, and there is a persistent need for efficient solutions that can provide access to high-quality and recently acquired human biospecimens.<ref name="MassettAss11">{{cite journal |title=Assessing the Need for a Standardized Cancer HUman Biobank (caHUB): Findings From a National Survey With Cancer Researchers |journal=Journal of the National Cancer Institute Monographs |author=Massett, H.A.; Atkinson, N.L.; Weber, D. et al. |volume=2011 |issue=42 |pages=8–15 |year=2011 |doi=10.1093/jncimonographs/lgr007 |pmid=21672890}}</ref> | |||
Revision as of 21:05, 1 June 2020
| Full article title | Bridging the collaboration gap: Real-time identification of clinical specimens for biomedical research |
|---|---|
| Journal | Journal of Pathology Informatics |
| Author(s) | Durant, Thomas J.S.; Gong, Guannan; Price, Nathan; Schilz, Wade L. |
| Author affiliation(s) | Yale New Haven Hospital, Yale New Haven Health |
| Primary contact | Email: Log in required |
| Year published | 2020 |
| Volume and issue | 11 |
| Article # | 14 |
| DOI | 10.4103/jpi.jpi_15_20 |
| ISSN | 2153-3539 |
| Distribution license | Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License |
| Website | http://www.jpathinformatics.org/article.asp |
| Download | http://www.jpathinformatics.org/temp/JPatholInform11114-7412119_203521.pdf |
 |
This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed. |
Abstract
Introduction: Biomedical and translational research often relies on the evaluation of patients or specimens that meet specific clinical or laboratory criteria. The typical approach used to identify biospecimens is a manual, retrospective process that exists outside the clinical workflow. This often makes biospecimen collection cost prohibitive and prevents the collection of analytes with short stability times. Emerging data architectures offer novel approaches to enhance specimen-identification practices. To this end, we present a new tool that can be deployed in a real-time environment to automate the identification and notification of available biospecimens for biomedical research.
Methods: Real-time clinical and laboratory data from Cloverleaf (Infor, NY, NY) were acquired within our computational health platform, which is built on open-source applications. Study-specific filters were developed in NiFi (Apache Software Foundation, Wakefield, MA, USA) to identify the study-appropriate specimens in real time. Specimen metadata were stored in Elasticsearch (Elastic N. V., Mountain View, CA, USA) for visualization and automated alerting.
Results: Between June 2018 and December 2018, we identified 2,992 unique specimens belonging to 2,815 unique patients, split between two different use cases. Based on laboratory policy for specimen retention and study-specific stability requirements, secure e-mail notifications were sent to investigators to automatically notify them of availability. The assessment of throughput on commodity hardware demonstrates the ability to scale to approximately 2,000 results per second.
Conclusion: This work demonstrates that real-world clinical data can be analyzed in real-time to increase the efficiency of biospecimen identification with minimal overhead for the clinical laboratory. Future work will integrate additional data types, including the analysis of unstructured data, to enable more complex cases and biospecimen identification.
Keywords: biobanking, biomedical research, biospecimen science, clinical specimens, real-time identification, translational research
Introduction
In the era of precision medicine, human biospecimens are an important resource for basic, translational, and clinical research and are increasingly needed to advance our understanding of human physiology, disease, treatment response, and outcomes. The field of biobanking has undergone significant optimization efforts by national and international communities to improve and harmonize biospecimen curation to support this need.[1][2] However, the operationalization and maintenance of biobanks is resource-intensive and often cost prohibitive for many institutions. In addition, long-term biobanking may be suboptimal for some types of testing, such as for studies that rely on labile analytes.[3][4] As a result, comprehensive access to human biospecimens remains limited, and there is a persistent need for efficient solutions that can provide access to high-quality and recently acquired human biospecimens.[5]
References
- ↑ van Ommen, G.-J.B.; Törnwall, O.; Bréchot, C. et al. (2015). "BBMRI-ERIC as a Resource for Pharmaceutical and Life Science Industries: The Development of Biobank-Based Expert Centres". European Journal of Human Genetics 23 (7): 893-900. doi:10.1038/ejhg.2014.235. PMC PMC4463510. PMID 25407005. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463510.
- ↑ Langhof, H.; Kahrass, H.; Illig, T. et al. (2018). "Current Practices for Access, Compensation, and Prioritization in Biobanks. Results From an Interview Study". European Journal of Human Genetics 26 (11): 1572–1581. doi:10.1038/s41431-018-0228-x. PMC PMC6189200. PMID 30089824. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6189200.
- ↑ Shabihkhani, M.; Lucey, G.M.; Wei, B. et al. (2014). "The Procurement, Storage, and Quality Assurance of Frozen Blood and Tissue Biospecimens in Pathology, Biorepository, and Biobank Settings". Clinical Biochemistry 47 (4–5): 258-66. doi:10.1016/j.clinbiochem.2014.01.002. PMC PMC3982909. PMID 24424103. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982909.
- ↑ Ellervik, C.; Vaught, J. (2015). "Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking". Clinical Chemistry 61 (7): 914-34. doi:10.1373/clinchem.2014.228783. PMID 25979952.
- ↑ Massett, H.A.; Atkinson, N.L.; Weber, D. et al. (2011). "Assessing the Need for a Standardized Cancer HUman Biobank (caHUB): Findings From a National Survey With Cancer Researchers". Journal of the National Cancer Institute Monographs 2011 (42): 8–15. doi:10.1093/jncimonographs/lgr007. PMID 21672890.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation. Grammar was cleaned up for smoother reading. In some cases important information was missing from the references, and that information was added.
