Journal:HEnRY: A DZIF LIMS tool for the collection and documentation of biospecimens in multicentre studies

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Full article title HEnRY: A DZIF LIMS tool for the collection and documentation of biomaterials in multicentre studies
Journal BMC Bioinformatics
Author(s) Heinen, Stepahine; Schulze, Nick; Franke, Bernd; Klein, Florian; Lehmann, Clara; Vehreschild, Maria J.G.T.; Gloistein, Claas;
Stecher, Melanie; Vehreschild, Jörg J.
Author affiliation(s) University of Cologne, German Center for Infection Research (DZIF), University Hospital Cologne, Goethe University Frankfurt
Primary contact Email: Contact form
Year published 2020
Volume and issue 21
Article # 290
DOI 10.1186/s12859-020-03596-1
ISSN 1471-2105
Distribution license Creative Commons Attribution 4.0 International
Website https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03596-1
Download https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03596-1 (PDF)

Abstract

Background: Well-characterized biological specimens of high quality have great potential for the acceleration of and quality improvement in translational biomedical research. To improve accessibility of local specimen collections, efforts have been made to create central repositories (biobanks) and catalogues. Available technical solutions for creating professional local specimen catalogues and connecting them to central systems are cost intensive and/or technically complex to implement. Therefore, the HIV-focused Thematic Translational Unit (TTU) of the German Center for Infection Research (DZIF) developed a laboratory information management system (LIMS) called HIV Engaged Research Technology (HEnRY) for implementation into the HIV Translational Platform (TP-HIV) at the DZIF and other research networks.

Results: HEnRY is developed at the University Hospital of Cologne. It is an advanced LIMS designed to manage the processing and storage of specimens and aliquots of different specimen types. Features include:

  • monitoring stored specimens and associated information;
  • finding and storing data via query tools or Structured Query Language (SQL);
  • preparation of summary documents, including scannable search lists;
  • centralized management of the practical laboratory part of multicentre studies (e.g., import of drawing schemes and specimen processing steps);
  • preparation of aliquot shipments, including associated documents to be added to shipments;
  • unique and secure identification of aliquots through use of customizable Quick Response (QR) code labels directly from HEnRY; and
  • support of aliquot data transmission to central registries.

In summary, HEnRY offers all features necessary for biobanking LIMS software. In addition, the structure of HEnRY provides sufficient flexibility to allow the implementation in other research areas.

Conclusion: HEnRY is a free biobanking tool published under the MIT license. While it was developed to support HIV research in Germany, the feature set and language options allow much broader applications and make this a powerful free research tool.

Keywords: LIMS, biobanking, sample documentation, sample storage, sample management, sample processing, DZIF, TP HIV, multicentre studies, TI biobanking

Introduction

A biobank can be described as a repository in which biological specimens and data of their respective donors are stored for use in biomedical research. It involves the systematic and standardized procurement, processing, annotation, storage, and ultimately distribution of biological specimens to researchers.[1] Biobanks enable cross-purpose research studies by rapidly providing sufficient and well-described specimens for experimental and translational experiments. Linkage of biological specimens with clinical data provides important insights to phenotypic disease information that is crucial in the current research environment.[2][3]

Today, the indexing, labelling, and storing of specimens in professional biobanks is usually managed by a laboratory information management system (LIMS), supporting the user with the administrative and coordinative tasks of specimen processing, as well as the collection and analysis of identified analytical data.[4][5] Ideally, a LIMS is also capable of exchanging data with other systems via software and hardware interfaces. Many LIMS on the market are also flexible, modular systems, which support the addition of functions according to the customer’s needs.

The features of a LIMS have changed over the years from a basic sample tracking tool to a resource planning system that manages multiple aspects of laboratory informatics. Common features of a LIMS include workflow management, record keeping, inventory management, data exchange interfaces, and reporting. A well-designed LIMS brings accuracy and accessibility to the flow of samples and laboratory data.[6][7][8][9] One particularly important aspect of a LIMS is the possibility for automation to increase processing speed while reducing workload, particularly for repetitive and predictable tasks.[8][10] By supporting the standardization of documentation and standard operating procedures (SOPs) for sample processing, a LIMS can also improve data and sample quality and reliability by minimizing documentation errors through automation.[1][11][12][13][14]

By using a LIMS with a database accessible to each employee, individually managed spreadsheets can be replaced. Representation of the collected and complex data is simplified by the use of database queries. Regular backups can ensure the safety and availability of laboratory data.

Most LIM systems on the market have high initial costs or license fees. Small or newly founded working groups usually lack the financial means to purchase such a system.[1] For the specific purpose of collecting and processing specimens of the HIV Translational Platform (TP-HIV) within the German Center for Infection Research (DZIF), we developed and here present the HIV Engaged Research Technology (HEnRY) LIMS. Due to excellent user feedback, we noticed that many of HEnRY’s features are required by a broad range of researchers. As such, we decided to release the tool under an open license and make it available to the community.

Implementation

Development

HEnRY is released under the MIT licence. The client has been under development by an agile structured team since 2014, using C#[15] with Windows Presentation Foundation (WPF)[16] and the .NET 4.5 framework.[17] An installer package for Windows platforms (Windows 7 up to Windows 10), as well as the source code are available upon request. The manual and short instructions for the program are available at http://www.tp-hiv.de/. The first production version of HEnRY was made available for participants of the TP-HIV on February 15th, 2017.

All data is stored in a Microsoft SQL database on Microsoft SQL Server 2012 or greater.[18] It is recommended to install the server and the databases in a protected network suitable for highly detailed and potentially stigmatizing patient data with considerable potential for misuse. For additional information, see Supplementary material 1, 2, and 3.

During the developmental process of HEnRY, a close collaboration with the laboratory staff, which represents the primary target group of the tool, and study coordinators was established. Both user groups gave continuous feedback to developed and requested features, which were tailored to their needs.

User feedback in the form of meetings and questionnaires was obtained at regular intervals. Requests and bugs were fixed in the context of monthly updates. Additionally, the lead developer accompanied the lab employees in their daily work routine with HEnRY to streamline the program to the actual workflow in the lab.

The HEnRY LIMS software has been in use at the University of Cologne since 2016, with currently seven active working groups.

Workflow

HEnRY specializes in the documentation of the storage and processing of blood samples and aliquots in analytically working laboratories. It simplifies and accelerates laboratory work, increases the quality of documentation, and minimizes potential sources of errors. Information about studies, patients, samples, aliquots, and processing steps is stored in a structured manner (see Fig. 1). This information can be exchanged via pseudonym export and import functions, which improves cooperation between different participants of the studies. Additional information can be found in Supplementary material 4, 5, and 6.


Fig1 Heinen BMCBioinfo2020 21.png

Figure 1. Snapshot of the biobanking view. The quick-view option of the box is opened.

Figure 2 shows a diagram of the workflow for multicenter studies and the use of HEnRY. An unlimited amount of users per study site is supported. Online access is available using the site's own Citrix access. A study supervisor or study coordinator can develop the study properties, drawing schemes, and processing steps and send the study design as an XML file[19] to other participating centers.


Fig2 Heinen BMCBioinfo2020 21.png

Figure 2. Scheme of HEnRY-usage and distribution of practical study data to participating centers in multicenter studies

In a setting of limited resources, HEnRY can be used as a standalone LIMS on one computer with, e.g., SQL Server Express editions for structured documentation of biomaterial and self-adhesive label creation. Via the transfer of XML files, data for biomaterial can be shared with other laboratories, clinics or project partners.

References

  1. 1.0 1.1 1.2 Somiari, S.B.; Somiari, R.I. (2020). "The Future of Biobanking: A Conceptual Look at How Biobanks Can Respond to the Growing Human Biospecimen Needs of Researchers". Advances in Experimental Medicine and Biology 864: 11–27. doi:10.1007/978-3-319-20579-3_2. PMID 26420610. 
  2. "United against infections". German Center for Infection Research. 2019. https://www.dzif.de/en/portrait. 
  3. "Biobanken – Vorreiter für FAIRes Teilen von Daten und Proben in der medizinischen Forschung". Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V.. 2018. http://www.biobanken.de/de-de/symposium.aspx. Retrieved 15 February 2018. 
  4. "What Is a LIMS?". Autoscribe Informatics Blog. Autoscribe Informatics, Inc. https://www.autoscribeinformatics.com/resources/blog/what-is-a-lims. Retrieved 20 August 2019. 
  5. Grand, A.; Geda, E.; Mignone, A.; Bertotti, A.; Fiori, A. (2019). "One tool to find them all: A case of data integration and querying in a distributed LIMS platform". Database 2019: baz004. doi:10.1093/database/baz004. PMC PMC6352757. PMID 30698777. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6352757. 
  6. Prasad, P.J.; Bodhe, G.L. (2012). "Trends in laboratory information management system". Chemometrics and Intelligent Laboratory Systems 118: 187–192. doi:10.1016/j.chemolab.2012.07.001. 
  7. Redrup, M.J.; Igarashi, H.; Schaefgen, J. et al. (2016). "Sample Management: Recommendation for Best Practices and Harmonization from the Global Bioanalysis Consortium Harmonization Team". AAPS Journal 18 (2): 290-3. doi:10.1208/s12248-016-9869-2. PMC PMC4779093. PMID 26821803. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779093. 
  8. 8.0 8.1 Machina, H.K.; Wild, D.J. (2013). "Electronic laboratory notebooks progress and challenges in implementation". Journal of Laboratory Automation 18 (4): 264–8. doi:10.1177/2211068213484471. PMID 23592569. 
  9. "Error: no |title= specified when using {{Cite web}}". International Society for Biological and Envioronmental Repositories. 2018. https://www.isber.org/page/BPR. Retrieved 21 August 2018. 
  10. McDowall, R.D. (1999). "The role of laboratory information management systems (LIMS) in analytical method validation". Analytica Chimica Acta 391 (2): 149–58. doi:10.1016/S0003-2670(99)00107-5. 
  11. Grizzle, W.E.; Gunter, E.W.; Sexton, K.C. et al. (2015). "Quality management of biorepositories". Biopreservation and Biobanking 13 (3): 183-94. doi:10.1089/bio.2014.0105. PMC PMC4559203. PMID 26035008. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559203. 
  12. Simeon-Dubach, D.; Zeisberger, S.M.; Hoerstrup, S.P. (2016). "Quality Assurance in Biobanking for Pre-Clinical Research". Transfusion Medicine and Hemotherapy 43 (5): 353-357. doi:10.1159/000448254. PMC PMC4559203. PMID PMC5073593. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559203. 
  13. "Quality Management". German Biobank Node. Federal Ministry of Education and Research. https://www.bbmri.de/biobanking/quality-management/?L=1. Retrieved 20 August 2019. 
  14. "Vision, Mission & Goals". European, Middle Eastern & African Society for Biopreservation and Biobanking. https://esbb.org/page/VisionMissionGoals. Retrieved 20 August 2019. 
  15. Microsoft (20 July 2015). "Introduction to the C# language and the .NET Framework". Microsoft Docs. https://docs.microsoft.com/en-us/dotnet/csharp/getting-started/introduction-to-the-csharp-language-and-the-net-framework. Retrieved 02 April 2019. 
  16. Microsoft (25 January 2018). "Windows Presentation Foundation". Microsoft Docs. https://docs.microsoft.com/de-de/dotnet/framework/wpf/. Retrieved 19 August 2019. 
  17. Microsoft. ".NET Framework documentation". Microsoft Docs. https://docs.microsoft.com/en-us/dotnet/framework/. Retrieved 02 April 2019. 
  18. Microsoft. "SQL Server 2016". https://www.microsoft.com/en-gb/sql-server/sql-server-2016. Retrieved 22 August 2018. 
  19. Quin, L. (11 October 2016). "Extensible Markup Language (XML)". W3C. https://www.w3.org/XML/. Retrieved 01 June 2018. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation, grammar, and spelling. In some cases important information was missing from the references, and that information was added. The original paper—likely translated from German—occasionally refers to biological samples as biomaterials; to avoid confusion with the concept of actual biomaterials used in medical devices, most instances of "biomaterial" were replaced with "biological specimen" or "biospecimen." Several URLs in the original no longer work; working URLs presumed to be the intended source were substituted for this version. Several superfluous citations to .NET and other technologies were either turned into external links or omitted for this version.