Journal:A model for design and implementation of a laboratory information management system specific to molecular pathology laboratory operations

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Full article title A model for design and implementation of a laboratory information management system specific to molecular pathology laboratory operations
Journal The Journal of Molecular Diagnostics
Author(s) Tomlinson, Eban; Goodman, Jennifer; Loftus, Margaret; Bitto, Stephen; Carpenter, Erica; Oddo, Richard; Judis, LuAnn; Ali, Shabab; Robinson, Wyatt E.; Carver, Miranda; Ganea, Mariana; McDonnell, Kristen; O'Neill, Diane; Starbuck, Jennifer; Johnson, Eric; Meister, Erik; Pohl, Jonathan; Spildener, Jessica; Shurtleff, Sheila; Sovie, Sheryl; Melendez, Cathleen; Krebs, Pamela; Riley, Jacquelyn D.; Wensel, Christine; Astbury, Caroline; Azzato, Elizabeth M.; Bosler, David S.; Brock, Jay E.; Cook, James R.; Cheng, Yu-Weu; Tu, Zheng J.; Cruise, M.; Henricks, Walter H.; Farkas, Daniel H.
Author affiliation(s) Semaphore Solutions, Cleveland Clinic
Primary contact Email: farkasd2 at ccf dot org
Year published 2022
Volume and issue S1525-1578(22)
Page(s) 00012-5
DOI 10.1016/j.jmoldx.2022.01.002
ISSN 1525-1578
Distribution license Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Website https://www.jmdjournal.org/article/S1525-1578(22)00012-5/fulltext
Download https://www.jmdjournal.org/action/showPdf?pii=S1525-1578%2822%2900012-5 (PDF)

Abstract

The Molecular Pathology Section of Cleveland Clinic (Cleveland, OH) has undergone enhancement of its testing portfolio and processes. An electronic- and paper-based data management system was replaced with a commercially available laboratory information management system (LIMS) solution, a separate bioinformatics platform, customized test-interpretation applications, a dedicated accessioning service, and a results-releasing solution. The LIMS solution manages complex workflows, large-scale data packets, and process automation. However, a customized approach was required for the LIMS since a survey of commercially available off-the-shelf (COTS) software solutions revealed none met the diverse and complex needs of Cleveland Clinic's molecular pathology service. The project utilized the expertise of clinical laboratorians, pathologists, genetics counselors, bioinformaticians, and systems analysts in partnering with software-engineering consultants to design and implement a solution. Concurrently, Agile software development best practices were formulated, which may be emulated for scalable and cost-effective laboratory-authored software.

Keywords: molecular pathology, laboratory information management system, LIMS, bioinformatics, software development, Agile-Scrum

Introduction

Data management needs in clinical molecular pathology laboratories differ in substantive ways from those in other clinical laboratories and anatomical pathology labs. [1,2,3,4] Conventional laboratory information systems (LISs) historically have not inherently supported the needs of molecular pathology laboratories to the extent that they have in other laboratory disciplines and operations. [2] Molecular pathology laboratories have often relied on a combination of manual methods, spreadsheets, and nonintegrated and/or modular software to meet data management and operational needs.

Such was the situation in the Molecular Pathology Section, Pathology & Laboratory Medicine Institute, Cleveland Clinic (Cleveland, OH) in early 2017. A revitalization and growth plan for the section—which included expansion of personnel, equipment, testing platforms, and test development—was undertaken. An improvement deemed fundamental to this re-invention process was a new laboratory information management system (LIMS) to reduce and eventually replace the outdated, largely paper- and electronic spreadsheet–based information and workflow management system.

While the overhaul of the laboratory service was substantial, the focus of this report is limited to a description of a replicable process for the modernization of information and workflow management specific to a clinical molecular pathology laboratory. The process employed a customer–vendor relationship. Out of necessity, the relationship was a partnership due to the complementary and nontechnical skill sets of each party. The overall goal was to digitize workflow based on paper and Excel (Microsoft, Redmond, WA) across a complex, multidisciplinary molecular pathology and cytogenomics clinical laboratory service. This digitization was accomplished through a custom-architected software solution.

This article describes a model for the design and implementation of a LIMS that meets the diverse information management needs of a full-service clinical molecular pathology laboratory, emphasizes the integral importance of a well-structured development process, and describes a novel application of modern software-based project management methods and third-party partnerships for building and deploying a LIMS suitable for a modern molecular pathology laboratory.

Materials and methods

References

Notes

This presentation is faithful to the original, with only a few minor changes to presentation, grammar, and punctuation. In some cases important information was missing from the references, and that information was added. Everything else remains true to the original article, per the "NoDerivatives" portion of the distribution license.