Custom software development for use in a clinical laboratory

A Model for Design and Implementation of a Laboratory Information-Management System Specific for Molecular Pathology Laboratory Operations

The Molecular Pathology Section, Cleveland Clinic (Cleveland, OH), has undergone enhancement of its testing portfolio and processes. An Excel 2013- and paper-based data-management system was replaced with a commercially available laboratory information-management system (LIMS) software application, a separate bioinformatics platform, customized test-interpretation applications, a dedicated sample-accessioning service, and a results-releasing software application. The customized LIMS solution manages complex workflows, large-scale data packets, and process automation. A customized approach was required because, in a survey of commercially available off-the-shelf software products, none met the diverse and complex needs of this molecular diagnostics 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-building best practices were formulated, which may be emulated for scalable and cost-effective laboratory-authored software.

Facilitating Test Status Information Communication in the Time of COVID-19

The Coronavirus 2019 pandemic has strained nearly every aspect of pathology practice, including preanalytic, analytic, and postanalytic processes. Much of the challenges result from high demand for limited severe acute respiratory syndrome coronavirus 2 testing capacity, a resource required to facilitate patient flow throughout the hospital system and society at large. At our institution, this led to unprecedented increases in inquiries from providers to laboratory staff relating to the expected time to result for their patients. The demand was great enough to require redeployment of staff to handle the laboratory call volume. Although these data are available in our laboratory information system, the data do not interface to our electronic health record system. We developed systems using the R statistical programming language that abstract the necessary data regarding severe acute respiratory syndrome coronavirus 2 polymerase chain reaction testing from our lab system in real time, store it, and present it to clinicians for on demand querying. These data have been accessed over 2500 times by over 100 distinct users. Median length of each user session is approximately 4.9 minutes. Because our lab information system does not persistently store tracking information while our system does, we have been able to iteratively recalculate time to result values for each tracking stop as workflows have changed over time. Facility with informatics and programming concepts coupled with clinical understanding have allowed us to swiftly develop and iterate on applications which provide efficiency gains, allowing laboratory resources to focus on generating test results for our patients.

An Analysis of the Effect of the COVID-19 Pandemic on Case Volumes in an Academic Subspecialty-Based Anatomic Pathology Practice

The recent COVID pandemic has had a major effect on anatomic pathology specimen volumes across the country. The effect of this pandemic on a subspecialty academic practice is presented. We used a data-driven approach to monitor the changing workloads in a granular fashion and dynamically adjust the scheduling of faculty and histology staff accordingly to minimize the number of people present on-site. At the peak of the pandemic locally, the main hospital in our health system had 450 COVID-positive inpatients. The surgical pathology specimen volume dropped to 13% of the pre-pandemic levels, and this occurred about 2 weeks before the peak of the inpatient census; cytology specimens (the majority of which are outreach gynecological) dropped to approximately 5% of the pre-pandemic volume, 4 weeks before the peak inpatient census. All of the surgical subspecialty services showed a significant decrease in volume, with hematopathology being the least affected (dropped to 30% of the pre-pandemic level). The genitourinary surgical subspecialty service (predominantly prostate and bladder biopsies) was the most affected (dropped to 1% of the pre-pandemic level) but was fastest to return as clinical operations began to return to normal. The only specimen type which showed a significant increase in turnaround time during the pandemic was our gynecologic cytology specimens and that occurred as the specimen volume returned. This was due to stay-at-home directives for the cytotechnologists and the fact that some of them were retasked to participate in our SARS-CoV-2 testing.

A Custom Microcontrolled and Wireless-Operated Chamber for Auditory Fear Conditioning

Animal behavioral paradigms, such as classical conditioning and operant conditioning, are an important tool to study the neural basis of cognition and behavior. These paradigms involve manipulating sensory stimuli in a way that learning processes are induced under controlled experimental conditions. However, the majority of the commercially available equipment did not offer flexibility to manipulate stimuli. Therefore, the development of most versatile devices would allow the study of more complex cognitive functions. The purpose of this work is to present a low-cost, customized and wireless-operated chamber for animal behavior conditioning, based on the joint operation of two microcontroller modules: Arduino Due and ESP8266-12E. Our results showed that the auditory stimulation system allows setting the carrier frequency in the range of 1 Hz up to more than 100 kHz and the sound stimulus can be modulated in amplitude, also over a wide range of frequencies. Likewise, foot-shock could be precisely manipulated regarding its amplitude (from ∼200 μA to ∼1500 μA) and frequency (up to 20 pulses per second). Finally, adult rats exposed to a protocol of cued fear conditioning in our device showed consistent behavioral response and electrophysiological evoked responses in the midbrain auditory pathway. Furthermore, the device developed in the current study represents an open source alternative to develop customized protocols to study fear memory under conditions of varied sensory stimuli.

Implementation of a Software Application for Presurgical Case History Review of Frozen Section Pathology Cases

Background:

The frozen section pathology practice at Mayo Clinic in Rochester performs ~20,000 intraoperative consultations a year (~70–80/weekday). To prepare for intraoperative consultations, surgical pathology fellows and residents review the case history, previous pathology, and relevant imaging the day before surgery. Before the work described herein, review of pending surgical pathology cases was a paper-based process requiring handwritten transcription from the electronic health record, a laborious and potentially error prone process.

Methods:

To facilitate more efficient case review, a modular extension of an existing surgical listing software application (Surgical and Procedure Scheduling [SPS]) was developed. The module (SPS-pathology-specific module [PM]) added pathology-specific functionality including recording case notes, prefetching of radiology, pathology, and operative reports from the medical record, flagging infectious cases, and real-time tracking of cases in the operating room. After implementation, users were surveyed about its impact on the surgical pathology practice.

Results:

There were 16 survey respondents (five staff pathologists and eleven residents or fellows). All trainees (11/11) responded that the application improved an aspect of surgical list review including abstraction from medical records (10/11), identification of possibly infectious cases (7/11), and speed of list preparation (10/11). The average reported time savings in list preparation was 1.4 h/day. Respondents indicated the application improved the speed (11/16), clarity (13/16), and accuracy (10/16) of morning report. During the workday, respondents reported the application improved real-time case review (14/16) and situational awareness of ongoing cases (13/16).

Conclusions:

A majority of respondents found the SPS-PM improved all preparatory and logistical aspects of the Mayo Clinic frozen section surgical pathology practice. In addition, use of the SPS-PM saved an average of 1.4 h/day for residents and fellows engaged in preparatory case review.

Open-source LIMS in Vietnam: The path toward sustainability and host country ownership

OBJECTIVE

The objectives of this case report are as follows: to describe the process of establishing a national laboratory information management system (LIMS) program for clinical and public health laboratories in Vietnam; to evaluate the outcomes and lessons learned; and to present a model for sustainability based on the program outcomes that could be applied to diverse laboratory programs.

METHODS

This case report comprises a review of program documentation and records, including planning and budgetary records of the donor, monthly reports from the implementer, direct observation, and ad-hoc field reports from technical advisors and governmental agencies. Additional data on program efficacy and user acceptance were collected from routine monitoring of laboratory policies and operational practices.

RESULTS

LIMS software was implemented at 38 hospital, public health and HIV testing laboratories in Vietnam. This LIMS was accepted by users and program managers as a useful tool to support laboratory processes. Implementation cost per laboratory and average duration of deployment decreased over time, and project stakeholders initiated transition of financing (from the donor to local institutions) and of system maintenance functions (from the implementer to governmental and site-level staff). Collaboration between the implementer in Vietnam and the global LIMS user community was strongly established, and knowledge was successfully transferred to staff within Vietnam.

CONCLUSION

Implementing open-sourced LIMS with local development and support was a feasible approach towards establishing a sustainable laboratory informatics program that met the needs of health laboratories in Vietnam. Further effort to institutionalize IT support capacity within key government agencies is ongoing.

Bar Coding and Tracking in Pathology

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology.

Laboratory Information Systems

Laboratory information systems (LISs) supply mission-critical capabilities for the vast array of information-processing needs of modern laboratories. LIS architectures include mainframe, client-server, and thin client configurations. The LIS database software manages a laboratory's data. LIS dictionaries are database tables that a laboratory uses to tailor an LIS to the unique needs of that laboratory. Anatomic pathology LIS (APLIS) functions play key roles throughout the pathology workflow, and laboratories rely on LIS management reports to monitor operations. This article describes the structure and functions of APLISs, with emphasis on their roles in laboratory operations and their relevance to pathologists.

Customizing Laboratory Information Systems: Closing the Functionality Gap

Highly customizable laboratory information systems help to address great variations in laboratory workflows, typical in Pathology. Often, however, built-in customization tools are not sufficient to add all of the desired functionality and improve systems interoperability. Emerging technologies and advances in medicine often create a void in functionality that we call a functionality gap. These gaps have distinct characteristics—a persuasive need to change the way a pathology group operates, the general availability of technology to address the missing functionality, the absence of this technology from your laboratory information system, and inability of built-in customization tools to address it. We emphasize the pervasive nature of these gaps, the role of pathology informatics in closing them, and suggest methods on how to achieve that. We found that a large number of the papers in the Journal of Pathology Informatics are concerned with these functionality gaps, and an even larger proportion of electronic posters and abstracts presented at the Pathology Informatics Summit conference each year deal directly with these unmet needs in pathology practice. A rapid, continuous, and sustainable approach to closing these gaps is critical for Pathology to provide the highest quality of care, adopt new technologies, and meet regulatory and financial challenges. The key element of successfully addressing functionality gaps is gap ownership—the ability to control the entire pathology information infrastructure with access to complementary systems and components. In addition, software developers with detailed domain expertise, equipped with right tools and methodology can effectively address these needs as they emerge.

Bar Coding and Tracking in Pathology

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology.

Laboratory Information Systems

Laboratory information systems (LISs) supply mission-critical capabilities for the vast array of information-processing needs of modern laboratories. LIS architectures include mainframe, client-server, and thin client configurations. The LIS database software manages a laboratory's data. LIS dictionaries are database tables that a laboratory uses to tailor an LIS to the unique needs of that laboratory. Anatomic pathology LIS (APLIS) functions play key roles throughout the pathology workflow, and laboratories rely on LIS management reports to monitor operations. This article describes the structure and functions of APLISs, with emphasis on their roles in laboratory operations and their relevance to pathologists.

Reqscan: An open source solution for laboratory requisition scanning, archiving and retrieval

Requisition storage and retrieval are an integral part of the outpatient laboratory testing process. It is frequently necessary to review an original requisition to confirm the ordering physician, patient demographics, diagnostic information, and requested tests. Manual retrieval of a paper requisition is time-consuming and tedious. Although commercial solutions exist for the scanning and archiving of barcoded paper requisitions, the tools to accomplish this are freely available from the open source software community. We present a simple dedicated piece of software, Reqscan, for scanning patient laboratory requisitions, finding all barcode information, and saving the requisition as a portable document format named according the barcode(s) found. This Python application offers a simple solution to patient requisition digitization. Reqscan has been successfully tested and implemented into routine practice for storage and retrieval of outpatient requisitions at St. Paul's Hospital, Department of Pathology and Laboratory Medicine in Vancouver, British Columbia, Canada.

Development and implementation of a custom integrated database with dashboards to assist with hematopathology specimen triage and traffic

BACKGROUND

At some institutions, including ours, bone marrow aspirate specimen triage is complex, with hematopathology triage decisions that need to be communicated to downstream ancillary testing laboratories and many specimen aliquot transfers that are handled outside of the laboratory information system (LIS). We developed a custom integrated database with dashboards to facilitate and streamline this workflow.

METHODS

We developed user-specific dashboards that allow entry of specimen information by technologists in the hematology laboratory, have custom scripting to present relevant information for the hematopathology service and ancillary laboratories and allow communication of triage decisions from the hematopathology service to other laboratories. These dashboards are web-accessible on the local intranet and accessible from behind the hospital firewall on a computer or tablet. Secure user access and group rights ensure that relevant users can edit or access appropriate records.

RESULTS

After database and dashboard design, two-stage beta-testing and user education was performed, with the first focusing on technologist specimen entry and the second on downstream users. Commonly encountered issues and user functionality requests were resolved with database and dashboard redesign. Final implementation occurred within 6 months of initial design; users report improved triage efficiency and reduced need for interlaboratory communications.

CONCLUSIONS

We successfully developed and implemented a custom database with dashboards that facilitates and streamlines our hematopathology bone marrow aspirate triage. This provides an example of a possible solution to specimen communications and traffic that are outside the purview of a standard LIS.

SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory

A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution.

Tracking in Anatomic Pathology

Bar code–based tracking solutions, long present in clinical pathology laboratories, have recently made an appearance in anatomic pathology (AP) laboratories. Tracking of AP “assets” (specimens, blocks, slides) can enhance laboratory efficiency, promote patient safety, and improve patient care. Routing of excess clinical material into research laboratories and biorepositories are other avenues that can benefit from tracking of AP assets. Implementing tracking is not as simple as installing software and turning it on. Not all tracking solutions are alike. Careful analysis of laboratory workflow is needed before implementing tracking to assure that this solution will meet the needs of the laboratory. Such analysis will likely uncover practices that may need to be modified before a tracking system can be deployed. Costs that go beyond simply that of purchasing software will be incurred and need to be considered in the budgeting process. Finally, people, not technology, are the key to assuring quality. Tracking will require significant changes in workflow and an overall change in the culture of the laboratory. Preparation, training, buy-in, and accountability of the people involved are crucial to the success of this process. This article reviews the benefits, available technology, underlying principles, and implementation of tracking solutions for the AP and research laboratory.