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.

Operationalizing COVID-19 testing: Who, what, when, where, why, and how.

The authors review the rationale behind and approaches to testing for COVID-19, the quality of currently available tests, the role of data analytics in strategizing testing, and using the electronic medical record and other programs designed to steward COVID-19 testing and follow-up of patients.

Logical Observation Identifiers Names and Codes for Laboratorians.

CONTEXT.­: The Logical Observation Identifiers Names and Codes (LOINC) system is supposed to facilitate interoperability, and it is the federally required code for exchanging laboratory data. OBJECTIVE.­: To provide an overview of LOINC, emerging issues related to its use, and areas relevant to the pathology laboratory, including the subtleties of test code selection and importance of mapping the correct codes to local test menus. DATA SOURCES.­: This review is based on peer-reviewed literature, federal regulations, working group reports, the LOINC database (version 2.65), experience using LOINC in the laboratory at several large health care systems, and insight from laboratory information system vendors. CONCLUSIONS.­: The current LOINC database contains more than 55 000 numeric codes specific for laboratory tests. Each record in the LOINC database includes 6 major axes/parts for the unique specification of each individual observation or measurement. Assigning LOINC codes to a laboratory's test menu should be a defined process. In some cases, LOINC can aid in distinguishing laboratory data among different information systems, whereby such benefits are not achievable by relying on the laboratory test name alone. Criticisms of LOINC include the complexity and resource-intensive process of selecting the most correct code for each laboratory test, the real-world experience that these codes are not uniformly assigned across laboratories, and that 2 tests that may have the same appropriately assigned LOINC code may not necessarily have equivalency to permit interoperability of their result data. The coding system's limitations, which subsequently reduce the potential utility of LOINC, are poorly understood outside of the laboratory.

Implementation of Whole Slide Imaging for Clinical Purposes: Issues to Consider From the Perspective of Early Adopters.

CONTEXT: - There is growing interest in the use of digital pathology, especially whole slide imaging, for diagnostic purposes. Many issues need to be considered when incorporating this technology into a clinical laboratory. The College of American Pathologists (CAP) established a Digital Pathology Committee to support the development of CAP programs related to digital pathology. One of its many initiatives was a panel discussion entitled "Implementing Whole-Slide Imaging for Clinical Use: What to Do and What to Avoid," given for 3 years at the CAP annual meetings starting in 2014. OBJECTIVES: - To review major issues to consider when implementing whole slide imaging for clinical purposes as covered during the panel discussion. DESIGN: - The views expressed and recommendations given are based primarily on the personal experience of the authors as early adopters of this technology. It is not intended to be an exhaustive review of digital pathology. RESULTS: - Implementation is best approached in phases. Early efforts are directed toward identifying initial clinical applications and assembling an implementation team. Scanner selection should be based on intended use and budget. Recognizing pathologist concerns over the use of digital pathology for diagnostic purposes, ensuring adequate training, and performing appropriate validation studies will enhance adoption. Once implemented, the transition period from glass slide to image-based diagnostics will be associated with challenges, especially those related to a hybrid glass slide-digital slide workflow. CONCLUSIONS: - With appropriate preparation, planning, and stepwise implementation, whole slide imaging can be used safely and reliably for frozen sections, consultation, quality assurance, and primary diagnosis.

Pathology Informatics Essentials for Residents: A Flexible Informatics Curriculum Linked to Accreditation Council for Graduate Medical Education Milestones.

CONTEXT: -Recognition of the importance of informatics to the practice of pathology has surged. Training residents in pathology informatics has been a daunting task for most residency programs in the United States because faculty often lacks experience and training resources. Nevertheless, developing resident competence in informatics is essential for the future of pathology as a specialty. OBJECTIVE: -To develop and deliver a pathology informatics curriculum and instructional framework that guides pathology residency programs in training residents in critical pathology informatics knowledge and skills, and meets Accreditation Council for Graduate Medical Education Informatics Milestones. DESIGN: -The College of American Pathologists, Association of Pathology Chairs, and Association for Pathology Informatics formed a partnership and expert work group to identify critical pathology informatics training outcomes and to create a highly adaptable curriculum and instructional approach, supported by a multiyear change management strategy. RESULTS: -Pathology Informatics Essentials for Residents (PIER) is a rigorous approach for educating all pathology residents in important pathology informatics knowledge and skills. PIER includes an instructional resource guide and toolkit for incorporating informatics training into residency programs that vary in needs, size, settings, and resources. PIER is available at http://www.apcprods.org/PIER (accessed April 6, 2016). CONCLUSIONS: -PIER is an important contribution to informatics training in pathology residency programs. PIER introduces pathology trainees to broadly useful informatics concepts and tools that are relevant to practice. PIER provides residency program directors with a means to implement a standardized informatics training curriculum, to adapt the approach to local program needs, and to evaluate resident performance and progress over time.

Pathology Informatics Essentials for Residents: A flexible informatics curriculum linked to Accreditation Council for Graduate Medical Education milestones.

CONTEXT: Recognition of the importance of informatics to the practice of pathology has surged. Training residents in pathology informatics have been a daunting task for most residency programs in the United States because faculty often lacks experience and training resources. Nevertheless, developing resident competence in informatics is essential for the future of pathology as a specialty. OBJECTIVE: The objective of the study is to develop and deliver a pathology informatics curriculum and instructional framework that guides pathology residency programs in training residents in critical pathology informatics knowledge and skills and meets Accreditation Council for Graduate Medical Education Informatics Milestones. DESIGN: The College of American Pathologists, Association of Pathology Chairs, and Association for Pathology Informatics formed a partnership and expert work group to identify critical pathology informatics training outcomes and to create a highly adaptable curriculum and instructional approach, supported by a multiyear change management strategy. RESULTS: Pathology Informatics Essentials for Residents (PIER) is a rigorous approach for educating all pathology residents in important pathology informatics knowledge and skills. PIER includes an instructional resource guide and toolkit for incorporating informatics training into residency programs that vary in needs, size, settings, and resources. PIER is available at http://www.apcprods.org/PIER (accessed April 6, 2016). CONCLUSIONS: PIER is an important contribution to informatics training in pathology residency programs. PIER introduces pathology trainees to broadly useful informatics concepts and tools that are relevant to practice. PIER provides residency program directors with a means to implement a standardized informatics training curriculum, to adapt the approach to local program needs, and to evaluate resident performance and progress over time.

Perceptions of pathology informatics by non-informaticist pathologists and trainees.

BACKGROUND: Although pathology informatics (PI) is essential to modern pathology practice, the field is often poorly understood. Pathologists who have received little to no exposure to informatics, either in training or in practice, may not recognize the roles that informatics serves in pathology. The purpose of this study was to characterize perceptions of PI by noninformatics-oriented pathologists and to do so at two large centers with differing informatics environments. METHODS: Pathology trainees and staff at Cleveland Clinic (CC) and Massachusetts General Hospital (MGH) were surveyed. At MGH, pathology department leadership has promoted a pervasive informatics presence through practice, training, and research. At CC, PI efforts focus on production systems that serve a multi-site integrated health system and a reference laboratory, and on the development of applications oriented to department operations. The survey assessed perceived definition of PI, interest in PI, and perceived utility of PI. RESULTS: The survey was completed by 107 noninformatics-oriented pathologists and trainees. A majority viewed informatics positively. Except among MGH trainees, confusion of PI with information technology (IT) and help desk services was prominent, even in those who indicated they understood informatics. Attendings and trainees indicated desire to learn more about PI. While most acknowledged that having some level of PI knowledge would be professionally useful and advantageous, only a minority plan to utilize it. CONCLUSIONS: Informatics is viewed positively by the majority of noninformatics pathologists at two large centers with differing informatics orientations. Differences in departmental informatics culture can be attributed to the varying perceptions of PI by different individuals. Incorrect perceptions exist, such as conflating PI with IT and help desk services, even among those who claim to understand PI. Further efforts by the PI community could address such misperceptions, which could help enable a better understanding of what PI is and is not, and potentially lead to increased acceptance by non-informaticist pathologists.

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.

Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

Pathology Informatics Essentials for Residents: A Flexible Informatics Curriculum Linked to Accreditation Council for Graduate Medical Education Milestones (a secondary publication).

CONTEXT: Recognition of the importance of informatics to the practice of pathology has surged. Training residents in pathology informatics has been a daunting task for most residency programs in the United States because faculty often lacks experience and training resources. Nevertheless, developing resident competence in informatics is essential for the future of pathology as a specialty. OBJECTIVE: To develop and deliver a pathology informatics curriculum and instructional framework that guides pathology residency programs in training residents in critical pathology informatics knowledge and skills, and meets Accreditation Council for Graduate Medical Education Informatics Milestones. DESIGN: The College of American Pathologists, Association of Pathology Chairs, and Association for Pathology Informatics formed a partnership and expert work group to identify critical pathology informatics training outcomes and to create a highly adaptable curriculum and instructional approach, supported by a multiyear change management strategy. RESULTS: Pathology Informatics Essentials for Residents (PIER) is a rigorous approach for educating all pathology residents in important pathology informatics knowledge and skills. PIER includes an instructional resource guide and toolkit for incorporating informatics training into residency programs that vary in needs, size, settings, and resources. PIER is available at http://www.apcprods.org/PIER (accessed April 6, 2016). CONCLUSIONS: PIER is an important contribution to informatics training in pathology residency programs. PIER introduces pathology trainees to broadly useful informatics concepts and tools that are relevant to practice. PIER provides residency program directors with a means to implement a standardized informatics training curriculum, to adapt the approach to local program needs, and to evaluate resident performance and progress over time.

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.

Pathologists' place in the electronic health record landscape.

With growth spurred by recent federal efforts, electronic health records (EHRs) are transforming the practice of medicine and have important implications for pathologists, their laboratories, and the patients they serve. Beyond new EHR-related regulatory requirements, EHRs fundamentally alter the way clinicians interact with laboratory information, including test order entry and result reviewing. This article is the first in a series of 5 related articles whose goal is to provide a "framework" for empowering pathologists to adapt to, and to succeed in, the era of expanding EHR use. This series aims to describe the environment for EHR uptake, to raise awareness of EHR-related issues that pathologists and laboratories face, and to explore new professional roles for pathologists as stewards of patients' laboratory information in EHRs.

Stand-alone laboratory information systems versus laboratory modules incorporated in the electronic health record.

The increasing availability of laboratory information management modules within enterprise electronic health record solutions has resulted in some institutional administrators deciding which laboratory information system will be used to manage workflow within the laboratory, often with minimal input from the pathologists. This article aims to educate pathologists on many of the issues and implications this change may have on laboratory operations, positioning them to better evaluate and represent the needs of the laboratory during this decision-making process. The experiences of the authors, many of their colleagues, and published observations relevant to this debate are summarized. There are multiple dimensions of the interdependency between the pathology laboratory and its information system that must be factored into the decision. Functionality is important, but management authority and gap-ownership are also significant elements to consider. Thus, the pathologist must maintain an active role in the decision-making process to ensure the success of the laboratory.

Management of laboratory data and information exchange in the electronic health record.

In the era of the electronic health record, the success of laboratories and pathologists will depend on effective presentation and management of laboratory information, including test orders and results, and effective exchange of data between the laboratory information system and the electronic health record. In this third paper of a series that explores empowerment of pathology in the era of the electronic health record, we review key elements of managing laboratory information within the electronic health record and examine functional issues pertinent to pathologists and laboratories in the exchange of laboratory information between electronic health records and both anatomic and clinical pathology laboratory information systems. Issues with electronic order-entry and results-reporting interfaces are described, and considerations for setting up these interfaces are detailed in tables. The role of the laboratory medical director as mandated by the Clinical Laboratory Improvement Amendments of 1988 and the impacts of discordance between laboratory results and their display in the electronic health record are also discussed.

Accreditation and regulatory implications of electronic health records for laboratory reporting.

The Clinical Laboratory Improvement Amendments of 1988 include strict regulations for reporting content, and it falls on the named director to ensure that this content is available to the caregiver. With the electronic health record serving as the conduit to the end user of the laboratory data, the laboratory generally, and the director specifically, must verify accurate transmission of these content components. An understanding of regulatory and accreditation requirements is essential both to allow the proper discharge of these mandated responsibilities and to enforce the role and authority that the pathologist must have to ensure that these requirements are satisfied by the reporting system. The regulatory requirements will be discussed in the context of the Clinical Laboratory Improvement Amendments of 1988 standards; however, interpretation and expansion on these regulations exist both in Clinical Laboratory Improvement Amendments of 1988 inspection guidelines from the Centers for Medicare and Medicaid Services and in accreditation program requirements. This regulatory expectation both places the laboratory director in a position of risk and provides leverage to ensure meaningful and accurate communication of laboratory information.

Pathologists as stewards of laboratory information.

Just as electronic health records are transforming the practice of medicine and health care information management, practicing in the era of the electronic health record offers opportunities, if not imperatives, for pathologists to take on new and "transformative" professional and leadership roles for the organizations they serve. Experience indicates that clinicians will perceive pathologists and laboratories as responsible for all aspects of laboratory testing and information management, including order entry and results reporting, even though such functions may fall beyond the control of the laboratory. As described and expanded upon in the previous 4 articles of this series, the use of electronic health records dictates changes in how clinicians interact with laboratory information. In this environment, pathologists are uniquely positioned to act as the stewards for laboratory information in electronic health records and throughout health care organizations.

The 2013 symposium on pathology data integration and clinical decision support and the current state of field.

BACKGROUND: Pathologists and informaticians are becoming increasingly interested in electronic clinical decision support for pathology, laboratory medicine and clinical diagnosis. Improved decision support may optimize laboratory test selection, improve test result interpretation and permit the extraction of enhanced diagnostic information from existing laboratory data. Nonetheless, the field of pathology decision support is still developing. To facilitate the exchange of ideas and preliminary studies, we convened a symposium entitled: Pathology data integration and clinical decision support. METHODS: The symposium was held at the Massachusetts General Hospital, on May 10, 2013. Participants were selected to represent diverse backgrounds and interests and were from nine different institutions in eight different states. RESULTS: The day included 16 plenary talks and three panel discussions, together covering four broad areas. Summaries of each presentation are included in this manuscript. CONCLUSIONS: A number of recurrent themes emerged from the symposium. Among the most pervasive was the dichotomy between diagnostic data and diagnostic information, including the opportunities that laboratories may have to use electronic systems and algorithms to convert the data they generate into more useful information. Differences between human talents and computer abilities were described; well-designed symbioses between humans and computers may ultimately optimize diagnosis. Another key theme related to the unique needs and challenges in providing decision support for genomics and other emerging diagnostic modalities. Finally, many talks relayed how the barriers to bringing decision support toward reality are primarily personnel, political, infrastructural and administrative challenges rather than technological limitations.