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.

Limited utilization of serologic testing in patients undergoing duodenal biopsy for celiac disease.

BACKGROUND: Clinical algorithms for the workup of celiac disease often recommend the use of serologic assays for initial screening, followed by duodenal biopsy for histologic confirmation. However, the majority of duodenal biopsies submitted to pathology for "rule out celiac" are negative. The objective of this study was to determine the underlying causes for this low diagnostic yield. METHODS: We performed a retrospective review of pathology reports from 1432 consecutive duodenal biopsies submitted for pathologic assessment to "rule out celiac" and correlated biopsy results with results for concurrent serologic testing for celiac autoantibodies. RESULTS: The majority of patients had no record of serologic testing prior to biopsy, and evidence of positive serology results was found in only 5% of patients. Most duodenal biopsies were submitted as part of a multi-site GI sampling strategy that included biopsies from other locations. In this context, serologic results correlated with the likelihood of significant duodenal and non-duodenal findings, and were also helpful in evaluating patients with indeterminate duodenal histology. CONCLUSIONS: The presence of a positive screening test for celiac autoantibodies does not appear to be a major driver in the decision to submit duodenal biopsies for evaluation of celiac disease, which accounts for the low incidence of findings in these samples. In patients where celiac serology testing was performed, the results were a good predictor of the likelihood of findings on biopsy.

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.

Telepathology for patient care: what am I getting myself into?

The vast advancements in telecommunications and converting medical information to a digital format have increased the number of applications within telemedicine. Telepathology, in simplest terms, is the practice of formally rendering a pathologic diagnosis based upon examination of an image rather than of a glass slide through traditional microscopy. The use of telepathology for clinical patient care has so far been limited to relatively few large academic institutions. Although a number of challenges remain, there is increasing demand for the use of information technology in pathology as a whole owing to the expansion of health care networks and the opportunity to enhance the quality of service delivered to patients. The software used to acquire, display, and manage digital images for clinical patient care may be subject to national and federal regulations just as is any other electronic information system. Despite the barriers, telepathology systems possess the capability to help manage pathology cases on a global scale, improve laboratory workload distribution, increase standardization of practice and enable new classes of ancillary studies to facilitate diagnosis and education even in the most remote parts of the earth.

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.

Poor interobserver agreement in the distinction of high-grade dysplasia and adenocarcinoma in pretreatment Barrett's esophagus biopsies.

OBJECTIVE: Grading Barrett's dysplasia at the lower end of the metaplasia-dysplasia spectrum (negative, indefinite, and low-grade dysplasia) suffers from poor interobserver agreement, even among gastrointestinal pathologists. Data evaluating interobserver agreement in Barrett's mucosal biopsies with changes at the upper end of the dysplasia spectrum (high-grade dysplasia, intramucosal, and submucosal adenocarcinoma) have not been published. The accurate categorization of pretreatment biopsies drives therapeutic decision making, but if the diagnostic distinction between cancer and high-grade dysplasia in Barrett's biopsies is inconsistent, then the use of these diagnoses to make management decisions is suspect. To this end, our aim was to assess interobserver reproducibility among a group of gastrointestinal pathologists in the interpretation of preresection biopsies. METHODS: All study pathologists agreed upon the histologic criteria distinguishing four diagnostic categories, including high-grade dysplasia; high-grade dysplasia with marked distortion of glandular architecture, cannot exclude intramucosal adenocarcinoma; intramucosal adenocarcinoma; and submucosally invasive adenocarcinoma. The histologic criteria were used to independently review preresection biopsies from 163 consecutive Barrett's esophagus patients with at least high-grade dysplasia who ultimately underwent esophagectomy. Reviewers recorded the specific histologic criteria used to categorize each case and Kappa statistics were calculated to assess interobserver agreement. RESULTS: Using kappa statistics, the overall agreement was only fair (kappa= 0.30). Agreement for high-grade dysplasia was moderate (kappa= 0.47), while agreement for high-grade dysplasia with marked architectural distortion, cannot exclude intramucosal adenocarcinoma and intramucosal adenocarcinoma were only fair (kappa= 0.21 and 0.30, respectively) and agreement for submucosal adenocarcinoma was poor (kappa= 0.14). CONCLUSIONS: The overall poor interobserver reproducibility among gastrointestinal pathologists who see a high volume of Barrett's cases calls into question treatment regimens based on the assumption that high-grade dysplasia, intramucosal adenocarcinoma, and submucosal adenocarcinoma can reliably be distinguished in biopsy specimens.

Medical laboratory informatics.

Laboratory informatics is the application of computers and information systems to information management in the pathology laboratory. Effective information management is crucial to the success of pathologists and laboratorians. Informatics has become one of the key pillars of pathology, and the requirement for skilled informaticists in the laboratory has quickly grown. This article provides a wide-ranging review of pertinent aspects of laboratory informatics, and deals with important technical and management processes. Topics covered include personal computing, networks, databases, fundamentals and advanced functions of the laboratory information system, interfaces and standards, digital imaging, coding, hospital information systems and electronic medical records.

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.

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.

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.

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.

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.