Seung Park

The history of pathology informatics: A global perspective

Pathology informatics has evolved to varying levels around the world. The history of pathology informatics in different countries is a tale with many dimensions. At first glance, it is the familiar story of individuals solving problems that arise in their clinical practice to enhance efficiency, better manage (e.g., digitize) laboratory information, as well as exploit emerging information technologies. Under the surface, however, lie powerful resource, regulatory, and societal forces that helped shape our discipline into what it is today. In this monograph, for the first time in the history of our discipline, we collectively perform a global review of the field of pathology informatics. In doing so, we illustrate how general far-reaching trends such as the advent of computers, the Internet and digital imaging have affected pathology informatics in the world at large. Major drivers in the field included the need for pathologists to comply with national standards for health information technology and telepathology applications to meet the scarcity of pathology services and trained people in certain countries. Following trials by a multitude of investigators, not all of them successful, it is apparent that innovation alone did not assure the success of many informatics tools and solutions. Common, ongoing barriers to the widespread adoption of informatics devices include poor information technology infrastructure in undeveloped areas, the cost of technology, and regulatory issues. This review offers a deeper understanding of how pathology informatics historically developed and provides insights into what the promising future might hold.

Anatomic pathology laboratory information systems: a review.

The modern anatomic pathology laboratory depends on a reliable information infrastructure to register specimens, record gross and microscopic findings, regulate laboratory workflow, formulate and sign out report(s), disseminate them to the intended recipients across the whole health system, and support quality assurance measures. This infrastructure is provided by Anatomic Pathology Laboratory Information Systems (APLIS), which have evolved over decades and now are beginning to support evolving technologies like asset tracking and digital imaging. As digital pathology transitions from “the way of the future” to “the way of the present,” the APLIS continues to be one of the key effective enablers of the scope and practice of pathology. In this review, we discuss the evolution, necessary components, architecture and functionality of the APLIS that are crucial to today’s practicing pathologist and address the demands of emerging trends on the future APLIS.

Handheld computing in pathology

Handheld computing has had many applications in medicine, but relatively few in pathology. Most reported uses of handhelds in pathology have been limited to experimental endeavors in telemedicine or education. With recent advances in handheld hardware and software, along with concurrent advances in whole-slide imaging (WSI), new opportunities and challenges have presented themselves. This review addresses the current state of handheld hardware and software, provides a history of handheld devices in medicine focusing on pathology, and presents future use cases for such handhelds in pathology.

Workflow Organization in Pathology

New technologies, analytic techniques, and computer-assisted diagnosis algorithms will change the way pathologists and clinicians interact with and use clinical data. Simultaneously, the artisanal nature of the culture and clinical practice of medicine have made them resistant to change. An understanding of workflow science will help pathologists prepare for the changes that lie ahead in anatomic and clinical pathology, better care for patients, and make better and more respectful use of existing human and other resources. This article provides a primer on workflow science, including historical perspective, review of current literature, and extrapolation of future trends.

Electronic Medical Records

An electronic health record (EHR), also known as an electronic medical record (EMR), is a patient’s medical chart accessed and modified in digital format. While an EMR is under the direct control of a hospital system or health care organization, a personal health record (PHR) is controlled by the patient. Increasingly more health care facilities and clinical practices are using EMRs. In the USA, EMR adoption has been accelerated by federal legislation that enforces clinicians to achieve “meaningful use” with certified EMRs. As a result, physicians are progressively placing more electronic orders for lab tests in the EMR. They also prefer to look up their patients’ results in the EMR. Since this paperless clinical practice is beginning to impact cytology, it is essential for cytopathology laboratories to be aware of this informatics trend.

Pathology informatics fellowship retreats: The use of interactive scenarios and case studies as pathology informatics teaching tools

Background: Last year, our pathology informatics fellowship added informatics-based interactive case studies to its existing educational platform of operational and research rotations, clinical conferences, a common core curriculum with an accompanying didactic course, and national meetings. Methods: The structure of the informatics case studies was based on the traditional business school case study format. Three different formats were used, varying in length from short, 15-minute scenarios to more formal multiple hour-long case studies. Case studies were presented over the course of three retreats (Fall 2011, Winter 2012, and Spring 2012) and involved both local and visiting faculty and fellows. Results: Both faculty and fellows found the case studies and the retreats educational, valuable, and enjoyable. From this positive feedback, we plan to incorporate the retreats in future academic years as an educational component of our fellowship program. Conclusions: Interactive case studies appear to be valuable in teaching several aspects of pathology informatics that are difficult to teach in more traditional venues (rotations and didactic class sessions). Case studies have become an important component of our fellowship′s educational platform.

Creation of a Queryable Toxicology Database Available to Forensic Pathologists

Purpose Forensic pathologists typically depend upon case reports or published compilations of case reports when determining the role a drug may have played in death. Case reports may provide a helpful range, but the cases reported are typically few and often lack information on circumstances surrounding death and autopsy findings. A searchable database recording circumstances, autopsy findings, drug concentrations, and the cause and manner of death would allow forensic pathologists to compare a specific case to similar cases, facilitating evaluation and interpretation of toxicology results. Method This project uses data extracted by computer programs from over 18 000 computer files of autopsy and toxicology reports generated between 2004 and 2012. Using PHP Hypertext Preprocessor and MariaDB, a relational database, we developed a webpage that stores the data and allows for complex queries. Results Users can search for cases by specifying drugs and medical conditions, demographics, height, body mass, and manner of death. The number of cases with a given drug for this eight-year span from one office is comparable to the numbers reported in compilations of case reports. Conclusion Our webpage enables a pathologist evaluating a case to search the database for cases with similar circumstances and findings. New cases are easily added to the database as they are completed. The database allows other institutions to contribute data and records the data source, which increases the usefulness of the database even more. This database provides pathologists a powerful new tool for the evaluation of toxicology findings in their practice.

Computer Extraction of Data from Autopsy and Toxicology Reports

Purpose Forensic autopsies contain a wealth of information ranging from toxicology results to organ masses. Extracting data by hand from years of reports is tedious. We report a computer program that extracts information from reports in Word, WordPerfect, or Portable Document Format (PDF). Methods The program consists of three Excel macros, written in Visual Basic for Applications, which extract information from autopsy and toxicology reports. The user selects a macro, chooses a folder of documents, and inputs key words to guide the search. The macros open each document in the folder sequentially, extract the desired values automatically, and enter the data into the respective case numbers row in a spreadsheet. Another macro combines data from the separate autopsy and toxicology reports by matching the unique case number. Extraction of PDF files is a two-step process involving batch conversion from PDF format to Word with subsequent extraction. Results We have developed a set of macros that extract data from autopsy and toxicology reports, such as age, race, height, manner and cause of death, and drug concentrations. Key words included autopsy headings, such as “Cardiovascular System” and units of measure such as “inches” or “pound.” We analyzed roughly 7000 cases and kept 3455 cases. Conclusions Our system rapidly procures data and places the information in a standardized format. This program will be hosted on our toxicology webpage for others to use. Future goals include combining data from other institutions and uploading the data to an online, queryable database.

Alchemy: A web 2.0 real-time quality assurance platform for human immunodeficiency Virus, hepatitis C Virus, and BK Virus quantitation assays

Background: The molecular diagnostics laboratory faces the challenge of improving test turnaround time (TAT). Low and consistent TATs are of great clinical and regulatory importance, especially for molecular virology tests. Laboratory information systems (LISs) contain all the data elements necessary to do accurate quality assurance (QA) reporting of TAT and other measures, but these reports are in most cases still performed manually: a time-consuming and error-prone task. The aim of this study was to develop a web-based real-time QA platform that would automate QA reporting in the molecular diagnostics laboratory at our institution, and minimize the time expended in preparing these reports. Methods: Using a standard Linux, Nginx, MariaDB, PHP stack virtual machine running atop a Dell Precision 5810, we designed and built a web-based QA platform, code-named Alchemy. Data files pulled periodically from the LIS in comma-separated value format were used to autogenerate QA reports for the human immunodeficiency virus (HIV) quantitation, hepatitis C virus (HCV) quantitation, and BK virus (BKV) quantitation. Alchemy allowed the user to select a specific timeframe to be analyzed and calculated key QA statistics in real-time, including the average TAT in days, tests falling outside the expected TAT ranges, and test result ranges. Results: Before implementing Alchemy, reporting QA for the HIV, HCV, and BKV quantitation assays took 45–60 min of personnel time per test every month. With Alchemy, that time has decreased to 15 min total per month. Alchemy allowed the user to select specific periods of time and analyzed the TAT data in-depth without the need of extensive manual calculations. Conclusions: Alchemy has significantly decreased the time and the human error associated with QA report generation in our molecular diagnostics laboratory. Other tests will be added to this web-based platform in future updates. This effort shows the utility of informatician-supervised resident/fellow programming projects as learning opportunities and workflow improvements in the molecular laboratory.

Application of Lean Principles to Preanalytic and Analytic Processes

Quality assurance (QA) efforts in the anatomical pathology (AP) laboratory today mainly involve analysis of batched assembly line-like workflow. Furthermore, the data that are generated are often hard to access due to limited laboratory information system (LIS) functionality as well as lack of LIS interoperability with interconnecting information systems. There are a number of “middleware” systems that offer business intelligence enabling extraction of valuable LIS data. Converting the anatomical laboratory workflow to a Lean process and using modern informatics tools such as bar-coded tracking systems in the AP lab results in more standardized workflow with automated processes leading to a reduction in errors, particularly in the preanalytical and analytical phases of the surgical pathology specimen life cycle. Creating auditable events in the workflow using barcodes and other technologies permits real-time data capture directly into the LIS that is available for real-time QA monitoring. Additional informatics tools such as synoptic reporting, computerized provider order entry (CPOE), and LIS-driven presign out random QA help to improve quality and reduce errors in AP.