Bruce A. Beckwith

Validating Whole Slide Imaging for Diagnostic Purposes in Pathology: Guideline from the College of American Pathologists Pathology and Laboratory Quality Center

CONTEXT There is increasing interest in using whole slide imaging (WSI) for diagnostic purposes (primary and/or consultation). An important consideration is whether WSI can safely replace conventional light microscopy as the method by which pathologists review histologic sections, cytology slides, and/or hematology slides to render diagnoses. Validation of WSI is crucial to ensure that diagnostic performance based on digitized slides is at least equivalent to that of glass slides and light microscopy. Currently, there are no standard guidelines regarding validation of WSI for diagnostic use. OBJECTIVE To recommend validation requirements for WSI systems to be used for diagnostic purposes. DESIGN The College of American Pathologists Pathology and Laboratory Quality Center convened a nonvendor panel from North America with expertise in digital pathology to develop these validation recommendations. A literature review was performed in which 767 international publications that met search term requirements were identified. Studies outside the scope of this effort and those related solely to technical elements, education, and image analysis were excluded. A total of 27 publications were graded and underwent data extraction for evidence evaluation. Recommendations were derived from the strength of evidence determined from 23 of these published studies, open comment feedback, and expert panel consensus. RESULTS Twelve guideline statements were established to help pathology laboratories validate their own WSI systems intended for clinical use. Validation of the entire WSI system, involving pathologists trained to use the system, should be performed in a manner that emulates the laboratorys actual clinical environment. It is recommended that such a validation study include at least 60 routine cases per application, comparing intraobserver diagnostic concordance between digitized and glass slides viewed at least 2 weeks apart. It is important that the validation process confirm that all material present on a glass slide to be scanned is included in the digital image. CONCLUSIONS Validation should demonstrate that the WSI system under review produces acceptable digital slides for diagnostic interpretation. The intention of validating WSI systems is to permit the clinical use of this technology in a manner that does not compromise patient care.

Development and evaluation of an open source software tool for deidentification of pathology reports

BackgroundElectronic medical records, including pathology reports, are often used for research purposes. Currently, there are few programs freely available to remove identifiers while leaving the remainder of the pathology report text intact. Our goal was to produce an open source, Health Insurance Portability and Accountability Act (HIPAA) compliant, deidentification tool tailored for pathology reports. We designed a three-step process for removing potential identifiers. The first step is to look for identifiers known to be associated with the patient, such as name, medical record number, pathology accession number, etc. Next, a series of pattern matches look for predictable patterns likely to represent identifying data; such as dates, accession numbers and addresses as well as patient, institution and physician names. Finally, individual words are compared with a database of proper names and geographic locations. Pathology reports from three institutions were used to design and test the algorithms. The software was improved iteratively on training sets until it exhibited good performance. 1800 new pathology reports were then processed. Each report was reviewed manually before and after deidentification to catalog all identifiers and note those that were not removed.Results1254 (69.7 %) of 1800 pathology reports contained identifiers in the body of the report. 3439 (98.3%) of 3499 unique identifiers in the test set were removed. Only 19 HIPAA-specified identifiers (mainly consult accession numbers and misspelled names) were missed. Of 41 non-HIPAA identifiers missed, the majority were partial institutional addresses and ages. Outside consultation case reports typically contain numerous identifiers and were the most challenging to deidentify comprehensively. There was variation in performance among reports from the three institutions, highlighting the need for site-specific customization, which is easily accomplished with our tool.ConclusionWe have demonstrated that it is possible to create an open-source deidentification program which performs well on free-text pathology reports.

Artifactual Hyperbilirubinemia Due to Paraprotein Interference

CONTEXT Paraprotein interference in automated chemistry is uncommon. We describe 2 patients with paraproteinemia and elevated total bilirubin levels measured erroneously using the Roche total bilirubin assay. OBJECTIVES To explain the mechanism of this artifactual hyperbilirubinemia and to determine its frequency in patients with monoclonal or increased immunoglobulins. MATERIALS AND METHODS The assay was performed manually using serum from 2 index patients and from control patients (without M proteins). Total bilirubin was also determined using another manufacturers assay. A prospective study was then undertaken using serum from 100 consecutive patients with various monoclonal gammopathies and from 13 patients with polyclonal hypergammaglobulinemia and cryoglobulins. For all patients, serum immunoglobulin (Ig) G, IgA, IgM, total and direct bilirubin, creatinine, and a direct spectrophotometric assessment of icterus were measured. RESULTS After the addition of assay reagents, a white precipitate formed in the reaction mixtures containing serum from the index patients, but not in other samples. This turbidity, rather than the expected color change to pink, increased the absorbance and falsely elevated the total bilirubin value. Serum from both index patients was anicteric, their direct bilirubin measurements were unaffected, and total bilirubin measured using an alternate assay was normal. Among the 113 patients studied, no additional spurious total bilirubin values were detected. CONCLUSION Paraprotein interference with the Roche automated total bilirubin assay is caused by precipitate formation. This interference is rare and probably idiosyncratic. Spurious hyperbilirubinemia from paraprotein interference may cause clinical confusion. If artifactual elevation of total bilirubin is suspected, the laboratory should examine the specimen for icterus (manually or by spectrophotometry) or measure total bilirubin using a different method.

Standardizing the use of whole slide images in digital pathology

Whole slide imaging/images (WSI) offers promising new perspectives for digital pathology. We launched an initiative in the anatomic pathology (AP) domain of integrating the healthcare enterprise (IHE) to define standards-based informatics transactions for integrating AP information and WSI. The IHE integration and content profiles developed as a result of this initiative successfully support the basic image acquisition and reporting processes in AP laboratories and provide a standard solution for sharing or exchanging structured AP reports in which observations can be explicitly bound to WSI or to regions of interest (ROI) in images.

Recent advances in standards for Collaborative Digital Anatomic Pathology.

ContextCollaborative Digital Anatomic Pathology refers to the use of information technology that supports the creation and sharing or exchange of information, including data and images, during the complex workflow performed in an Anatomic Pathology department from specimen reception to report transmission and exploitation. Collaborative Digital Anatomic Pathology can only be fully achieved using medical informatics standards. The goal of the international integrating the Healthcare Enterprise (IHE) initiative is precisely specifying how medical informatics standards should be implemented to meet specific health care needs and making systems integration more efficient and less expensive.ObjectiveTo define the best use of medical informatics standards in order to share and exchange machine-readable structured reports and their evidences (including whole slide images) within hospitals and across healthcare facilities.MethodsSpecific working groups dedicated to Anatomy Pathology within multiple standards organizations defined standard-based data structures for Anatomic Pathology reports and images as well as informatic transactions in order to integrate Anatomic Pathology information into the electronic healthcare enterprise.ResultsThe DICOM supplements 122 and 145 provide flexible object information definitions dedicated respectively to specimen description and Whole Slide Image acquisition, storage and display. The content profile “Anatomic Pathology Structured Report” (APSR) provides standard templates for structured reports in which textual observations may be bound to digital images or regions of interest. Anatomic Pathology observations are encoded using an international controlled vocabulary defined by the IHE Anatomic Pathology domain that is currently being mapped to SNOMED CT concepts.ConclusionRecent advances in standards for Collaborative Digital Anatomic Pathology are a unique opportunity to share or exchange Anatomic Pathology structured reports that are interoperable at an international level. The use of machine-readable format of APSR supports the development of decision support as well as secondary use of Anatomic Pathology information for epidemiology or clinical research.

Protein Electrophoresis and Immunoglobulin Analysis in HIV-Infected Patients

We studied the prevalence and nature of immunoglobulin abnormalities in HIV-1-infected patients in the era of highly active antiretroviral therapy. Protein electrophoreses (PEP) were performed on and quantitative immunoglobulin levels obtained in samples from 320 consecutive HIV-1-infected patients. Samples with possible PEP abnormalities underwent immunofixation. The PEP pattern was normal in 83.8% of samples, 8.1% had subtle oligoclonal banding, and 4.4% had a low-concentration (<5% of total protein) monoclonal band. Hypogammaglobulinemia and polyclonal hypergammaglobulinemia accounted for 1.9% each. In multivariate analysis, younger age (odds ratio [OR], 1.06 with each decreasing year of life; 95% confidence interval [CI], 1.02-1.11; P = .016), female sex (OR, 2.4; 95% CI, 1.13-5.11; P = .02), viral load (OR, 1.50 with each increasing logarithmic viral load of 1.0; 95% CI, 1.14-1.98; P = .004), and CD4 cell count (> or =350 vs <350/microL [0.35 x 10(9)/L]) (OR, 2.71; 95% CI, 1.09-6.75; P = .032) were associated with monoclonal or oligoclonal banding. These results suggest that younger HIV-1-infected patients with a more robust immune system (higher CD4 cell count), which is stimulated by uncontrolled viremia, are most likely to have an augmented B-cell response to HIV infection. One manifestation of this B-cell response is low-concentration monoclonal banding in 4.4% of the patients studied.

Analysis of On-Line Clinical Laboratory Manuals and Practical Recommendations

CONTEXT On-line clinical laboratory manuals are a valuable resource for medical professionals. To our knowledge, no recommendations currently exist for their content or design. OBJECTIVE To analyze publicly accessible on-line clinical laboratory manuals and to propose guidelines for their content. DESIGN We conducted an Internet search for clinical laboratory manuals written in English with individual test listings. Four individual test listings in each manual were evaluated for 16 data elements, including sample requirements, test methodology, units of measure, reference range, and critical values. Web sites were also evaluated for supplementary information and search functions. RESULTS We identified 48 on-line laboratory manuals, including 24 academic or community hospital laboratories and 24 commercial or reference laboratories. All manuals had search engines and/or test indices. No single manual contained all 16 data elements evaluated. An average of 8.9 (56%) elements were present (range, 4-14). Basic sample requirements (specimen and volume needed) were the elements most commonly present (98% of manuals). The frequency of the remaining data elements varied from 10% to 90%. CONCLUSIONS On-line clinical laboratory manuals originate from both hospital and commercial laboratories. While most manuals were user-friendly and contained adequate specimen-collection information, other important elements, such as reference ranges, were frequently absent. To ensure that clinical laboratory manuals are of maximal utility, we propose the following 13 data elements be included in individual test listings: test name, synonyms, test description, test methodology, sample requirements, volume requirements, collection guidelines, transport guidelines, units of measure, reference range, critical values, test availability, and date of latest revision.

A core curriculum for clinical fellowship training in pathology informatics

Background: In 2007, our healthcare system established a clinical fellowship program in Pathology Informatics. In 2010 a core didactic course was implemented to supplement the fellowship research and operational rotations. In 2011, the course was enhanced by a formal, structured core curriculum and reading list. We present and discuss our rationale and development process for the Core Curriculum and the role it plays in our Pathology Informatics Fellowship Training Program. Materials and Methods: The Core Curriculum for Pathology Informatics was developed, and is maintained, through the combined efforts of our Pathology Informatics Fellows and Faculty. The curriculum was created with a three-tiered structure, consisting of divisions, topics, and subtopics. Primary (required) and suggested readings were selected for each subtopic in the curriculum and incorporated into a curated reading list, which is reviewed and maintained on a regular basis. Results: Our Core Curriculum is composed of four major divisions, 22 topics, and 92 subtopics that cover the wide breadth of Pathology Informatics. The four major divisions include: (1) Information Fundamentals, (2) Information Systems, (3) Workflow and Process, and (4) Governance and Management. A detailed, comprehensive reading list for the curriculum is presented in the Appendix to the manuscript and contains 570 total readings (current as of March 2012). Discussion: The adoption of a formal, core curriculum in a Pathology Informatics fellowship has significant impacts on both fellowship training and the general field of Pathology Informatics itself. For a fellowship, a core curriculum defines a basic, common scope of knowledge that the fellowship expects all of its graduates will know, while at the same time enhancing and broadening the traditional fellowship experience of research and operational rotations. For the field of Pathology Informatics itself, a core curriculum defines to the outside world, including departments, companies, and health systems considering hiring a pathology informatician, the core knowledge set expected of a person trained in the field and, more fundamentally, it helps to define the scope of the field within Pathology and healthcare in general.

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.

Standards for Digital Pathology and Whole Slide Imaging

In this chapter, the goal is to discuss various types of standards which are relevant to digital pathology images, especially whole slide imaging (WSI), discussing the role they play as well as their current status. We will consider standards primarily in relation to their use in the clinical practice of pathology. In the last ten years much work has been done to extend the DICOM medical imaging standard to include additional metadata relevant to pathology images and specimens as well as to accommodate the special requirements of whole slide microscopic images. This work, along with efforts underway in other organizations, such as HL7 and Integrating the Healthcare Enterprise are laying the foundations for standards based interoperability in pathology that should allow for integration of digital imaging into the clinical workflow of pathologists.