Proceedings of the Association for Pathology Informatics Bootcamp 2022.

The Pathology Informatics Bootcamp, held annually at the Pathology Informatics Summit, provides pathology trainees with essential knowledge in the rapidly evolving field of Pathology Informatics. With a focus on data analytics, data science, and data management in 2022, the bootcamp addressed the growing importance of data analysis in pathology and laboratory medicine practice. The expansion of data-related subjects in Pathology Informatics Essentials for Residents (PIER) and the Clinical Informatics fellowship examinations highlights the increasing significance of these skills in pathology practice in particular and medicine in general.

Laboratory Test Names Matter: A Survey on What Works and What Doesn't Work for Orders and Results.

Context.—: Health care providers were surveyed to determine their ability to correctly decipher laboratory test names and their preferences for laboratory test names and result displays.

Objective.

Comprehensive Genomic Profiling of High-Risk Pediatric Cancer Patients Has a Measurable Impact on Clinical Care.

Purpose: Profiling of pediatric cancers through deep sequencing of large gene panels and whole exomes is rapidly being adopted in many clinical settings. However, the most impactful approach to genomic profiling of pediatric cancers remains to be defined.

Methods: We conducted a prospective precision medicine trial, using whole-exome sequencing of tumor and germline tissue and whole-transcriptome sequencing (RNA Seq) of tumor tissue to characterize the mutational landscape of 127 tumors from 126 unique patients across the spectrum of pediatric brain tumors, hematologic malignancies, and extracranial solid tumors.

Influence of user-centered clinical decision support on pediatric blood product ordering errors.

Background: Children are at increased risk from transfusion-related medical errors. Clinical decision support (CDS) can enhance pediatric providers' decision-making regarding transfusion practices including indications, volume, rate, and special processing instructions. Our objective was to use CDS in a pediatric health system to reduce:blood product-related safety events from ordering errors;special processing ordering errors for patients with T-cell dysfunction, sickle cell disease (SCD), or thalassemia;transfusions administered faster than 5 mL/kg/h.

Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group.

The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as several other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians, and patients in the ability to generate, communicate, consume, and use genomic test results.

A Survey of LOINC Code Selection Practices Among Participants of the College of American Pathologists Coagulation (CGL) and Cardiac Markers (CRT) Proficiency Testing Programs.

Context.—: Biomedical terminologies such as Logical Observation Identifiers, Names, and Codes (LOINC) were developed to enable interoperability of health care data between disparate health information systems to improve patient outcomes, public health, and research activities.

Objective.

Expanding the Scope of The Journal of Molecular Diagnostics to the Informatics Subdivision of the Association for Molecular Pathology.

This editorial describes the expanded scope of The Journal of Molecular Diagnostics, to include informatics-based articles.

Host Genome Variation is Associated with Neurocognitive Outcome in Survivors of Pediatric Medulloblastoma.

Host genome analysis is a promising source of predictive information for long-term morbidity in cancer survivors. However, studies on genetic predictors of long-term outcome, particularly neurocognitive function following chemoradiation in pediatric oncology, are limited. Here, we evaluated variation in host genome of long-term survivors of medulloblastoma and its association with neurocognitive outcome.

A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health Record.

Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. Although text documents are useful for human readability and initial use, they are not conducive for data retrieval and reuse.

Considerations for Genomic Data Privacy and Security when Working in the Cloud.

Next-generation sequencing produces large amounts of data. The complexity and data management issues associated with next-generation sequencing have led many laboratories to turn to cloud services, especially when internal information technology infrastructure is inadequate to support data requirements. In addition, public cloud repositories of variants are being increasingly utilized, and their data sets are being populated through crowdsourcing submissions of human genetic variation identified within laboratories.

Twenty Years of Digital Pathology: An Overview of the Road Travelled, What is on the Horizon, and the Emergence of Vendor-Neutral Archives.

Almost 20 years have passed since the commercial introduction of whole-slide imaging (WSI) scanners. During this time, the creation of various WSI devices with the ability to digitize an entire glass slide has transformed the field of pathology. Parallel advances in computational technology and storage have permitted rapid processing of large-scale WSI datasets.

Laboratory Information Systems and Instrument Software Lack Basic Functionality for Molecular Laboratories.

Laboratory information systems (LISs) have some basic functionality necessary for molecular workflow that is glaringly absent. This study determined functionality gaps of LISs in molecular laboratories and the associated impact to workflow, efficiency, and security by collecting anonymous survey data from clinical laboratory professionals. A 34-question survey (30 required + 4 optional) was compiled using an online survey tool.

The Impact of Disruption of the Care Delivery System by Commercial Laboratory Testing in a Children's Health Care System.

Context.—: Disruption of outpatient laboratory services by routing the samples to commercial reference laboratories may seem like a cost-saving measure by the payers, but results in hidden costs in quality and resources to support this paradigm.

Objective.

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.

Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines.

Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment.

Context: -Next-generation sequencing (NGS) is revolutionizing the discipline of laboratory medicine, with a deep and direct impact on patient care. Although it empowers clinical laboratories with unprecedented genomic sequencing capability, NGS has brought along obvious and obtrusive informatics challenges. Bioinformatics and clinical informatics are separate disciplines with typically a small degree of overlap, but they have been brought together by the enthusiastic adoption of NGS in clinical laboratories.

Standards for Clinical Grade Genomic Databases.

Context: Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation.

Computational Pathology: A Path Ahead.

Context: We define the scope and needs within the new discipline of computational pathology, a discipline critical to the future of both the practice of pathology and, more broadly, medical practice in general.

Objective: To define the scope and needs of computational pathology.

Data Sources: A meeting was convened in Boston, Massachusetts, in July 2014 prior to the annual Association of Pathology Chairs meeting, and it was attended by a variety of pathologists, including individuals highly invested in pathology informatics as well as chairs of pathology departments.

Reduced red blood cell transfusion in cardiothoracic surgery after implementation of a novel clinical decision support tool.

Background: Packed red blood cell (PRBC) transfusion can increase short- and long-term adverse outcomes and health care costs. We compared the transfusion practices in cardiothoracic surgery before and after implementation of a novel clinical decision support (CDS) tool.

Study Design: The transfusion CDS tool was implemented within computerized provider order entry of a multi-institutional urban hospital system in September 2012.

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.

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.