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Pathobiology : Journal of... 2016The future paradigm of pathology will be digital. Instead of conventional microscopy, a pathologist will perform a diagnosis through interacting with images on computer... (Review)
Review
The future paradigm of pathology will be digital. Instead of conventional microscopy, a pathologist will perform a diagnosis through interacting with images on computer screens and performing quantitative analysis. The fourth generation of virtual slide telepathology systems, so-called virtual microscopy and whole-slide imaging (WSI), has allowed for the storage and fast dissemination of image data in pathology and other biomedical areas. These novel digital imaging modalities encompass high-resolution scanning of tissue slides and derived technologies, including automatic digitization and computational processing of whole microscopic slides. Moreover, automated image analysis with WSI can extract specific diagnostic features of diseases and quantify individual components of these features to support diagnoses and provide informative clinical measures of disease. Therefore, the challenge is to apply information technology and image analysis methods to exploit the new and emerging digital pathology technologies effectively in order to process and model all the data and information contained in WSI. The final objective is to support the complex workflow from specimen receipt to anatomic pathology report transmission, that is, to improve diagnosis both in terms of pathologists' efficiency and with new information. This article reviews the main concerns about and novel methods of digital pathology discussed at the latest workshop in the field carried out within the European project AIDPATH (Academia and Industry Collaboration for Digital Pathology).
Topics: Humans; Image Interpretation, Computer-Assisted; Image Processing, Computer-Assisted; Microscopy; Telepathology
PubMed: 27100343
DOI: 10.1159/000443482 -
Modern Pathology : An Official Journal... Dec 2022Artificial intelligence (AI) solutions that automatically extract information from digital histology images have shown great promise for improving pathological... (Review)
Review
Artificial intelligence (AI) solutions that automatically extract information from digital histology images have shown great promise for improving pathological diagnosis. Prior to routine use, it is important to evaluate their predictive performance and obtain regulatory approval. This assessment requires appropriate test datasets. However, compiling such datasets is challenging and specific recommendations are missing. A committee of various stakeholders, including commercial AI developers, pathologists, and researchers, discussed key aspects and conducted extensive literature reviews on test datasets in pathology. Here, we summarize the results and derive general recommendations on compiling test datasets. We address several questions: Which and how many images are needed? How to deal with low-prevalence subsets? How can potential bias be detected? How should datasets be reported? What are the regulatory requirements in different countries? The recommendations are intended to help AI developers demonstrate the utility of their products and to help pathologists and regulatory agencies verify reported performance measures. Further research is needed to formulate criteria for sufficiently representative test datasets so that AI solutions can operate with less user intervention and better support diagnostic workflows in the future.
Topics: Humans; Artificial Intelligence; Forecasting; Datasets as Topic; Pathology
PubMed: 36088478
DOI: 10.1038/s41379-022-01147-y -
Biopreservation and Biobanking Aug 2019Herein we propose an ambitious confrontation of the current coral reef crisis through the establishment of a "Coral Hospital." In an analogous manner to a human...
Herein we propose an ambitious confrontation of the current coral reef crisis through the establishment of a "Coral Hospital." In an analogous manner to a human hospital, "sick" corals will first be diagnosed either or in the hospital's diagnostic "clinic" such that the root cause of illness can be discerned (e.g., disease, high temperatures, or pollutant stress). Then, corals will be "treated" (when necessary) and allowed to "convalesce" in precisely controlled coral husbandry facilities. Upon "rehabilitation," the recovered corals will be returned to their home reef (if this reef was not found to have degraded), or, alternatively, to a site featuring oceanographic conditions favoring a high level of health, as determined by husbandry experiments performed in other hospital "wards." When possible, diagnostic data from the sick corals (i.e., the underlying cause of sickness) will be used to guide environmental remediation schemes aimed at promoting coral resilience in the ocean. If the home reef improves to an appreciable extent during the time the corals are "hospitalized," these corals could be replanted there upon rehabilitation. Regardless of the site of outplanting, recuperated corals will be monitored over time to validate the "quality of care" in the hospital. In the event that the home reefs suffer to such an extent that environmental mitigation is no longer possible, coral gametes will be collected and cryopreserved such that they may be fertilized, reared , and later reseeded once/if global marine conditions again permit coral survival.
Topics: Animals; Coral Reefs; Cryopreservation; Pathology, Molecular; Preservation, Biological
PubMed: 30907622
DOI: 10.1089/bio.2018.0137 -
The Journal of Molecular Diagnostics :... Dec 2023Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide... (Review)
Review
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
Topics: Humans; United States; Cell-Free Nucleic Acids; Pathology, Molecular; Consensus; Pathologists; Neoplasms
PubMed: 37806433
DOI: 10.1016/j.jmoldx.2023.09.004 -
The Medical Journal of Australia May 2020To estimate the carbon footprint of five common hospital pathology tests: full blood examination; urea and electrolyte levels; coagulation profile; C-reactive protein...
OBJECTIVES
To estimate the carbon footprint of five common hospital pathology tests: full blood examination; urea and electrolyte levels; coagulation profile; C-reactive protein concentration; and arterial blood gases.
DESIGN, SETTING
Prospective life cycle assessment of five pathology tests in two university-affiliated health services in Melbourne. We included all consumables and associated waste for venepuncture and laboratory analyses, and electricity and water use for laboratory analyses.
MAIN OUTCOME MEASURE
Greenhouse gas footprint, measured in carbon dioxide equivalent (CO e) emissions.
RESULTS
CO e emissions for haematology tests were 82 g/test (95% CI, 73-91 g/test) for coagulation profile and 116 g/test (95% CI, 101-135 g/test) for full blood examination. CO e emissions for biochemical tests were 0.5 g/test CO e (95% CI, 0.4-0.6 g/test) for C-reactive protein (low because typically ordered with urea and electrolyte assessment), 49 g/test (95% CI, 45-53 g/test) for arterial blood gas assessment, and 99 g/test (95% CI, 84-113 g/test) for urea and electrolyte assessment. Most CO e emissions were associated with sample collection (range, 60% for full blood examination to 95% for coagulation profile); emissions attributable to laboratory reagents and power use were much smaller.
CONCLUSION
The carbon footprint of common pathology tests was dominated by those of sample collection and phlebotomy. Although the carbon footprints were small, millions of tests are performed each year in Australia, and reducing unnecessary testing will be the most effective approach to reducing the carbon footprint of pathology. Together with the detrimental health and economic effects of unnecessary testing, our environmental findings should further motivate clinicians to test wisely.
Topics: Australia; Carbon Footprint; Humans; Pathology; Phlebotomy; Specimen Handling
PubMed: 32304240
DOI: 10.5694/mja2.50583 -
Emerging Topics in Life Sciences Dec 2022Cognitive dysfunction, particularly attentional impairment, is a core feature of many psychiatric disorders, yet is inadequately addressed by current treatments....
Cognitive dysfunction, particularly attentional impairment, is a core feature of many psychiatric disorders, yet is inadequately addressed by current treatments. Development of targeted therapeutics for the remediation of attentional deficits requires knowledge of underlying neurocircuit, cellular, and molecular mechanisms that cannot be directly assayed in the clinic. This level of detail can only be acquired by testing animals in cross-species translatable attentional paradigms, in combination with preclinical neuroscience techniques. The 5-choice continuous performance test (5C-CPT) and rodent continuous performance test (rCPT) represent the current state of the art of preclinical assessment of the most commonly studied subtype of attention: sustained attention, or vigilance. These tasks present animals with continuous streams of target stimuli to which they must respond (attention), in addition to non-target stimuli from which they must withhold responses (behavioral inhibition). The 5C-CPT and rCPT utilize the same measures as gold-standard clinical continuous performance tests and predict clinical efficacy of known pro-attentional drugs. They also engage common brain regions across species, although efforts to definitively establish neurophysiological construct validity are ongoing. The validity of these tasks as translational vigilance assessments enables their use in characterizing the neuropathology underlying attentional deficits of animal models of psychiatric disease, and in determining therapeutic potential of drugs ahead of clinical testing. Here, we briefly review the development and validation of such tests of attentional functioning, as well as the data they have generated pertaining to inattention, disinhibition, and impulsivity in psychiatric disorders.
Topics: Neuropathology; Neurophysiology; Neurosciences; Cognition
PubMed: 36408755
DOI: 10.1042/ETLS20220009 -
Critical Reviews in Clinical Laboratory... Aug 2019Large laboratory systems that include facilities with a range of capabilities and capacity are being created within consolidated healthcare systems. This paradigm shift... (Review)
Review
Large laboratory systems that include facilities with a range of capabilities and capacity are being created within consolidated healthcare systems. This paradigm shift is being driven by administrators and payers seeking to achieve resource efficiencies and to conform practice to the requirements of computerization as well as the adoption of electronic medical records. Although standardization and harmonization of practice improves patient care outcomes and operational efficiencies, administratively driven practice conformity (conformity to opinion) also has serious drawbacks and may lead to significant system failure. Juxtaposition of the distinct philosophical approaches of physicians and scientists (i.e. "professionalism") versus administrators and managers (i.e. "managerialism") towards bringing about conformity of the laboratory system inherently creates conflict. Despite an administrative edict to "perform all tests using the same methods" regardless of available "best practice" evidence to do so, medical/scientific input on these decisions is critical to ensure quality and safety of patient care. Innovation within the laboratory system, including the adoption of advanced technologies, practices, and personalized medicine initiatives, will be enabled by balancing the relentless drive by non-medical administration to meet "business" requirements, the medical responsibility to provide the best care possible, and customizing practice to meet individual patient care needs.
Topics: Clinical Laboratory Services; Decision Making; Humans; Pathology; Professionalism; Reference Standards; Risk Assessment
PubMed: 31060412
DOI: 10.1080/10408363.2019.1615408 -
Archives of Pathology & Laboratory... Jan 2022The presence of allogeneic contamination impacts clinical reporting in cancer next-generation sequencing specimens. Although consensus guidelines recommend the...
CONTEXT.—
The presence of allogeneic contamination impacts clinical reporting in cancer next-generation sequencing specimens. Although consensus guidelines recommend the identification of contaminating DNA as a part of quality control, implementation of contamination assessment methods in clinical molecular diagnostic laboratories has not been reported in the literature.
OBJECTIVE.—
To develop and implement a method to assess allogeneic contamination in clinical cancer next-generation sequencing specimens.
DESIGN.—
We describe a method to detect contamination based on the evaluation of single-nucleotide polymorphic sites from tumor-only specimens. We validate this method and apply it to a large cohort of cancer sequencing specimens.
RESULTS.—
Identification of specimen contamination was validated via in silico and in vitro mixtures, and reference range and reproducibility were established in a panel of normal specimens. The algorithm accurately detects an episode of systemic contamination due to reagent impurity. We prospectively applied this algorithm across 7571 clinical cancer specimens from a targeted next-generation sequencing panel, in which 262 specimens (3.5%) were predicted to be affected by greater than 5% contamination.
CONCLUSIONS.—
Allogeneic contamination can be inferred from intrinsic cancer next-generation sequencing data without paired normal sequencing. The adoption of this approach can be useful as a quality control measure for laboratories performing clinical next-generation sequencing.
Topics: High-Throughput Nucleotide Sequencing; Humans; Neoplasms; Pathology, Molecular; Polymorphism, Single Nucleotide; Reproducibility of Results
PubMed: 34015814
DOI: 10.5858/arpa.2020-0679-OA -
The Journal of Molecular Diagnostics :... May 2022Systematic implementation of bioinformatics resources for next generation sequencing (NGS)-based clinical testing is an arduous undertaking. One of the key challenges... (Review)
Review
Systematic implementation of bioinformatics resources for next generation sequencing (NGS)-based clinical testing is an arduous undertaking. One of the key challenges involves developing an ecosystem of information technology infrastructure for enabling scalable and reproducible bioinformatics services that is resilient and secure for handling genetic and protected health information, often embedded in an existing non-bioinformatics-oriented infrastructure. Container technology provides an ideal and infrastructure-agnostic solution for molecular laboratories developing and using bioinformatics pipelines, whether on-premise or using the cloud. A container is a technology that provides a consistent computational environment and enables reproducibility, scalability, and security when developing NGS bioinformatics analysis pipelines. Containers can increase the bioinformatics team's productivity by automating and simplifying the maintenance of complex bioinformatics resources, as well as facilitate validation, version control, and documentation necessary for clinical laboratory regulatory compliance. Although there is increasing popularity in adopting containers for developing NGS bioinformatics pipelines, there is wide variability and inconsistency in the usage of containers that may result in suboptimal performance and potentially compromise the security and privacy of protected health information. In this article, the authors highlight the current state and provide best or recommended practices for building, using containers in NGS bioinformatics solutions in a clinical setting with focus on scalability, optimization, maintainability, and data security.
Topics: Computational Biology; Ecosystem; High-Throughput Nucleotide Sequencing; Humans; Pathology, Molecular; Reproducibility of Results; Software
PubMed: 35189355
DOI: 10.1016/j.jmoldx.2022.01.006 -
American Journal of Clinical Pathology Sep 2022The aim of this study was to assess expectations of performance that exist in the marketplace for entry-level pathologists' assistants (PathAs), defined as recent...
OBJECTIVES
The aim of this study was to assess expectations of performance that exist in the marketplace for entry-level pathologists' assistants (PathAs), defined as recent graduates of a pathologists' assistant program on their first day of employment.
METHODS
A voluntary, anonymous survey was distributed to pathologist and PathA members of the American Society for Clinical Pathology by email. We assessed 98 professional activities of PathAs using a 5-point scale of expectations based on levels of trust placed in them. We also collected demographic information.
RESULTS
A total of 728 participants responded to this survey, including 280 pathologists and 448 PathAs. We classified 98 activities according to expectations: independent performance (20/98), developing independence (48/98), and not expected of PathAs (5/98). Some activities (25/98) were indeterminate yet likely represent areas of developing independence.
CONCLUSIONS
This study demonstrates an expectation for entry-level PathAs to perform some activities included in the scope of practice independently but eventually to develop independent proficiency for most professional activities. A minority of activities were identified as responsibilities that are not expected of PathAs. Entry-level PathAs, therefore, remain "works in progress," with an expectation for independent performance of core activities while developing abilities in many areas of professional practice.
Topics: Humans; Motivation; Pathologists; Pathology, Clinical; Surveys and Questionnaires; United States
PubMed: 35760554
DOI: 10.1093/ajcp/aqac065