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. The curriculum included lectures on databases, programming, analytics, machine learning basics, and specialized topics like anatomic pathology data analysis and dashboarding.

Chronic Lymphocytic Leukemia Presenting as Bilateral Periorbital Edema Treated With Low-dose Radiation Therapy.

Ocular manifestations in chronic lymphocytic leukemia (CLL) have been reported in 30% to 40% of patients and may be a result of direct tissue infiltration, concomitant blood dyscrasias, or a result of therapeutic intervention. Leukemia cutis, defined as infiltration of the epidermis or dermis by neoplastic lymphocytes, is rare. Herein, we present a case report of a patient with leukemia who presented with periorbital edema and ecchymosis. This is the first known case to date of periorbital CLL successfully treated with low-dose radiation therapy (4 Gy in 2 fractions). Clinicians should be aware of the possibility of ocular involvement from CLL, given the importance of prompt diagnosis and treatment.

NK/T-cell Lymphoma With Orbital Involvement: A Case Report and Systematic Review of the Literature.

PURPOSE: To present the clinical course of a patient with recurrent NK/T-cell lymphoma (NKTL) involving the orbit and to review the literature on patients with NKTL involving the orbit. METHODS: The PubMed database was searched for all cases of NKTL involving orbital, intraocular, or adnexal ocular structures. RESULTS: Ninety-six patients were included in the final analysis. The mean age of diagnosis was 48.1 ± 16.8 years. The patients were 53/96 (55.2%) male and 43/96 (44.8%) female. Tumor location varied and included the orbit in 80/96 (83.3%), nasosinus in 56/96 (58.3%), uvea in 11/96 (11.5%), lacrimal gland in 9/96 (9.4%), lacrimal drainage system in 11/96 (11.5%), and conjunctiva in 7/96 (7.3%) cases. Management included surgical debulking in 29/96 (30.2%) cases, radiotherapy in 52/96 (54.2%) cases, and chemotherapy in 82/96 (85.4%) cases. Median survival was 6 months (95% CI: 5-9). Chemotherapy (hazard ratio = 0.80, 95% CI: 0.67-0.95, p = 0.013), radiotherapy (hazard ratio = 0.75, 95% CI: 0.64-0.87, p < 0.001), and orbital involvement being a recurrence of disease (hazard ratio = 0.79, 95% CI: 0.67-0.95, p = 0.009) were associated with improved survival. Advanced Ann Arbor stage (III-IV) at diagnosis (hazard ratio = 1.22, 95% CI: 1.08-1.38, p = 0.001), vision loss (hazard ratio = 1.18, 95% CI: 1.04-1.34, p = 0.009), proptosis (hazard ratio = 1.15, 95% CI: 1.01-1.30, p = 0.035) and periorbital swelling (hazard ratio = 1.15, 95% CI: 1.00-1.33, p = 0.048) were associated with poor survival. CONCLUSIONS: NK/T-cell lymphoma involving the orbit, globe, or ocular adnexa heralds a poor prognosis where early diagnosis and therapy are critical. The use of radiotherapy and chemotherapy is associated with improved survival.

Computational pathology in 2030: a Delphi study forecasting the role of AI in pathology within the next decade.

BACKGROUND: Artificial intelligence (AI) is rapidly fuelling a fundamental transformation in the practice of pathology. However, clinical integration remains challenging, with no AI algorithms to date in routine adoption within typical anatomic pathology (AP) laboratories. This survey gathered current expert perspectives and expectations regarding the role of AI in AP from those with first-hand computational pathology and AI experience. METHODS: Perspectives were solicited using the Delphi method from 24 subject matter experts between December 2020 and February 2021 regarding the anticipated role of AI in pathology by the year 2030. The study consisted of three consecutive rounds: 1) an open-ended, free response questionnaire generating a list of survey items; 2) a Likert-scale survey scored by experts and analysed for consensus; and 3) a repeat survey of items not reaching consensus to obtain further expert consensus. FINDINGS: Consensus opinions were reached on 141 of 180 survey items (78.3%). Experts agreed that AI would be routinely and impactfully used within AP laboratory and pathologist clinical workflows by 2030. High consensus was reached on 100 items across nine categories encompassing the impact of AI on (1) pathology key performance indicators (KPIs) and (2) the pathology workforce and specific tasks performed by (3) pathologists and (4) AP lab technicians, as well as (5) specific AI applications and their likelihood of routine use by 2030, (6) AI's role in integrated diagnostics, (7) pathology tasks likely to be fully automated using AI, and (8) regulatory/legal and (9) ethical aspects of AI integration in pathology. INTERPRETATION: This systematic consensus study details the expected short-to-mid-term impact of AI on pathology practice. These findings provide timely and relevant information regarding future care delivery in pathology and raise key practical, ethical, and legal challenges that must be addressed prior to AI's successful clinical implementation. FUNDING: No specific funding was provided for this study.

Systems approach to enhance Lynch syndrome diagnosis through tumour testing.

BACKGROUND: Guidelines recommend universal mismatch repair (MMR) tumour testing of colorectal adenocarcinomas (CRCs) to screen for Lynch syndrome (LS). However, its implementation remains disjointed and referral for genetic testing dismal, particularly among minorities. We aimed to increase referral, cancer genetic testing and eventually LS diagnosis by developing the CLEAR LS (Closed Loop Enhanced Assessment and Referral for Lynch Syndrome) intervention, a systems approach which in the second phase was automated. METHODS: This is a cohort study of all patients diagnosed with CRC at an academic centre between 1 January 2012, when implementation of universal CRC testing began, and 31 January 2021. The original cohort spanned through 31 May 2015. Tumour testing included MMR immunohistochemistry, followed by BRAF V600E/MLH1 promoter methylation testing when indicated. The intervention included a manual phase (1 June 2015 through 31 July 2018), which systematised pathology screening and cancer genetics (CG) referral mechanisms, and an automated phase (1 August 2018 through 31 January 2021) using computer programming. RESULTS: A total of 249/1541 CRC (17.38%) had MMR loss of expression and 129 (8.37%) qualified for CG evaluation. Referral was 27.58% in the original cohort and 92.1% in the intervention (p<0.001). Patients seen by CG among referred were 27.58% in the original cohort and 74.3% in the intervention (p two-sided<0.001). The distribution of race/ethnicity among patients qualifying and referred for CG evaluation was not significantly different across cohorts. LS diagnosis increased from 0.56% (original cohort) to 1.43% (intervention). Cost per new diagnosis of LS decreased from US$173 675 to $87 960 from original cohort to intervention. CONCLUSION: Implementation of systematic case identification and referral support mechanisms significantly increased the proportion of patients undergoing genetic testing and doubled the percentage of patients diagnosed with LS with no referral differences across racial/ethnic groups.

Bilateral dacryoadenitis as the initial presentation of ANCA-associated vasculitis in a pediatric patient.

A 14-year-old female presented with 2 weeks of progressive right eye pain, erythema, and proptosis. Examination demonstrated an enlarged palpable mass along the right superior lateral orbit and bilateral conjunctival petechiae. Of note, she was asymptomatic on the left side, and the petechiae were present only on the superior bulbar conjunctiva with eyelid eversion. Imaging demonstrated bilateral lacrimal gland enhancement. Testing was significant for elevated inflammatory markers, but otherwise negative workup. Biopsy of the right lacrimal gland demonstrated acute-on-chronic inflammation without evidence of lymphoproliferative disease. On repeat testing, myeloperoxidase antibody levels (MPO/p-ANCA) were elevated, indicative of an underlying immune-mediated vasculitis. This case illustrates a rare presentation of ANCA-associated vasculitis in a pediatric patient. It further demonstrates the phenomenon of initial negative serology and subsequent auto-antibody seroconversion in a patient with localized granulomatosis with polyangiitis.

Local recurrence of uveal melanoma and concomitant brain metastases associated with an activating telomerase promoter mutation seven years after secondary enucleation.

Purpose: To describe a case of local recurrence of uveal melanoma with concomitant brain metastases after secondary enucleation. Observations: A 73 year-old patient presented with dizziness and gait instability. MRI of the orbits and brain showed an anophthalmic socket with an orbital implant and an associated optic nerve mass as well as multiple mass lesions in the brain. The patient's history was significant for secondary enucleation for uveal melanoma recurrence seven years prior to presentation. Histopathology of the enucleated eye revealed no signs of extrascleral extension or optic nerve invasion. Biopsy of the optic nerve mass confirmed recurrent uveal melanoma with somatic mutations in GNAQ (Q209L) and the telomerase (TERT) promoter (c.1-124C > T) found on targeted next-generation sequencing (NGS). The same mutations were found in the primary tumor in the patient's archived enucleation samples. Conclusions: Local recurrence of uveal melanoma can occur after enucleation and is associated with an increased risk of systemic metastases. It is important for clinicians to monitor patients for local recurrence and systemic metastases even after enucleation. Genetic biomarkers may play an important role in identifying tumors at highest risk of local recurrence and metastasis. To our knowledge, this is the first case study to describe the TERT promoter mutation c.1-124C > T in the setting of recurrent uveal melanoma.

Necrotic Uveal Melanoma Mimics Orbital Cellulitis: A Review.

Background: Uveal melanoma is the most common primary intraocular malignancy in adults, often resulting in painless vision loss. We report a case of necrotic uveal melanoma presenting with orbital inflammation mimicking orbital cellulitis and present a comprehensive review of the literature and tabulation of reported cases. Summary: Our review found 44 published reports of spontaneously necrotic uveal melanoma involving 55 patients. Of these reports, 26 patients (47%) presented with orbital cellulitis. Presenting symptoms of necrotic uveal melanoma with orbital cellulitis included proptosis (82.8%), pain (80.7%), vision loss (61.5%), and restricted extraocular movements (46.2%). Key Messages: Uveal melanoma can rarely mimic orbital cellulitis. Autoinfarction and tumor necrosis causes secondary orbital inflammation. Intraocular malignancy must remain in the differential for patients with orbital inflammation and vision loss.

Primary Mesenchymal Tumors of the Thyroid Gland: A Modern Retrospective Cohort Including the First Case of TFE3-Translocated Malignant Perivascular Epithelioid Cell Tumor (PEComa).

Primary mesenchymal tumors of the thyroid gland are extremely rare, with only case reports and small case series documented in the English literature, many of which were published prior to the era of molecular pathology. In the current study, we aim to present a contemporary multi-centric cohort of thyroid mesenchymal tumors. Nineteen primary thyroid mesenchymal tumors were collected from three tertiary centers. Their clinicopathologic features, immunoprofile, molecular alterations, and outcome were described. Eight cases were classified as benign or intermediate with solitary fibrous tumor being the most common histotype (n = 3). The remaining 11 cases were malignant, including three angiosarcomas, one epithelioid hemangioendothelioma, one adamantinoma-like Ewing sarcoma, one biphasic synovial sarcoma, one malignant melanocytic peripheral nerve sheath tumor (melanotic schwannoma), one myxofibrosarcoma, and two undifferentiated pleomorphic/spindle sarcomas (one of which was radiation-induced). Six tumors showed characteristic diagnostic translocations. We herein also described the first case of thyroid malignant perivascular epithelioid cell tumor (PEComa) with RBM10-TFE3 fusion in a 35-year-old female patient. Thyroid mesenchymal tumors, benign or malignant, are rare with a broad spectrum of possible diagnoses. A comprehensive examination to include histology, immunohistochemistry, and molecular testing is essential for the correct diagnosis and to distinguish them from anaplastic thyroid carcinoma. PEComa may occur as a primary tumor of the thyroid gland, expanding the histologic spectrum of thyroid mesenchymal tumors.

Molecular Markers in Maternal Blood Exosomes Allow Early Detection of Fetal Alcohol Spectrum Disorders.

Prenatal alcohol exposure can cause developmental abnormalities (fetal alcohol spectrum disorders; FASD), including small eyes, face and brain, and neurobehavioral deficits. These cannot be detected early in pregnancy with available imaging techniques. Early diagnosis could facilitate development of therapeutic interventions. Banked human fetal brains and eyes at 9−22 weeks' gestation were paired with maternal blood samples, analyzed for morphometry, protein, and RNA expression, and apoptotic signaling. Alcohol (EtOH)-exposed (maternal self-report) fetuses were compared with unexposed controls matched for fetal age, sex, and maternal race. Fetal brain-derived exosomes (FB-E) were isolated from maternal blood and analyzed for protein, RNA, and apoptotic markers. EtOH use by mothers, assessed by self-report, was associated with reduced fetal eye diameter, brain size, and markers of synaptogenesis. Brain caspase-3 activity was increased. The reduction in eye and brain sizes were highly correlated with amount of EtOH intake and caspase-3 activity. Levels of several biomarkers in FB-E, most strikingly myelin basic protein (MBP; r > 0.9), correlated highly with morphological abnormalities. Reduction in FB-E MBP levels was highly correlated with EtOH exposure (p < 1.0 × 10−10). Although the morphological features of FAS appear long before they can be detected by live imaging, FB-E in the mother's blood may contain markers, particularly MBP, that predict FASD.

Cilioretinal Artery Occlusion as the Presenting Manifestation of Left Atrial Myxoma.

Purpose: This work reports a case of left atrial myxoma presenting with cilioretinal artery occlusion. Methods: A case report is discussed. Results: A 57-year-old man was referred for acute vision loss in the left eye after a workup including electrocardiogram, magnetic resonance imaging of the brain without contrast, computed tomography angiography of the head and neck, erythrocyte sedimentation rate, and C-reactive protein had negative results. Examination revealed cilioretinal artery occlusion with visible emboli. Because an echocardiogram was not performed, the patient was referred to the emergency department. Echocardiogram revealed a large left atrial mass prolapsing into the left ventricle. The mass was excised, and pathology showed myxoma. Conclusions: This is the first case to our knowledge of isolated cilioretinal artery occlusion as the initial presentation of an atrial myxoma. Thorough and complete workup was crucial to averting further morbidity and mortality.

Measuring Faculty Effort: A Quantitative Approach That Aligns Personal and Institutional Goals in Pathology at Yale.

US medical schools increasingly seek ways to reduce costs and improve productivity. One aspect of this effort has been the development of performance-based incentives for individual faculty. A myriad of such plans exist. Typically, they incentivize clinical revenue generation but vary widely in how teaching, investigation, and administrative contributions are recognized. In Pathology at Yale, we have developed a transparent metrically driven approach that recognizes all missions and allows faculty significant control over their career path. Although some metrics derive from traditional measures such as workload relative value units and one's level of grant support, the key concept underpinning our approach is to define one's contributions not in terms of the revenue generated, but rather on the effort devoted to each of our missions, benchmarked against national or local standards. Full-time faculty are paid a competitive rank-based salary and are expected to contribute at least 100% effort in support of the school's missions: clinical, research, education, administration, and professional service. Metrics define the effort assigned to each activity. Faculty achieving greater than 100% effort receive bonus compensation in proportion to their excess effort. By codifying explicitly how such effort is recognized into a single metric (% effort), we achieve a process that better aligns the professional and personal goals of faculty with the aims of the school. To facilitate its implementation, we have developed a web-based software platform called SWAY (Standardized Workload Analysis at Yale) that enables faculty to monitor their progress and record their activities in real time.

An independent assessment of an artificial intelligence system for prostate cancer detection shows strong diagnostic accuracy.

Prostate cancer is a leading cause of morbidity and mortality for adult males in the US. The diagnosis of prostate carcinoma is usually made on prostate core needle biopsies obtained through a transrectal approach. These biopsies may account for a significant portion of the pathologists' workload, yet variability in the experience and expertise, as well as fatigue of the pathologist may adversely affect the reliability of cancer detection. Machine-learning algorithms are increasingly being developed as tools to aid and improve diagnostic accuracy in anatomic pathology. The Paige Prostate AI-based digital diagnostic is one such tool trained on the digital slide archive of New York's Memorial Sloan Kettering Cancer Center (MSKCC) that categorizes a prostate biopsy whole-slide image as either "Suspicious" or "Not Suspicious" for prostatic adenocarcinoma. To evaluate the performance of this program on prostate biopsies secured, processed, and independently diagnosed at an unrelated institution, we used Paige Prostate to review 1876 prostate core biopsy whole-slide images (WSIs) from our practice at Yale Medicine. Paige Prostate categorizations were compared to the pathology diagnosis originally rendered on the glass slides for each core biopsy. Discrepancies between the rendered diagnosis and categorization by Paige Prostate were each manually reviewed by pathologists with specialized genitourinary pathology expertise. Paige Prostate showed a sensitivity of 97.7% and positive predictive value of 97.9%, and a specificity of 99.3% and negative predictive value of 99.2% in identifying core biopsies with cancer in a data set derived from an independent institution. Areas for improvement were identified in Paige Prostate's handling of poor quality scans. Overall, these results demonstrate the feasibility of porting a machine-learning algorithm to an institution remote from its training set, and highlight the potential of such algorithms as a powerful workflow tool for the evaluation of prostate core biopsies in surgical pathology practices.

An Analysis of the Effect of the COVID-19 Pandemic on Case Volumes in an Academic Subspecialty-Based Anatomic Pathology Practice.

The recent COVID pandemic has had a major effect on anatomic pathology specimen volumes across the country. The effect of this pandemic on a subspecialty academic practice is presented. We used a data-driven approach to monitor the changing workloads in a granular fashion and dynamically adjust the scheduling of faculty and histology staff accordingly to minimize the number of people present on-site. At the peak of the pandemic locally, the main hospital in our health system had 450 COVID-positive inpatients. The surgical pathology specimen volume dropped to 13% of the pre-pandemic levels, and this occurred about 2 weeks before the peak of the inpatient census; cytology specimens (the majority of which are outreach gynecological) dropped to approximately 5% of the pre-pandemic volume, 4 weeks before the peak inpatient census. All of the surgical subspecialty services showed a significant decrease in volume, with hematopathology being the least affected (dropped to 30% of the pre-pandemic level). The genitourinary surgical subspecialty service (predominantly prostate and bladder biopsies) was the most affected (dropped to 1% of the pre-pandemic level) but was fastest to return as clinical operations began to return to normal. The only specimen type which showed a significant increase in turnaround time during the pandemic was our gynecologic cytology specimens and that occurred as the specimen volume returned. This was due to stay-at-home directives for the cytotechnologists and the fact that some of them were retasked to participate in our SARS-CoV-2 testing.

Autopsy Services and Emergency Preparedness of a Tertiary Academic Hospital Mortuary for the COVID-19 Public Health Emergency: The Yale Plan.

Pathology Autopsy and Mortuary Services have been front and center in the severe acute respiratory syndrome coronavirus 2 (SARS-Co-V-2) pandemic. The sheer number of fatalities from the pandemic have been unlike any other in recent memory and needed the rapid creation of new protocols and paradigms to manage the situation. This required rapidly escalating mortuary capacity to manage the increased fatalities from the pandemic with the establishment of lines of communication and networking with governmental entities, institution of new policies for patient flow, and implementation of worker infection control and well-being plans. Autopsies also assumed a crucial role, both to provide insight into the pathomechanisms of a novel disease and to allow tissue retrieval necessary to power research directed towards finding a vaccine. We here outline the plan adopted by the Yale Autopsy and Mortuary Services, in alignment with the institutional mission of high-quality patient care, education, research and health care worker safety and well-being, as the Corona Virus Disease of 2019 (COVID-19) pandemic surged in Connecticut. In the early response phase, ensuring sufficient mortuary capacity necessarily took center stage. As we enter the recovery and plateau phase of the pandemic, setting up a process for a rapid and safe autopsy, that will meet educational and research needs while ensuring the safety of our workforce is being implemented.

Histopathologic changes in cadaver eyes after MicroPulse and continuous wave transscleral cyclophotocoagulation.

OBJECTIVE: The purpose of this study was to compare the acute histological effects of MicroPulse transscleral cyclophotocoagulation (MPCPC) using the MicroPulse P3 Device and continuous wave transscleral cyclophotocoagulation (CWCPC) on the ciliary body and adjacent structures in human cadaver eyes. METHODS: Quadrants of 6 human cadaver eyes from 3 different donors were subjected to traditional CWCPC, slow burn CWCPC, MPCPC, or no treatment (internal control). Sutures were used to differentiate different treatment areas on each eye. Differential inking was applied after treatments to aid in microscopic correlation. All specimens were subject to standard histologic processing. Tissue sections were cut at 4 microns and stained with hematoxylin and eosin according to established protocols. Pathologic evaluation by light microscopy was confirmed by a senior pathologist blinded to treatment groups. RESULTS: In all 6 eyes, tissues treated with traditional and low burn CWCPC showed variable coagulative tissue damage to the ciliary body compared with untreated tissues. Minimal histologic changes were identified within the ciliary processes, although variable pigment clumping and streaming were noted within the pigmented ciliary epithelium. In contrast to CWCPC, MPCPC-treated tissues showed only minimal coagulative tissue damage to the ciliary body. Variable pigment clumping and streaming, however, were also noted in the pigmented ciliary epithelium in MPCPC-treated tissues. CONCLUSIONS: In human cadaver eyes, MPCPC treatment caused less tissue disruption to the ciliary body compared with traditional and low burn CWCPC treatments. MPCPC may be a less destructive and more selective method of cyclophotocoagulation when compared with traditional and low burn CWCPC.

Angiolymphoid Hyperplasia with Eosinophilia with Clinical Presentation Concerning for Juvenile Temporal Arteritis.

A 20-year-old boy presented with a mass superotemporal to the right eyebrow of 1 month's duration without a history of recent trauma. Complete examination and workup, including laboratory analysis, Doppler ultrasound imaging, and magnetic resonance imaging, suggested a diagnosis of juvenile temporal arteritis. Excisional biopsy and histopathology contradicted the preoperative workup and yielded the final diagnosis of angiolymphoid hyperplasia with eosinophilia, a rare eosinophilic dermatosis of unknown etiology. This case highlights the need for better characterization of temporal vascular tumors in the pediatric population.

Dabrafenib and Trametinib for BRAF-Mutated Conjunctival Melanoma.

BACKGROUND: Conjunctival melanoma is a potentially lethal malignancy of the ocular surface. There have been no therapeutic advancements made in the past several decades despite increasing prevalence of the disease. METHODS: The authors report the case of a 52-year-old Caucasian male with unresectable, recurrent conjunctival melanoma with V600 BRAF mutation who was treated with systemic BRAF/MEK inhibition. RESULTS: There was complete regression of local disease within the first 9 months. The patient remains without local recurrence or systemic metastasis at 1 year. CONCLUSION: This is the first reported case of conjunctival melanoma with complete response to BRAF/MEK inhibition. As long as targeted therapy remains an option, patients with conjunctival melanoma should undergo mutational profiling of their tumor.

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.­: To ascertain the utilization rate and accuracy of LOINC terminology mapping to 10 commonly ordered tests by participants of the College of American Pathologists (CAP) Proficiency Testing program. DESIGN.­: Questionnaires were sent to 1916 US and Canadian laboratories participating in the 2018 CAP coagulation (CGL) and/or cardiac markers (CRT) surveys requesting information on practice setting, instrument(s) and test method(s), and LOINC code selection and usage in the laboratory and electronic health records. RESULTS.­: Ninety of 1916 CGL and/or CRT participants (4.7%) responded to the questionnaire. Of the 275 LOINC codes reported, 54 (19.6%) were incorrect: 2 codes (5934-2 and 12345-1) (0.7%) did not exist in the LOINC database and the highest error rates were observed in the property (27 of 275, 9.8%), system (27 of 275, 9.8%), and component (22 of 275, 8.0%) LOINC axes. Errors in LOINC code selection included selection of the incorrect component (eg, activated clotting time instead of activated partial thromboplastin time); selection of panels that can never be used to obtain an individual analyte (eg, prothrombin time panel instead of international normalized ratio); and selection of an incorrect specimen type. CONCLUSIONS.­: These findings of real-world LOINC code implementation across a spectrum of laboratory settings should raise concern about the reliability and utility of using LOINC for clinical research or to aggregate data.