Early experience with formalin-fixed paraffin-embedded (FFPE) based commercial clinical genomic profiling of gliomas-robust and informative with caveats.

BACKGROUND: Commercial targeted genomic profiling with next generation sequencing using formalin-fixed paraffin embedded (FFPE) tissue has recently entered into clinical use for diagnosis and for the guiding of therapy. However, there is limited independent data regarding the accuracy or robustness of commercial genomic profiling in gliomas. METHODS: As part of patient care, FFPE samples of gliomas from 71 patients were submitted for targeted genomic profiling to one commonly used commercial vendor, Foundation Medicine. Genomic alterations were determined for the following grades or groups of gliomas; Grade I/II, Grade III, primary glioblastomas (GBMs), recurrent primary GBMs, and secondary GBMs. In addition, FFPE samples from the same patients were independently assessed with conventional methods such as immunohistochemistry (IHC), Quantitative real-time PCR (qRT-PCR), or Fluorescence in situ hybridization (FISH) for three genetic alterations: IDH1 mutations, EGFR amplification, and EGFRvIII expression. RESULTS: A total of 100 altered genes were detected by the aforementioned targeted genomic profiling assay. The number of different genomic alterations was significantly different between the five groups of gliomas and consistent with the literature. CDKN2A/B, TP53, and TERT were the most common genomic alterations seen in primary GBMs, whereas IDH1, TP53, and PIK3CA were the most common in secondary GBMs. Targeted genomic profiling demonstrated 92.3%-100% concordance with conventional methods. The targeted genomic profiling report provided an average of 5.5 drugs, and listed an average of 8.4 clinical trials for the 71 glioma patients studied but only a third of the trials were appropriate for glioma patients. CONCLUSIONS: In this limited comparison study, this commercial next generation sequencing based-targeted genomic profiling showed a high concordance rate with conventional methods for the 3 genetic alterations and identified mutations expected for the type of glioma. While it may not be feasible to exhaustively independently validate a commercial genomic profiling assay, examination of a few markers provides some reassurance of its robustness. While potential targeted drugs are recommended based on genetic alterations, to date most targeted therapies have failed in glioblasomas so the usefulness of such recommendations will increase with development of novel and efficacious drugs.

Cervical cytology with a diagnosis of atypical squamous cells, cannot exclude high-grade squamous intraepithelial lesion (ASC-H): a follow-up study with corresponding histology and significance of predicting dysplasia by human papillomavirus (HPV) DNA testing.

OBJECTIVES: To evaluate the clinical significance of "atypical squamous cells, cannot exclude high-grade squamous intraepithelial lesion" ASC-H by comparing the original cytologic findings with follow-up tissue biopsies, and its association with high-risk HPV. METHODS: A total of 235,518 ThinPrep Pap tests were performed at our institution from January 2008 through December 2010, but only 727 (0.3%) of these cases were diagnosed as ASC-H. RESULTS: Of the 309 cases diagnosed as ASC-H on cytology for which follow-up histologic material was available, 120 (38.8%) were definitively diagnosed as high-grade dysplasia (CIN 2/3) and 75 (24.2%) showed features of low-grade dysplasia (CIN 1). We observed that the incidence of dysplasia in patients less than 30 years of age was 73.4% (113/154) and 48.3% (14/29) in patients greater than 49 years of age (p = 0.001). There were 71 cases for which high-risk HPV DNA testing was conducted. HPV DNA was found to be positive in 41 of the dysplastic cases (CIN 1 = 18 cases and CIN 2/3 = 23) and negative in six of the dysplastic cases (CIN1 = 2 and CIN2/3 = 4). CONCLUSION: We conclude that cases diagnosed as ASC-H should be followed-up with caution as they are strongly associated with dysplasia of any grade (63.1%), especially high-grade dysplasia (38.8%). Reflex HPV DNA testing is an important predictor of dysplasia with a positive predictive value of 87.2% in our study.

Artificial intelligence for human gunshot wound classification.

Certain features are helpful in the identification of gunshot entrance and exit wounds, such as the presence of muzzle imprints, peripheral tears, stippling, bone beveling, and wound border irregularity. Some cases are less straightforward and wounds can thus pose challenges to an emergency room doctor or forensic pathologist. In recent years, deep learning has shown promise in various automated medical image classification tasks. This study explores the feasibility of using a deep learning model to classify entry and exit gunshot wounds in digital color images. A collection of 2418 images of entrance and exit gunshot wounds were procured. Of these, 2028 entrance and 1314 exit wounds were cropped, focusing on the area around each gunshot wound. A ConvNext Tiny deep learning model was trained using the Fastai deep learning library, with a train/validation split ratio of 70/30, until a maximum validation accuracy of 92.6% was achieved. An additional 415 entrance and 293 exit wound images were collected for the test (holdout) set. The model achieved an accuracy of 87.99%, precision of 83.99%, recall of 87.71%, and F1-score 85.81% on the holdout set. Correctly classified were 88.19% of entrance wounds and 87.71% of exit wounds. The results are comparable to what a forensic pathologist can achieve without other morphologic cues. This study represents one of the first applications of artificial intelligence to the field of forensic pathology. This work demonstrates that deep learning models can discern entrance and exit gunshot wounds in digital images with high accuracy.

Metastatic renal cell carcinoma to the pancreas: diagnostic significance of fine-needle aspiration cytology.

BACKGROUND: Renal cell carcinoma rarely metastasizes to the pancreas. Diagnosing a neoplasm that is metastatic to the pancreas by fine-needle aspiration (FNA) cytology is often challenging. A detailed clinical history may prove to be beneficial. CASE REPORTS: A total of 729 pancreatic FNAs were performed from January 2005 through August 2012 at our institution. Among these, we found 3 patients with a prior history of a malignant renal neoplasm who presented with a pancreatic mass: 2 in the tail and 1 in the head. Radiographically, they ranged in size from 2.5 to 7.0 cm. Microscopic evaluation of cytologic material obtained during endoscopic ultrasound-guided FNA (EUS-FNA) revealed cohesive clusters of atypical cells with clear cytoplasm and prominent nucleoli surrounded by a thin capillary network. The neoplastic cells were immunoreactive with CD10 (cases 2 and 3). A diagnosis of metastatic clear cell renal cell carcinoma was rendered for each case based on the morphologic features and immunohistochemical staining pattern of the neoplastic cells. Histologic comparison with the available slides of the corresponding primary renal neoplasm confirmed the diagnosis. CONCLUSION: We conclude that EUS-FNA of pancreatic masses is an important, effective, and accurate diagnostic modality for early diagnosis of both primary and metastatic neoplasms of the pancreas.

Autopsy Histopathologic Cardiac Findings in 2 Adolescents Following the Second COVID-19 Vaccine Dose.

CONTEXT.­: Myocarditis in adolescents has been diagnosed clinically following the administration of the second dose of an mRNA vaccine for coronavirus disease 2019 (COVID-19). OBJECTIVE.­: To examine the autopsy microscopic cardiac findings in adolescent deaths that occurred shortly following administration of the second Pfizer-BioNTech COVID-19 dose to determine if the myocarditis described in these instances has the typical histopathology of myocarditis. DESIGN.­: Clinical and autopsy investigation of 2 teenage boys who died shortly following administration of the second Pfizer-BioNTech COVID-19 dose. RESULTS.­: The microscopic examination revealed features resembling a catecholamine-induced injury, not typical myocarditis pathology. CONCLUSIONS.­: The myocardial injury seen in these postvaccine hearts is different from typical myocarditis and has an appearance most closely resembling a catecholamine-mediated stress (toxic) cardiomyopathy. Understanding that these instances are different from typical myocarditis and that cytokine storm has a known feedback loop with catecholamines may help guide screening and therapy.

Biobanking of Cerebrospinal Fluid.

Cerebrospinal fluid (CSF) is a physiologically essential fluid produced by the brain that is involved in protecting the brain and in the exchange of nutrients and waste products. CSF has long been utilized to confirm clinical suspicion of various infectious and inflammatory disorders, such as meningitis and multiple sclerosis. However, there has been increasing interest in collecting CSF in order to study the clinical significance of additional biomarkers. This chapter outlines the procedures necessary to collect, process, store, and utilize CSF obtained for the purposes of biobanking from both living and deceased patients.

Autopsy Biobanking: Biospecimen Procurement, Integrity, Storage, and Utilization.

An autopsy is a specialized surgical procedure consisting of external and internal examination of a deceased individual for the purposes of documenting abnormalities and determining or confirming medical diagnoses that may have contributed to their death. One of the benefits of an autopsy is the opportunity to collect and store biospecimens for the purposes of biobanking. This chapter outlines the procedures necessary to procure, store, and utilize biospecimens obtained during an autopsy. With the emergence of molecular diagnostics, this chapter also discusses factors that influence the integrity of autopsy biospecimens prior to procurement. These include the postmortem interval, as well as premortem factors such as the patient's agonal state, biospecimen temperature, and pH.

Domestic and International Shipping of Biospecimens.

The packaging and shipment of biospecimens is a multistep process for which a distinct set of regulations needs to be followed, depending on whether a biospecimen is shipped domestically or internationally and whether the shipment contains hazardous materials. Shipments may be delayed if these regulations are not followed. Once learned, the process is straightforward. Major principles include double or triple packaging, adequate absorbent material, appropriate coolant, accurate labeling, and complete documentation. Training in packaging and shipping is often offered at major biomedical institutions and is a requirement to avoid shipping biohazards.

Glioblastoma following treatment with fingolimod for relapsing-remitting multiple sclerosis.

Glioblastoma is an uncommon and aggressive primary brain tumor with incidence of 3 per 100,000 annually. We report a 50-year-old woman diagnosed with glioblastoma within threeyears of induction of fingolimod therapy for relapsing-remitting multiple sclerosis. Fingolimod, an immunomodulating agent used in the treatment of relapsing-remitting multiple sclerosis, has also been suggested to impart a cardioprotective role in heart failure and arrhythmia via activation of P21-activated kinase-1 (Pak1). In the brain, Pak1 activation has been shown to correlate with decreased survival time amongst patients with glioblastoma. A molecular mechanism underlying a link between fingolimod use and glioblastoma development may involve activation of Pak1. To our knowledge, this is the first report of a potential association between fingolimod use and glioblastoma development.

Primary inflammatory malignant fibrous histiocytoma of the breast: a case report of an unusual variant and review of the literature.

Malignant fibrous histiocytoma (MFH) is the most common soft tissue sarcoma of adults, but its presence in the breast is rare. We report a case of primary inflammatory MFH in a 72-year-old Caucasian female with no previous medical history and no prior radiation exposure. She presented with a palpable mass that was suspicious for malignancy on mammography. Histologic evaluation of the core needle biopsy revealed sheets of large, pleomorphic neoplastic cells within a dense background of acute and chronic inflammatory cells. The neoplastic cells exhibited a moderate to abundant amount of finely vacuolated cytoplasm and atypical nuclei with vesicular nuclear chromatin and prominent nucleoli. Mitotic activity was readily identified, and foci of necrosis were noted. The neoplastic cells were immunoreactive with CD68, alpha 1-antitrypsin, alpha 1-antichymotrypsin, and vimentin. The diagnosis of MFH was rendered after thorough microscopic examination of the entire mass following mastectomy. MFH of the breast is a diagnosis of exclusion. The definitive treatment of MFH is surgical, either with wide local excision or total mastectomy. The roles of sentinel lymph node biopsy, axillary lymph node dissection, chemotherapy, and radiation have yet to be definitively clarified. The prognosis of MFH of the breast is generally poor.