IDH1 mutated acute myeloid leukemia in a child with metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria.

D-2-hydroxyglutaric aciduria (D-2-HGA) is a rare metabolic disorder characterized by developmental delay, hypotonia, and bi-allelic mutations in D-2-hydroxyglutarate dehydrogenase (D2HGDH) or a single gain-of-function mutation in isocitrate dehydrogenase 2 (IDH2). Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria (MC-HGA) is a type of D-2-HGA that has been previously reported in ten patients (OMIM 614875), three of whom had somatic mosaicism for R132 variants in isocitrate dehydrogenase 1 (IDH1). We describe a 3-year-old boy with MC-HGA who subsequently developed acute myeloid leukemia (AML) and was found to have an IDH1 R132C mutation in a leukemic bone marrow sample. Further testing revealed presence of somatic mosaicism for IDH1 R132C variant, suggesting an association of IDH1 in inducing myeloid leukemogenesis.

Development of a Scoring Rubric Assessing Medical Students' Explanations of Pathology Reports.

CONTEXT.­: With increasing availability of immediate patient access to pathology reports, it is imperative that all physicians be equipped to discuss pathology reports with their patients. No validated measures exist to assess how pathology report findings are communicated during patient encounters. OBJECTIVE.­: To pilot a scoring rubric evaluating medical students' communication of pathology reports to standardized patients. DESIGN.­: The rubric was iteratively developed using the Pathology Competencies for Medical Education and Accreditation Council for Graduate Medical Education pathology residency milestones. After a brief training, third- and fourth-year medical students completed 2 standardized patient encounters, presenting simulated benign and malignant pathology reports. Encounters were video recorded and scored by 2 pathologists to calculate overall and item-specific interrater reliability. RESULTS.­: All students recognized the need for pathology report teaching, which was lacking in their medical curriculum. Interrater agreement was high for malignant report scores (intraclass correlation coefficient, 0.65) but negligible for benign reports (intraclass correlation coefficient, 0). On malignant reports, most items demonstrated good interrater agreement, except for discussing the block (cassette) summary, explaining the purpose of the pathology report, and acknowledging uncertainty. Participating students (N = 9) felt the training was valuable given their limited prior exposure to pathology reports. CONCLUSIONS.­: This pilot study demonstrates the feasibility of using a structured rubric to assess the communication of pathology reports to patients. Our findings also provide a scalable example of training on pathology report communication, which can be incorporated in the undergraduate medical curriculum to equip more physicians to facilitate patients' understanding of their pathology reports.

Trilateral retinoblastoma in a patient with Peutz-Jeghers syndrome.

Germline loss of function mutations in tumor suppressor genes RB1 and LKB1/STK11 are associated with the autosomal dominant cancer predisposing syndromes familial retinoblastoma and Peutz-Jeghers syndrome (PJS), respectively. We present a rare case of a young woman with trilateral retinoblastoma diagnosed as an infant who survived and was then diagnosed with PJS as a teenager. There was no family history of either disorder. Analysis of the LKB1/STK11 gene sequence identified a germline frameshift mutation (c.107del) leading to a nonsense mutation near the N-terminus of the protein, confirming a clinical diagnosis of Peutz-Jeghers syndrome. Extensive RB1 gene analysis failed to detect germline mutations or deletions, and immunohistochemical analysis of her ocular tumors demonstrated nuclear staining of immunoreactive pRB. This result suggests that the RB1 gene is intact. We estimate the chance of trilateral retinoblastoma and PJS occurring in the same individual at approximately 1 in 134 billion live births, and we discuss the possibility that this case could be explained by a putative modifier of pRB action that is associated with the LKB1/STK11 pathway.

Realizing the Dream of Precision Oncology: A Solution for All Patients.

MICRO-ABSTRACT: As molecularly informed oncology care has increasingly become standard practice for patients with cancer, society must prioritize equitable access to genetic testing that guides subsequent care. Despite the availability of genomic testing laboratories, published guidelines, US Food and Drug Administration-approved targeted therapies, financial assistance programs, and clinical decision tools, precision medicine remains out of reach for many patients. While there has been modest improvement in testing rates in recent years, molecular testing and targeted therapy for cancer patients continue to vary by practice setting and patient insurance status, and racial and socioeconomic disparities persist. National standards and centralized solutions are needed to promote the equitable distribution of patient benefit from precision medicine technology. Although various online resources are currently available, no single all-encompassing precision oncology tool currently exists. A one-stop shop to address all aspects of precision oncology-tissue selection and test ordering, interpretation of results, prescribing targeted therapies, and enrolling patients in clinical trials-would disrupt cancer care. Recent advances in artificial intelligence, digital pathology, and data science provide an opportunity for stakeholders to partner together to leverage these technologies to develop this unified, freely accessible, national solution. Whether locoregionally, nationally, or internationally, only collaborative efforts can fully realize the potential of technological advancements in molecular pathology and oncology therapeutics for all cancer patients.

Interdisciplinary Quality Improvement Led by the Molecular Pathology Laboratory Expedites Diagnosis of Acute Promyelocytic Leukemia.

OBJECTIVES: Acute promyelocytic leukemia (APL) requires emergent treatment while definitive laboratory results are pending. Following the death of a patient whose diagnosis was delayed, we sought to improve our institution's workflow by using the EPIDEM (Exploration, Promotion, Implementation, Documentation, Evaluation, Modification) quality improvement model. METHODS: APL is confirmed by identifying translocation t(15;17)(q24;q21) PML-RARA by using either molecular or cytogenetic methods on peripheral blood or bone marrow specimens. We used the EPIDEM model to decrease the turnaround time (TAT) of molecular diagnosis by improving communication and developing reflex testing. We additionally compared 32 APL cases against a control group of 18 suspected APL cases. RESULTS: Our review of 687 multiplex polymerase chain reaction orders and 33 PML-RARA orders (January 2012 to April 2021) showed an initial TAT decrease from 4.48 days to 2.71 days (P < .0001), which further decreased to 0.64 days (P < .0001) after implementation of the PML-RARA qualitative assay. Compared with patients suspected of having APL, patients with confirmed APL had higher dimerized plasmin fragment D (P = .0145), lower fibrinogen (P ≤ .0001), and lower WBC (P ≤ .0001). CONCLUSIONS: By using the EPIDEM model, with its emphasis on local context, culture, and resources, improved communication and workflow changes enabled us to reduce the time needed to diagnose APL to 0.64 days and identify potential locally derived screening cutoffs.

Reshaping the binding channel of a novel GH113 family ß-mannanase from Paenibacillus cineris (PcMan113) for enhanced activity.

Endo-ß-mannanases are important enzymes for degrading lignocellulosic biomass to generate mannan, which has significant health effects as a prebiotic that promotes the development of gut microbiota. Here, a novel endo-ß-mannanase belonging to glycoside hydrolase (GH) family 113 from Paenibacillus cineris (PcMan113) was cloned, expressed and characterized, as one of only a few reported GH113 family ß-mannanases. Compared to other functionally and structurally characterized GH113 mannanases, recombinant PcMan113 showed a broader substrate spectrum and a better performance. Based on a structural homology model, the highly active mutant PcMT3 (F110E/N246Y) was obtained, with 4.60- and 5.53-fold increases of enzyme activity (towards KG) and catalytic efficiency (kcat/Km, against M5) compared with the WT enzyme, respectively. Furthermore, molecular dynamics (MD) simulations were conducted to precisely explore the differences of catalytic activity between WT and PcMT3, which revealed that PcMT3 has a less flexible conformation, as well as an enlarged substrate-binding channel with decreased steric hindrance and increased binding energy in substrate recognition. In conclusion, we obtained a highly active variant of PcMan113 with potential for commercial application in the manufacture of manno-oligosaccharides.

Relative sensitivity of anterior nares and nasopharyngeal swabs for initial detection of SARS-CoV-2 in ambulatory patients: Rapid review and meta-analysis.

Nasopharyngeal (NP) swabs are considered "gold standard" for diagnosing SARS-CoV-2 infections, but anterior nares or mid-turbinate swabs (nasal swabs) are often used. We performed a meta-analysis comparing the sensitivity of nasal and nasopharyngeal swabs against a composite reference standard for the initial diagnosis of SARS-CoV-2 infection in ambulatory patients. The study is registered on PROSPERO (CRD42020221827). Data sources included studies appearing between January 1, 2020 and March 20, 2021, identified by searches of PubMed, medRxiv and bioRxiv. Studies included at least 20 subjects who simultaneously provided nasal and nasopharyngeal specimens for reverse transcription-polymerase chain reaction testing, and for which confusion matrices could be constructed. Authors individually assessed studies for inclusion and compared assessments. Each author independently extracted all data elements; differences were reconciled by review of initial data sources. Extracted data included specimen site, patient characteristics, collection site, and confusion matrices comparing results for nasal and nasopharyngeal swabs. Assessed against a composite reference standard, anterior nares swabs are less sensitive (82% - 88%) than nasopharyngeal swabs (98%). For populations with 10% specimen positivity, the negative predictive values of all swab types were greater than 98%. Mid-turbinate and anterior nares swabs seem to perform similarly. The lower sensitivity associated with nasal swab SARS-CoV-2 diagnosis is justified by the ability to screen more patients and reduced personal protective equipment requirements. Our conclusions are limited by the small number of studies and the significant heterogeneity of study designs and study outcomes.

Genetic testing for young-onset colorectal cancer: case report and evidence-based clinical guidelines.

BACKGROUND: Young-onset colorectal cancer is clinicopathologically different from older-onset colorectal cancer and tends to occur in patients with hereditary germline conditions such as Lynch syndrome and familial adenomatous polyposis. CASE REPORT: We describe the case of a 44-year-old man with a paternal history of colon polyps, a personal 2-year history of hematochezia, and a diagnosis of rectal cancer. Further clinical evaluation of the patient at our institution determined the cancer to be stage IIIA. The patient underwent genetic counseling and testing, which indicated he was negative for the most common familial cancer syndromes. After treatment with neoadjuvant chemoradiotherapy, surgery, and adjuvant chemotherapy, the patient has done well. We review the hereditary cancer syndromes and genetic tests to consider for patients with early-onset colorectal cancer. CONCLUSIONS: This case underscores the importance of following cancer-screening guidelines.

EPIDEM: A Model for Quality Improvement.

BACKGROUND: Existing quality improvement (QI) models have been used with varied success in health care. We developed the EPIDEM Model of Quality Improvement to apply QI principles to health care and promote a widespread culture of quality and patient safety. METHODS: The EPIDEM acronym can be used to teach and remember the steps of process improvement: explore relevant issues and contextual factors, promote to the right people, implement timely solutions, document steps, evaluate with meaningful measures, and make modifications to improve interventions further. RESULTS: The EPIDEM model requires no previous QI training and can be used in conjunction with other QI tools. Our model uniquely emphasizes understanding local context, culture, and resources throughout the QI process. CONCLUSIONS: We hope that this new QI model will help facilitate an "EPIDEMic" of healthcare QI for our institution and others by providing a foundational framework to successfully implement QI initiatives.

Using the EPIDEM Model of Quality Improvement to Increase Value of BCR-ABL1 Tests.

Objectives: As pathologists and laboratorians, we can enhance patient care by promoting the appropriate ordering of diagnostic tests. Our goal was to improve the ordering of BCR-ABL1 tests by using the EPIDEM model of quality improvement. Methods: We applied the EPIDEM model, which emphasizes understanding local context, culture, and resources, to explore inappropriate BCR-ABL1 ordering, promote and implement a new reflexive testing strategy in-house, document and evaluate effectiveness, and make stepwise modifications. Results: Multiple quality improvement interventions correlated with cost savings and decreased total errors and incorrect orders for both BCR-ABL1 major and minor positive patients. Furthermore, our laboratory built stronger collaborative relationships with colleagues within and outside of pathology. Conclusions: Our molecular pathology laboratory successfully used the EPIDEM model of quality improvement to improve the ordering of BCR-ABL1 tests and promote better patient care by focusing on educational efforts and modification of laboratory workflow.

A Novel Approach to Improving Utilization of Laboratory Testing.

CONTEXT: - The incorporation of best practice guidelines into one's institution is a challenging goal of utilization management, and the successful adoption of such guidelines depends on institutional context. Laboratorians who have access to key clinical data are well positioned to understand existing local practices and promote more appropriate laboratory testing. OBJECTIVE: - To apply a novel approach to utilization management by reviewing international clinical guidelines and current institutional practices to create a reliable mechanism to improve detection and reduce unnecessary tests in our patient population. DESIGN: - We targeted a frequently ordered genetic test for HFE-related hereditary hemochromatosis, a disorder of low penetrance. After reviewing international practice guidelines, we evaluated 918 HFE tests and found that all patients with new diagnoses had transferrin saturation levels that were significantly higher than those of patients with nonrisk genotypes (72% versus 42%; P < .001). RESULTS: - Our "one-button" order that restricts HFE genetic tests to patients with transferrin saturation greater than 45% is consistent with published practice guidelines and detected 100% of new patients with HFE-related hereditary hemochromatosis. CONCLUSIONS: - Our proposed algorithm differs from previously published approaches in that it incorporates both clinical practice guidelines and local physician practices, yet requires no additional hands-on effort from pathologists or clinicians. This novel approach to utilization management embraces the role of pathologists as leaders in promoting high-quality patient care in local health care systems.

Comparison of Two Point-of-Care CYP2C19 Genotyping Assays for Genotype-Guided Antiplatelet Therapy.

BACKGROUND: CYP2C19 polymorphisms contribute about 12% of the variability in the antiplatelet effect of clopidogrel, which is commonly prescribed for patients undergoing percutaneous coronary intervention. For these patients, rapid turnaround time of CYP2C19 genotyping may be critical. We validated and compared the performance of two point-of-care CYP2C19 genotype tests, Nanosphere Verigene CYP2C19 Nucleic Acid Test and Spartan RX CYP2C19 System. MATERIALS AND METHODS: Our CLIA certified Molecular Diagnostic Laboratory performed 99 Verigene tests and 108 Spartan RX CYP2C19 assays. We compared performance and genotype results between the two platforms, across runs, and among technologists. Based on our validation results, we started offering CYP2C19 genotyping using the Spartan RX CYP2C19 assay for post-percutaneous coronary intervention patients. RESULTS: Laboratory validation genotype results were consistent between both assays when the assays produced results (100% accuracy); however, the Verigene CYP2C19 had a 33% no call rate. In contrast, Spartan consistently showed accurate results. Using a newly established clinical workflow, we assayed 342 post-percutaneous coronary intervention patients with the Spartan test. Within one hour of submitting patient samples, ordering physicians were notified of any clinically significant results and provided clinical decision support. CONCLUSIONS: Every approach has its limitations, but our practice of using the Spartan RX CYP2C19 test in our acute cardiac workflow provides accurate and rapid results to guide clinical decision-making at the point-of-care. Prospective follow-up is ongoing to evaluate outcomes and effectiveness of CYP2C19 testing.

Next-generation sequencing of liquid-based cytology non-small cell lung cancer samples.

BACKGROUND: The detection of mutated epidermal growth factor receptor (EGFR) in non-small cell lung cancer (NSCLC) with residual cell pellets derived from liquid-based cytology (LBC) samples (eg, endoscopic ultrasound-guided fine-needle aspiration) has been validated with allele-specific polymerase chain reaction. The aim of this study was to validate next-generation sequencing (NGS) technology for detecting gene mutations with residual cell pellets from LBC. METHODS: Archived DNA extracted from LBC samples of adenocarcinoma stored in PreservCyt with a known EGFR mutation status was retrieved. Genomic DNA was multiplex-amplified and enriched with Ion AmpliSeq Cancer Hotspot Panel v2 chemistry and the OneTouch 2 instrument; this was followed by semiconductor sequencing on the Ion Personal Genome Machine platform. The mutation hotspots of 6 NSCLC-related genes (BRAF, EGFR, ERBB2, KRAS, MET, and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α [PIK3CA]) were analyzed with NextGENe and Torrent Suite bioinformatics tools. RESULTS: The commonly identified EGFR sequence changes, including 4 L858R mutations, 3 exon 19 deletions, and 1 exon 20 insertion, were in 100% concordance between the assay platforms. Less common NSCLC variants were also found in the mutation hotspots of ERBB2, KRAS, MET, and PIK3CA genes. CONCLUSIONS: NSCLC mutation analysis using NGS can be successfully performed on residual cell pellets derived from LBC samples. This approach allows the simultaneous examination of multiple mutation hotspots in a timely manner to improve patient care. Cancer Cytopathol 2017;125:178-187. © 2016 American Cancer Society.

Mosaicism in a patient with Down syndrome reveals post-fertilization formation of a Robertsonian translocation and isochromosome.

It has been estimated that a few hundred children are born each year in the United States with translocation Down syndrome. About 5% of the cases with Down syndrome carry a Robertsonian translocation involving chromosome 21. The case described here is a patient with Down syndrome who showed mosaicism for two cell lines. Each cell line contains a different, de novo acrocentric rearrangement. We constructed somatic cell hybrids from the patient's cells and determined the parental origins of the rearrangements by molecular and fluorescence in situ hybridization (FISH) analyses. The analysis showed that the rob(14q21q) formed between a paternally inherited chromosome 21 and a maternally inherited chromosome 14, indicating that this rearrangement formed post-zygotically. Further molecular analysis also determined that the rea(21q21q) is an isochromosome of paternal origin. The cell line containing the isochromosome is unbalanced, resulting in trisomy 21. Because the same paternal chromosome 21 was involved in both the isochromosome and the Robertsonian translocation, we speculate that an unstable chromosome 21 was stabilized either through formation of a rob(14q21q) or through formation of an isochromosome. The mechanism proposed for the formation of the rob(14q21q) in this case is different from that for most de novo rob(14q21q), but similar to a previously reported mosaic case of Down syndrome.