bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple Hepatic Microabscesses Caused by Magnusiomyces Clavatus in a Patient with Acute Myeloid Leukemia: A Case Report
Authors: Pokharel A , Elzieny M , Wey E , Zhang P L 
Published: November 2023

Abstract

Introduction/Objective
Invasive fungal infections can result in significant complications for acute myeloid leukemia (AML) patients undergoing induction chemotherapy. While Candida and Aspergillus are the most common fungal pathogens, Magnusiomyces clavatus (Geotrichum clavatum) is a rare fungal pathogen that has been reported to cause invasive infection in immunocompromised patients. Here, we report a case of fungemia and hepatic microabscess with Magnusiomyces clavatus in an 18-year-old female with AML.

Methods/Case Report
An 18-year-old female with AML in remission after induction chemotherapy presented with fevers. Further work-up revealed fungemia on her blood culture. While awaiting culture speciation, numerous hepatic lesions were identified on the abdominal CT scan, which were biopsied. The liver biopsy showed aggregates of fungi with septate hyphae on silver-stained sections. The initial morphologic differential diagnosis included Aspergillus and Mucormycosis. Her blood cultures ultimately revealed fungemia with Magnusiomyces clavatus (Geotrichum clavatum), a yeast that is rising in prevalence, particularly among neutropenic and leukemic patients. The morphology of fungi detected in the liver biopsy resembled Magnusiomyces clavatus and a subsequent PCR testing confirmed that the fungi present was Magnusiomyces clavatus. She was started on voriconazole and liposomal amphotericin B. She became afebrile with no growth on blood cultures for several days and was discharged to outpatient follow-up.

Results (if a Case Study enter NA)
N/A

Conclusion
This case highlights the clinical significance of Magnusiomyces clavatus in immunocompromised patients, particularly those with AML, and emphasizes the importance of considering rare fungal pathogens in such patients who present with fever. Treatment with voriconazole and liposomal amphotericin B can be helpful in relieving symptoms.
From research genomics to clinical genetics: Insourcing next generation sequencing in a pediatric and women’s hospital
Authors: Asinas J M 
Published: November 2023

Abstract

Introduction/Objective
The Sidra Medicine Clinical Genomics Laboratory (CGL) offers rapid and cost-effective next- generation sequencing (NGS) solutions such as Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) which support various research initiatives in Qatar. With the current worldwide trend in precision and personalized medicine, the Pathology Genetics (PG) division is required to provide in-house diagnostic genetic testing to clinical patient groups. The main objective of this quality initiative project is to decrease the cost of NGS send-out tests and to perform patient testing in-house. The CGL NGS workflow and processes must be validated to comply with the clinical accreditation requirements of the College of American Pathologists (CAP).

Methods/Case Report
Assay performance metrics are considered for the validation of the Illumina NovaSeq 6000 NGS platform. Sample library preparation is performed in PG while sequencing and data analysis is based in CGL. NGS quality assurance in CGL involves the use of Illumina PhiX control mixed with the pooled library. To maintain the high throughput and low-cost NGS approach, Illumina S4 flow cells are used with efficient library pooling techniques. The TAT of clinical samples for WES and WGS analysis in CGL is around 14 days which includes sequencing, data conversion, and bioinformatics.

Results (if a Case Study enter NA)
A Service Level Agreement (SLA) between Sidra Research and Sidra Pathology was created to define the workflow and services provided by both departments with clear lines of responsibility and accountability. A quality manual is also written to describe the QMS of the genomics laboratory and outlines the various NGS services offered. CGL protocols are transferred to CAP-approved SOP templates for standardization with pathology documentation. For quality improvement, the NGS workflow in CGL is continuously developed to improve the data produced and TAT.

Conclusion
The collaboration between the two departments maximized the available infrastructures of Sidra Medicine, saved costly send-out tests, improved the TAT of genetic analysis, and most importantly enhanced healthcare outcomes and related clinical diagnostics in alignment with the National Health Strategy (NHS) of the country. Accreditation propels good QMS in laboratory services hence this quality initiative fulfills Sidra Medicine’s vision to provide total precision diagnosis and personalized medicine leading to the delivery of exceptional care to rank amongst the top medical centers internationally.
Development of a Companion Diagnostic for a Targeted Protein Degradation Therapy: Ultrasensitive and Minimally-Invasive Detection of SALL4 Oncoproteins for Therapeutic Monitoring
Authors: Liu J , Senussi Y , Melkonian A , Walt D R , Chai L 
Published: November 2023

Abstract

Introduction/Objective
Spalt-Like Transcription Factor 4 (SALL4), a member of the SALL family, is a regulator of embryonic stem cell development that plays a crucial role in cell renewal and proliferation. SALL4 expression is normally repressed in most adult organs but is reactivated in a multitude of cancers and upon treatment with hypomethylating agents (HMA). Research in the past 20 years established SALL4 as a novel, druggable cancer target. SALL4 targeting therapies (inhibitors and degraders) are under pre-clinical development. There are currently no FDA/CLIA approved SALL4 diagnostic tests beyond tissue immunohistochemistry (IHC). Therefore, there is outstanding clinical need for the development and validation of a less invasive and sufficiently-sensitive SALL4 expression assay which can be used for selecting, and monitoring patients on SALL4-targeting therapy such as molecular glue degraders, as well as monitoring patients on HMA treatment.

Methods/Case Report
Using the Simoa (Single Molecule Array) platform, a bead-based digital enzyme-linked immunosorbent assay, we cross-tested 5 commercial SALL4 antibodies and 13 antibody pair combinations, using the best antibody pair to test the matrix effects of human plasma, buffy coats, and bone marrow aspirates. For quantitative assay development, we successfully expressed and purified full-length SALL4 which will be used to calibrate the standard curve and determine the assay’s limit of quantification.

Results (if a Case Study enter NA)
The best antibody pair can detect both SALL4A and SALL4B isoforms, with stronger signal detected with the SALL4A isoform. We successfully optimized detection of SALL4 in bone marrow and peripheral blood matrix, and tested the utility of the assay for quantifying the efficacy of SALL4 degrader drugs and with hypomethylating agent treatment, using cell culture system. We also optimized multiple pre-analytic steps, including our cell lysis protocol, isolation of buffy coats using density gradient separation, and sample collection method comparison.

Conclusion
We developed an ultrasensitive SALL4 expression assay will be useful for monitoring patients on HMA treatment and SALL4-targeting therapy such as molecular glue degraders. There is ongoing effort to use MGB Biobank peripheral blood samples to validate SALL4 Simoa for patients with myelodysplastic syndrome (MDS), acute myeloid leukaemia (AML), and liver cancer.
Diagnostic Value of Concurrent Endoscopic Ultrasound-Guided Fine-Needle Aspiration and Fine-Needle Core Biopsy in Cytology Categories of Pancreatic Solid Lesions: An Institutional Experience
Authors: Mousavi S , Mirzaei Baboli K , Salehiazar S , Rector A R 
Published: November 2023

Abstract

Introduction/Objective
Endoscopic ultrasound is the current standard of care in the evaluation of pancreatic solid lesions. Two methods have been employed in obtaining EUS-guided pancreatic specimens; fine needle aspiration (EUS-FNA) and fine needle core biopsy (EUS-FNB). EUS-FNA may have certain limitations, including the inability to assess the histological architecture and a limited sample size for immunohistochemical staining on cell blocks. EUS- FNB, which employs a larger needle for core biopsy, was developed to address these limitations. However, it is still uncertain which method is better suited for specific lesions. In this study, we evaluated the diagnostic efficacy of concurrent EUS-FNA and EUS-FNB from pancreatic solid lesions.

Methods/Case Report
We reviewed our institutional database for cases that had EUS-FNA from pancreatic solid lesions with a subsequent definitive diagnosis on histology. Similarly, the concurrent EUS-FNB findings were recorded. The cases were categorized based on the World Health Organization pancreaticobiliary cytology reporting system. Furthermore, the absolute risk of malignancy (ARM) of each diagnostic category (defined as the presence of high-grade dysplasia or worse on the histologic follow-up) was calculated.

Results (if a Case Study enter NA)
A total of 108 cases were reviewed for the study from 1/1/2019 to 6/1/2022. The patients were 47% male and 53% female with an average age of 68. No case was categorized as non-diagnostic or neoplastic high-grade. There were 20 benign, 7 atypical, 3 neoplastic low-grade, 6 suspicious for malignancy, and 72 malignant cases, and the associated ARM related to each category was 40%, 86%, 33%, 33%, and 96% respectively. Concurrent EUS-FNB was performed in 23 cases in total (12 in malignant and 11 in other categories). EUS-FNB exhibited 95% positive and 100% negative predictive values (PPV and NPV) in all categories combined and 89% PPV and 100% NPV in non-malignant and indeterminate categories (categories II, III, IV, VI) for correlating to the histologic follow-up.

Conclusion
Cases diagnosed in all categories except the malignant category demonstrated ARM rates higher than expected. When approaching a solid pancreatic lesion, EUS-FNB may increase the diagnostic value, especially in cases of non-malignant and indeterminate categories. Moreover, categorizing the cases in the benign category may require additional supporting data, and placing them in the nondiagnostic category may be more appropriate warranting re-sampling if there is a clinical vs pathologic discrepancy.
A Rare Case of High grade Epithelioid Malignant Neoplasm with CAM 5.2 Expression and (EML4–ALK) Fusion in a Pediatric Patient
Authors: Aljumaili Z , Zhao B , Tchakarov A 
Published: November 2023

Abstract

Introduction/Objective
ALK (anaplastic lymphoma kinase) fusions have been identified in lymphomas and diverse cancer types including carcinomas, melanomas and mesenchymal neoplasms such as inflammatory myofibroblastic tumors (IMT), epithelioid fibrous histiocytoma (EFH). Herein we present a (non IMT, non EFH) ALK rearranged aggressive epithelioid neoplasm.

Methods/Case Report
We report a 17-year-old male with a 14.0 cm mediastinal mass and extensive metastatic disease involving brain, bones, pleura and lymph nodes. The tumor was made of epithelioid like cell with round nuclei, prominent nucleoli and a moderate amount of cytoplasm, arranged in a nested pattern. Ki-67 showed a high proliferative index, &gt;70%. The tumor cells were positive for CAM 5.2; weakly positive for AE1/3, ALK, CD30; focally positive for p63, p53, S100. Additional stains including CD117, PLAP, OCT-4, Sall-4, glypican-3, synaptophysin, chromogranin, CK5/6, p40, pan-melanoma, myogenin, CD99, WT1, CD34, CD45, CD138, MUM1, CD2, CD4, CD5, CD3, CD7, CD15, CD23, CD31, CD20, CD79a, CD15, PAX8, PAX5, CD43, MPO, desmin, D2-40, Calretinin, ERG,
SOX-10, PD-L1 and NUT-1 were all negative. Both BRG and INI1 were retained. The keratin positivity and the lack of “hallmark” cells made anaplastic large cell lymphoma (ALCL) less likely. The absence of desmin and CD30 excluded the rare epithelioid IMT sarcoma. Next-generation sequencing detected an (EML4–ALK) fusion. A diagnosis of high- grade epithelioid malignant neoplasm with (EML4–ALK) fusion was made.
Most cases of this category were described as low grade-appearing spindled cells within a myxoid stroma arranged in fascicles (+S100, +CD34) and have unaggressive behavior. Only three cases, were characterized by epithelioid high- grade morphology and metastatic nature. They shared features like little collagenous stroma, conspicuous mitotic activity and tumor necrosis.

Results (if a Case Study enter NA)
NA

Conclusion
Identification of kinase fusions was essential for precise classification, better knowledge of this epithelioid high grade malignant neoplasm and for targeted therapy purposes. The significant clinicopathologic heterogeneity of this emerging group requires further investigation.
LC/MS-MS quantification of myo-inositol: a novel biomarker for kidney disease
Authors: Omosule Catherine , Blair Connor , Herries Elizabeth , Ladenson Jack , Farnsworth Christopher , Dietzen Dennis , Gaut Joseph 
Published: November 2023

Abstract
Creatinine is the primary biomarker used for assessing kidney function in patients with suspected acute and chronic kidney injury. However, creatinine, a product of muscle creatine metabolism, is an imperfect proxy for renal function because it is subject to non-renal interferences including muscle mass, diet, and medications. Creatinine is particularly problematic as a biomarker of acute kidney injury (AKI) due to relatively high renal function reserve, requiring considerable kidney damage and time for a clinically significant change in creatinine to be detected. Given that AKI and chronic kidney injury (CKD) are associated with high mortality, morbidity, and contribute significantly to health care costs, there is an unmet need for highly sensitive and specific biomarkers for assessing renal function in patients.
Myo-inositol oxygenase (MIOX) is a novel biomarker limitedly expressed in the proximal renal tubules. MIOX concentrations are elevated in mice with renal injury and in critically ill patients with AKI. Our previously published studies have demonstrated that elevation in MIOX concentrations precedes changes in creatinine concentrations by approximately 54 hours. Importantly, MIOX facilitates the conversion of myo-inositol to glucuronic acid.
We developed a robust LC-MS/MS method to quantify myo-inositol in human plasma, hypothesizing that following renal injury (acute and chronic), plasma concentrations of myo-inositol will increase, and will correlate with increases in serum creatinine concentrations. A healthy outpatient cohort was identified from samples obtained from out-patients with normal plasma creatinine, eGFR&gt;60, as well as normal urine protein: creatinine ratio, albumin: creatinine ratio, or urinalysis results that were pan-negative/pan-normal. Remnant samples from out-patients with clinically staged CKD who have not initiated dialyses were selected for the CKD group.
In healthy adult out-patients with stable renal function, the central 95th% distribution of plasma myo-inositol concentrations was 16.61 - 44.2 uM (Median 27.7uM, 95% CI: 26.7-28-7). No sex-based differences in plasma myo-inositol were observed. We also observed excellent correlation between plasma myo-inositol and serum creatinine concentrations (r=0.84, 95% CI: 80-88), as well as excellent sensitivity (99%) and specificity (100%) at a myo-inositol concentration of 50.22uM for differentiating patients with stable kidney function from those with CKD. Patients with CKD exhibited higher plasma myo-inositol concentrations (p value &lt;0.0001) with a central 95% percentile of 51.2-309.1 uM (Median 104.1 uM, 95% CI: 92.3- 113.6).
These results imply that myo-inositol concentrations increase in accord with renal injury and MIOX buildup in patients with kidney dysfunction, making it a potential biomarker for renal impairment.
Evaluation of different microbead volumes in a single antigen bead assay for HLA antibody detection
Authors: Frick Robert , Wetter Lauren , Phelan Donna , Liu Chang , Tang Mei San 
Published: November 2023

Abstract

OBJECTIVE
S: The multiplexed single antigen bead (SAB) assay is now commonly used for detection of antibodies to human leukocyte antigens (HLA) in the management of solid organ transplantation. Serum is incubated with microbeads individually coated with unique HLA antigens and the presence of antibody is detected using a secondary antibody. Due to its cost, laboratories may use a lower-than-recommended volume of reagent microbeads, although the impact of microbead volume on assay performance has not been reported. The present study seeks to determine the concordance of an SAB assay when different microbead volumes were used. Although this is also a required laboratory practice when modifications are made to an FDA-cleared assay, requirements for the validation of a multiplexed assay are currently not well-standardized. Hence, this study may also serve as an example framework for validating a clinical multiplexed assay.

METHODS
SAB (LabScreen, One Lambda) was performed on 14 patient specimens [Mei San T1] selected to provide a range of class I and II HLA antibody levels. Each specimen was tested using three microbead volumes of 5 μL (manufacturer-recommended), 3 μL and 2.5 μL. All reactions were tested in a single session to minimize sources of variability. A mean fluorescence intensity (MFI) of ≥ 2000 was used to define positive beads, which is also the institutional threshold for defining incompatible antigens in solid organ transplantation. Concordance between different bead volumes was calculated using Cohen’s Kappa. Bland-Altman plots were used to visualize bias. All analyses were performed at individual bead level.

RESULTS
Kappa values were: 0.91 (class I) and 0.95 (class II) for 3 μL vs. 5 μL; 0.90 (class I) and 0.93 (class II) for 2.5 μL vs. 5 µL; 0.97 (class I) and 0.93 (class II) for 2.5 μL vs. 3 μL. Positive bias in MFI values was observed with lower bead volumes and was most pronounced in the 2.5 μL vs. 5 μL comparison; in contrast, MFI values between 2.5 µL and 3 µL were more similar.

CONCLUSION
Lower-than-recommended microbead volume may be used in the SAB assay without significant impact on classification of incompatible antigens. Although positive bias in MFI values was observed with lower microbead volumes, the impact on positive vs. negative beads assignment was minimal. Since the tested microbead volumes represented 12.5-20% of the total reaction volume, such a change could have caused a matrix effect and impacted antibody-bead binding, leading to differences in MFI values. Hence, individual laboratories modifying the SAB assay should validate such modifications before implementation to ensure the accuracy of HLA antibody assignment.
Automated Machine Learning-Based Diagnosis and Molecular Characterization of Acute Leukemias using Flow Cytometry Data
Authors: Lewis Joshua , Cooper Lee , Jaye David , Pozdnyakova Olga 
Published: November 2023

Abstract
Current flow cytometric analysis of blood and bone marrow samples for the diagnosis of acute leukemias relies heavily on manual intervention in both the processing and analysis steps, introducing significant subjectivity into the resulting diagnosis and increasing diagnostic turn-around time. Additionally, concurrent molecular characterization of these samples via cytogenetics and targeted sequencing panels can take multiple days, thereby delaying patient diagnosis and treatment. Attention-based multi-instance learning models are machine learning models that can make accurate predictions and generate interpretable insights regarding the classification of a sample from multiple events/cells; while these models have been developed for anatomic pathology applications, they have yet to be applied to flow cytometry data. By utilizing 1,820 flow cytometry samples from 2019-2022 at Brigham and Women’s Hospital, we developed attention-based multi-instance machine learning models for automated diagnosis of acute leukemia, including differentiation of acute myeloid leukemia (AML) from B-lymphoblastic leukemia/lymphoma (B-ALL). Additionally, using concurrent cytogenetic and targeted sequencing data from 674 acute leukemia samples, machine learning models for prediction of molecular aberrancies from flow cytometry data were developed. Machine learning models were created using the TabNet deep learning architecture and VIME self-supervised training algorithm, which are state-of-the-art approaches towards machine learning from tabular data including flow cytometry data. Attention-based multi-instance models demonstrated strong performance for the automated diagnosis of acute leukemia versus non-leukemia samples (AUROC 0.869), as well as the separation of AML from B-ALL samples (AUROC 0.971). These models also accurately predicted cytogenetic aberrancies among AML samples, including t(15;17);PML::RARA (AUROC 1.00), as well as mutations including NPM1 (AUROC 0.725). These models do not require any manual intervention including compensation or gating, and additionally provide quantitative scores for the relative importance of different flow cytometry events and markers for the diagnosis of a particular sample. These importance scores can be integrated into flow cytometry analysis software for visualization and interpretation by hematopathologists. In this study, we have demonstrated the capability of machine learning models to provide automated diagnoses of acute leukemia, as well as accurately predict cytogenetic and molecular aberrancies in blood and bone marrow samples using flow cytometry data. This automated workflow can significantly decrease diagnostic turn-around time and ultimately improve patient outcomes.
Optimized method to enhance the limit of detection for large FLT3 internal tandem duplications
Authors: Hubler Zita , Ficor Tracy , Stroup Brooke , Parikh Bijal 
Published: November 2023

Abstract
Internal tandem duplications (ITDs) in the fms-related tyrosine kinase 3 gene (FLT3) are recurrently detected in acute myeloid leukemia (AML) and are associated with a poor prognosis. Evaluation for the presence of ITDs in AML is considered standard of care; detection alters risk stratification and therapeutic selection. ITDs can range in size, being a minimum of three base pairs to over 300 base pairs. Larger ITDs are considered rare; however, it is unclear whether this represents true prevalence or a consequence of conventional assay design. The FDA-approved companion diagnostic test for the detection of FLT3 ITDs has a six times higher limit of detection for large ITDs (~300 bp) compared to medium or small ITDs. Further, the conventionally used short-read sequencing approaches to detect ITDs can also struggle to detect larger duplications. Therefore, it is unknown how many patients may have large ITDs that have gone undetected. We developed an approach to improve the detection limit for large ITDs that uses polymerase chain reaction (PCR) and capillary electrophoresis (CE) with a spiked-in reference. Larger ITDs undergo a predictable and reproducible negative PCR bias, which can be adjusted once the effect has been quantitatively characterized. FLT3 ITDs are reported as an allele ratio, the ratio of the ITD to the wild-type allele, as a biomarker for prognosis; the spike-in reference allows for quantification of an allele ratio despite distinct CE run conditions for the ITD and wild-type alleles. Using existing commercially available controls and manufactured plasmid controls, sensitivity was optimized, including temperature, injection time, polymerase, and PCR primers. With this method, the detection limit for large ITD variants is comparable to the limit of detection for medium and small ITDs in the FDA-approved companion diagnostic assay. We now have a robust tool to evaluate the accuracy, precision, linearity, and limit of detection at different ITD lengths. Enhanced identification of large FLT3 ITDs may modify the prevalence estimates of large ITDs in AML and ultimately alter patient management.