bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of indeterminate SARS-CoV-2 results with repeat testing on an alternative platform
Authors: Lynn T , Martinez R M 
Published: October 2021

Abstract

Introduction/Objective
Accurate SARS-CoV-2 results are crucial for patient management and infection prevention. Result confidence decreases with low viral load because near the assay’s limit of detection (LOD), test results may alternate between positive and negative, as characterized by Poisson distribution for target analytes at low density. Low positive results may indicate past infection, early infection, a vaccinated individual with low level viral shed, or a false-positive result. EUA methods provide guidance on test interpretation, but laboratories should assess clinical accuracy. The purpose of this study was to assess clinical accuracy of specimens with low positive results.

Methods/Case Report
Respiratory specimens were tested by Cepheid Xpert® Xpress SARS-CoV-2 assay with positive results up to a Ct of 45. A low positive (defined as Ct ≥35), which could not be confirmed by Hologic Aptima® SARS-CoV-2 assay was reported as indeterminate and repeat testing recommended. Repeat testing occurred by Cepheid, Hologic, BioFire, Roche, or Quest assays. Retrospectively, final results were extracted from the LIS (Epic Beaker, Madison, WI, version May 2020) for 5-months (12/1/2020 to 5/31/2021), and chart review performed.

Results (if a Case Study enter NA)
A total of 19,969 tests were performed; 10.4% (n=2,083) were positive, 89% (n=17,728) negative, and 0.79% (n=158) indeterminate. Previous infection (up to 3 months prior) was documented in 18% (n=28) of indeterminate results and defined as true positive. Of remaining indeterminate results, 43% (n=68) had repeat testing as recommended by laboratory; 26% (n=18) were positive and 74% (n=50) were negative. The average number of days between indeterminate and negative result was 7.25 (range 1-38).

Conclusion
Result discordance occurred in &lt; 1% of all samples, excellent agreement. For low positive samples, discordance was higher, as expected. It’s impossible to determine if negative results from the 50 repeat samples were false-positive by Cepheid or false-negative by other methods. In summary, 32% (50/158) of indeterminant samples did not repeat as positive. Overall concordance was high and results fluctuate when low virus is present. In absence of symptoms, we conclude repeat testing is not routinely recommended. Laboratories must recognize that normal variability occurs near assay LOD and must critically assess performance against other methods with similar LODs to fully assess performance of EUA methods.
Next generation sequencing identifies potential PARP inhibitor sensitive mutations
Authors: Humble R , Bossler A 
Published: October 2021

Abstract

Introduction/Objective
Poly ADP-ribose polymerase (PARP) inhibitors are a novel and important drug class targeting homologous recombination DNA repair defects (HRD) and have been approved for use in breast, pancreatic and ovarian cancers. Originally targeted for loss of function mutations in BRCA1 and BRCA2, many other genes are involved in the HRD pathway; Rimar et al detailed 19 DNA repair genes associated with homologous recombination and PARP inhibitor sensitivity. Our 214 gene NGS panel, Iowa Cancer Mutation Profile, includes BRCA1, BRCA2 and 15 other HRD pathway genes. We reviewed cases from the prior 12 months to determine the frequency of HRD7 pathway gene variants in various tumor types with potential PARP inhibitor sensitivity.

Methods/Case Report
Iowa Cancer Mutation Profile NGS test results from June 4, 2020 through May 7, 2021 were reviewed for variants involving ATM, ATR, BAP1, BLM, BRCA1, BRCA2, CDK12, CHEK1, CHEK2, FANCA, FANCC, FANCD2, MRE11A, NBN, PALB2, RAD51c and RAD51d, categorized as pathogenic, likely pathogenic or of unknown significance and had the tumor type identified. Additional chart review for PARP inhibitor therapy was performed in cases of breast, pancreatic, and ovarian cancer.

Results (if a Case Study enter NA)
A total of 599 cases were reviewed with 234 found to have variants in genes with possible PARP inhibitor sensitivity. Of these 2% (n=8) and 11% (n=43) of variants were categorized as pathogenic or likely pathogenic while most (n=334) were categorized as variants of unknown significance. The pathogenic and likely pathogenic variants included mutations in ATM (n=13), BRCA2 (n=12), BAP1 (n=8), FANCA (n=5), BRCA1 (n=4),
NBM (n=3), FANCD2 (n=2), ATR (n=1), CDK12 (n=1), FANCC (n=1), and RAD51d (n=1), and frameshift (n=19) and nonsense (n=19) alterations were most common. Non-small cell lung cancer was the most frequent tumor type identified (n=78). At this time no PARP inhibitors were identified for use in cases of breast (n=9), pancreatic (n=3) and ovarian cancer (n=33).

Conclusion
Review of our institutional results for mutations in HRD pathway genes identified possible PARP inhibitor sensitivity in 8% (46 of 599) of cases during the period of review in a wide variety of tumor types. Our results suggest that variants with possible sensitivity to PARP inhibitor therapy are frequently identified from many tumor types and should be a component of solid tumor mutation profiling.
Semi-automated validation and quantification of CTLA-4 in 90 different Tumor entities using multiple antibodies and artificial intelligence
Authors: Dum D , Blessin N C , Henke T L , Mandelkow T , Bady E , Raedler J , Simon R , Sauter G , Lennartz M , Wilczak W , Burandt E 
Published: October 2021

Abstract

Introduction/Objective
Introduction: CTLA-4 is an inhibitory immune checkpoint receptor and a negative regulator of anti-tumor T-cell function. This study aimed at a comparative analysis of CTLA-4+ entities. cells between different tumor

Methods/Case Report
Methods: To quantify CTLA-4+ cells, 4,582 tumor samples from 90 different tumor entities as well as 608 samples of 76 different normal tissue types were analyzed by immunohistochemistry in a tissue microarray format. Two different antibody clones (MSVA-152R and CAL49) were validated and quantified using a deep learning framework for automated exclusion of unspecific immunostaining.

Results (if a Case Study enter NA)
Results: Comparing both CTLA-4 antibodies revealed a clone dependent unspecific staining pattern in adrenal cortical adenoma (63%) for MSVA-152R and in pheochromocytoma (67%) as well as hepatocellular carcinoma (36%) for CAL49. After automated exclusion of non-specific staining reaction (3.6%), a strong correlation was observed for the densities of CTLA-4+ lymphocytes obtained by both antibodies (r=0.87; p&lt;0.0001). The mean density of CTLA-4+cells was 674±1482 cells/ mm2 and ranged from 71±175 cells/mm2 in leiomyoma to 5916±3826 cells/mm2 in Hodgkin’s lymphoma. Within epithelial tumors, the density of CTLA-4+ lymphocytes were higher in squamous cell (421±467 cells/ mm2) and urothelial carcinomas (419±347 cells/ mm2) than in adenocarcinomas (269±375 cells/ mm2) and renal cell neoplasms (256±269 cells/ mm2). A high CTLA-4+ cell density was linked to low pT category (p&lt;0.0001), absent lymph node metastases (p=0.0354), and PD-L1 expression in tumor cells or inflammatory cells (p&lt;0.0001 each). A high CTLA-4/CD3-ratio was linked to absent lymph node metastases (p=0.0295) and to PD-L1 positivity on immune cells (p&lt;0.0026).

Conclusion
Marked differences exist in the number of CTLA-4+ lymphocytes between tumors. Analyzing two independent antibodies by a deep learning framework can facilitate automated quantification of immunohistochemically analyzed target proteins such as CTLA-4.
Comparison of Abbott COVID-19 testing Platforms for timely results- CMCVAMC experience
Authors: Patel S , Petersen J M , Jhala D 
Published: October 2021

Abstract

Introduction/Objective
COVID-19 is a new disease, caused by the SARS-CoV-2 coronavirus capable of causing severe disease and death. The Alinity-m has a high throughput and random-access features that are not on the Abbott m2000, both of which had been validated and brought into clinical use for high throughput SARS-CoV-2 testing. The additional features of Alinity-m would be expected to improve turnaround time; however, there are no published reports in the English literature comparing the turnaround time between the Abbott m2000 and Alinity-m.

Methods/Case Report
A retrospective quality assurance search for all SARS-CoV-2 tests performed on the Abbott m2000 and Alinity-m (both Chicago IL) between February 1st 2021 to March 1st, 2021, to capture the turnaround time differences for the Abbott m2000 versus the Alinity-m for the month after the Alinity-m was brought into clinical service after validation.

Results (if a Case Study enter NA)
There was a total of 318 tests performed on the Abbott m2000 and 1329 tests performed on the Alinity-m during this time period. The average turnaround time on the Alinity was 6 hours, compared with 11 hours on the Abbott m2000. This difference was statistically significant by the t-test (p-value = &lt;0.01). Both the optimized throughput and random-access features of the Alinity-m contributed significantly to this improvement.
The Alinity-m is capable of producing results within 115 minutes for the first specimen and then 3 minutes for each sequential specimen. On the other hand, the Abbott m2000 must be batched in limited 8-12 hour runs without random access capability. All the results were reported and communicated to the clinical teams, so the timely patient management can be administrated and surveillance of the same can be done in real time.

Conclusion
Alinity M has a significant advantage for a random access as well as improved TAT for detection of SARS-CoV-2, leading to prompt patient care and management.
Extraction-free rapid cycle RT-qPCR and extreme RT-PCR for SARS-CoV-2 virus detection
Authors: Lownik J C , Farrar J S , Way G , Martin R K 
Published: October 2021

Abstract

Introduction/Objective
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostic testing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has faced substantial supply chain shortages and noteworthy delays in result reporting after sample collection. Supply chain shortages have been most evident in reagents for RNA extraction and rapid diagnostic testing. In this study, we explored the kinetic limitations of extraction-free rapid cycle RT-qPCR for SARS-CoV-2 virus detection using the commercially available capillary based LightCycler.

Methods/Case Report
We optimized reverse transcription and PCR under extraction-free and rapid thermocycling conditions utilizing hydrolysis probe-based detection methods using a Roche LightCycler.

Results (if a Case Study enter NA)
This protocol improves detection speed while maintaining the sensitivity and specificity of hydrolysis probe-based detection. Percentage agreement between the developed assay and previously tested positive patient samples was 97.6% (n= 40/41) and negative patient samples was 100% (40/40). We further demonstrate that using purified RNA, SARS-CoV-2 testing using extreme RT-PCR and product verification by melting can be completed in less than 3 minutes.

Conclusion
We developed a protocol for sensitive and specific RT-qPCR of SARS-CoV-2 RNA from nasopharyngeal swabs in less than 20 minutes, with minimal hands-on time requirements. Overall, these studies provide a framework for increasing the speed of SARS-CoV-2 and other infectious disease testing.
Intraoperative Assessment of IDH Mutation Status and Tumor Invasioni in Glioma
Authors: Brown H , Chen R , Cooks R , Garcia D , Chaichana K , Quinones-Hinojosa A , Jentoft M , Middlebrooks E 
Published: October 2021

Abstract

Introduction/Objective
Maximizing surgical resection in gliomas, while avoiding compromising non-infiltrated tissue, is associated with survival benefit. Current methodologies are suboptimal in providing rapid, intraoperative molecular characterization of tissue. We address this unmet need by using desorption electrospray ionization mass spectrometry (DESI-MS) for the intraoperative molecular assessment of gliomas.

Methods/Case Report
This prospective study uses intraoperative DESI-MS analysis of fresh tissue to evaluate IDH mutations via 2-hydroxyglutarate intensity and TCP via measurement of N-acetylaspartic acid (NAA) intensity and characteristic lipid profiles in less than three minutes. Blinded review of the tissue smears by a neuropathologist is used to validate IDH mutation status and TCP estimates.

Results (if a Case Study enter NA)
Presently, 529 biopsies from 85 enrolled patients have been collected and analyzed at two institutions. TCP assessment based on NAA intensity in 203 biopsies at the first institution yielded sensitivity, specificity, and accuracy values of 91, 76, and 83%, whereas TCP estimates via characteristic lipid profiles yielded 76, 85, and 81%, respectively. Assessment of IDH mutation status of 71 core biopsies yielded sensitivity, specificity, and accuracy values of 89, 100, and 94%. Ongoing validation of the methodology is being performed at a second institution, where we have collected 282 biopsies from 36 patients. IDH mutation assessment of the first 15 patients indicate 100% sensitivity, specificity, and accuracy.

Conclusion
This study represents the first and largest study using DESI-MS for the intraoperative evaluation of IDH status and TCP measurement in gliomas. Prospectively, we propose to modify our DESI-MS system to allow estimation of IDH mutation status and TCP in surgical cavities without the need for a biopsy by placing a surgical material along the margin and transferring material from the blot to a microscope slide prior to DESI-MS analysis. We envision molecular analysis by DESI-MS as a complementary technique to histopathology capable of providing additional clinical information in near real-time.
Assessment of Comprehensive Mutational Profiling in T-lymphoblastic leukemia/lymphoma (T-ALL/LBL): A Single Center Experience
Authors: Reddy N C , Reddy A C , Reddy K S 
Published: October 2021

Abstract

Introduction/Objective
T-lymphoblastic leukemia/lymphoma (T-ALL/LBL) is a malignancy arising from immature precursor T cells with T-ALL involving bone marrow/blood and T-LBL occurring in the thymus and nodal/extranodal sites. Studies have now revealed &gt;100 recurrently altered genes that are not necessarily disease initiating but can provide diagnostic, prognostic, and predictive information which can then be utilized in personalized therapy.

Methods/Case Report
Next-generation sequencing was performed on DNA and/or RNA extracted from blood/marrow aspirates or tissue at an external CLIA-certified, CAP-accredited laboratory. The hematology panel sequenced DNA of 406 genes, introns of 31 gene rearrangements, and RNA of 265 genes.
This retrospective single-center study highlights salient findings noted in genomic profiles of 15 T-ALL/LBL cases out of 83 total patients with ALL from 2018-2021. While the majority were B-ALL cases, T-ALL accounted for 18%, and all but 1 case were pediatric patients (ages 9-21 years).

Results (if a Case Study enter NA)
In our pediatric cohort (14 patients; 9 males, 5 females), as in literature, NOTCH signaling was most frequently involved with NOTCH1 (50%) and FBXW7 (36%) mutations, followed by those in cell cycle process CDKN2A/2B (36%) and PTEN (28%) mutations. Other mutations: PHF6 (21%), BCOR and TAL1 (14%) each. The prognostic effect of mutations: NOTCH1 favorable, FBXW7 no effect but trend toward favorable when FBXW7 co-occurs with NOTCH1 while PTEN is unfavorable (3 patients had relapses). Some unusual or useful findings: a patient diagnosed initially as AML with aberrant CD3 was re-classified as early T-cell precursor ALL, supported by RELN mutation (occurs in 4% ETP-ALL). The adult with NOTCH1 and BCOR mutations in addition to BCR-ABL1 fusion was diagnosed as having T-ALL blasts with CML. We could not study detailed nuances in mutational profiles of T-ALL vs T-LBL with only 1 case of T-LBL showing FBXW7, PTEN, NF1, RB1, BCOR and NRAS mutations (latter is typically noted in pediatric T-LBL cases).

Conclusion
Clinical molecular testing in our pediatric T-ALL patients revealed gene alterations that provide refinement of diagnosis, prognosis, and risk stratification. It also contributes a useful data set for further analysis and potential use of clinically actionable therapeutic targets in some cases. Longer term follow-up incorporating therapy and outcomes information would be valuable.
Massive Perivillous Fibrin Deposition-A Cause of Recurrent Fetal Demise: A Case Report
Authors: Pandiri M , Kashikar R 
Published: October 2021

Abstract

Introduction/Objective
Massive perivillous fibrin deposition (MPFD) and maternal floor infarction (MFI) are rare placental lesions reported in less than 1% of all pregnancies and have a significant risk of recurrence ranging from 12% to 78%. MPFD/MFI is associated with high rates of adverse perinatal outcomes including preterm delivery, severe intrauterine growth restriction, spontaneous abortion, cystic renal cell dysplasia, fetal metabolic disease with reported mutations in the LCHAD (long-chain 3-hydroxy acyl-CoA-dehydrogenase) gene, neonatal death and long- term neurological impairment.

Methods/Case Report
We report a case of MFPD in a 28-year-old female gravida 3 para 1 with one uncomplicated pregnancy and one therapeutic abortion. The current pregnancy was complicated by abruption resulting in intrauterine fetal demise at 32 weeks of gestation. The placenta was examined. Grossly, the placenta weighed 260 grams (small placenta for the dates) with an eccentrically inserted three vessel umbilical cord and a diffuse, firm pale grey cut surface with focal cystic areas. The histological examination revealed MPFD characterized by extensive transmural perivillous fibrinoid material with encasement of almost entire chorionic villi (transmural type). The villi were viable but fibrotic with focal syncytiotrophoblastic necrosis and focal mild chronic inflammation. The etiology of MPFD is not well understood, but risk factors that have been reported include maternal thrombophilia, coagulopathies, and autoimmune diseases. Given the clinical associations, MFI/MPFD should be reported promptly to the obstetrician and pediatrician. As per the current literature, a combination of thrombolytic therapy (aspirin and heparin), intravenous immunoglobulin and a statin (pravastatin) helps to correct angiogenic/antiangiogenic imbalance which has been thought to be associated with recurrent MFI/MPFD.

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

Conclusion
In summary, we present this rare recurring entity of MPFD to emphasize the awareness of this condition and the importance of placental examination in all abortions and fetal abnormalities/demise.
Mature tertiary lymphoid structures in lung adenocarcinoma are associated with better progression free survival
Authors: Obeng R , Parihar V , Alexis D , Behera M , Owonikoko T , Pillai R , Ramalingam S , Sica G , Ahmed R 
Published: October 2021

Abstract

Introduction/Objective
The presence of inducible lymphoid structures known as tertiary lymphoid structures in the tumor microenvironment has been shown to correlate with positive clinical outcome. However, the maturation states of lymphoid aggregates in lung adenocarcinoma are not completely understood.

Methods/Case Report
Seventy tumor samples from 69 patients diagnosed with lung adenocarcinoma (Stages I to III) between 2013 and 2015 were included in the study. The presence and maturation states of the lymphoid structures within the tumors were evaluated by conventional and 26 samples were further analyzed by multiplexed immunohistochemistry of formalin fixed paraffin embedded tissues and then quantified. Mature lymphoid follicles containing germinal centers were identified by the presence of CD21+ and BCL-6+ cells in an organized configuration within tight clusters of T and B cells.

Results (if a Case Study enter NA)
Samples with fully mature lymphoid structures (germinal centers) had larger tumors and higher disease stage. The number of mature lymphoid structures correlated with the total number of lymphoid aggregates present in the tumor microenvironment. Additionally, tumor samples with ≥10 mature lymphoid structures had more primary follicles. While there was no difference in overall survival, progression free survival was significantly longer in patients who had ≥10 mature lymphoid structures in comparison with patients who had &lt;10 mature structures.

Conclusion
In conclusion, a spectrum of lymphoid aggregates in different stages of maturation are present in lung adenocarcinoma. An increase in the number of mature lymphoid structures may be associated with progression free survival in patients with lung adenocarcinoma.
Heterotopic Ossification in Benign and Malignant Renal Neoplasms
Authors: Badeti S , Deb P Q , Heller D , Fitzhugh V , Weiss R 
Published: October 2021

Abstract

Introduction/Objective
Heterotopic bone formation in renal neoplasms is a rare phenomenon. Ossification with or without marrow elements has been reported in both benign and malignant renal tumors. Due to its rarity, the epidemiological and clinical features of this finding are not well-documented. Herein, we have examined heterotopic ossification in renal neoplasms and summarized the epidemiological and clinical features of this entity.

Methods/Case Report
A database search on PubMed, Scopus, and Google Scholar was performed using a combination of proper search terms. Full article texts of all search results were reviewed with reference lists screened for additional articles matching the search criteria. The demographic details of the patients, disease characteristics, treatment, and outcomes were all extracted from full text articles and were summarized in a pre-standardized form. The inclusion criteria were set as any epithelial renal neoplasm with histological evidence of heterotopic ossification. A case of clear cell renal cell carcinoma (CCRCC) with heterotopic ossification diagnosed in our institution is included in the study.

Results (if a Case Study enter NA)
A total of 30 cases were found of renal neoplasms with bone formation. The majority of patients were between the ages of 40 to 60. The male to female ratio was 1:1. The majority (19/30) were histologically diagnosed as CCRCC, the most common subtype of kidney tumor with a few cases diagnosed as chromophobe RCC (4/30), papillary RCC (3/30), and cystic nephroma (2/30). Of the neoplasms reported, tumor size varied from 3.0 cm to 28.8 cm.

Conclusion
Heterotopic ossification of renal neoplasms often presents a diagnostic challenge to the radiologist as other benign conditions such as extramedullary hematopoiesis can be in the differential. The rarity of this phenomenon renders pre-surgical diagnosis difficult. Our study documents this phenomenon to be seen in a variety of renal neoplasms and underscores the necessity to be aware of this rare entity.