bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation and Implementation of molecular RT-PCR COVID-19 Testing Platforms
Authors: Patel S , Jhala D 
Published: October 2021

Abstract

Introduction/Objective
COVID-19 is caused by the SARS-CoV-2 coronavirus that has led to a worldwide pandemic with an unprecedented need for fast and accurate testing under FDA Emergency Use Authorizations (EUA). Despite the promise of the Alinity-m as an upgrade from the Abbott m2000 for optimization of high throughput testing and random access for laboratory workflow, validation studies comparing Alinity-m to already used Abbott m2000 are sparse in the literature, particularly for the veteran population.

Methods/Case Report
The validation study for the Alinity m (Chicago IL) was performed in three parts 1) Method to method sample/patient correlation study, 2) precision study (at 250 virus copies/mL, 500 virus copies/mL and 1000 virus copies/mL versus 4 negatives), and 3) verification and confirmation of the accuracy of the assay at the lower limit of detection (LOD). For the validation study. The patient specimens were used side by side for both assays. The results from the Abbott m2000 (Chicago IL), which was already established in our lab, were used as a reference for validation.

Results (if a Case Study enter NA)
The validation with a method to method correlation included 157 valid specimens from which concordant results were obtained for all 157 specimens on both the Alinity-m and Abbott m2000. The precision or reproducibility of the Alinity-m was verified at all concentrations. The limit of detection verification on diluted samples determined the limit of detection to be 20 virus copies/mL (&gt;95% of dilution samples agreed with positive results at this level), which confirmed even below the manufacturer provided LOD of 100 virus copies/mL.

Conclusion
Alinity m was validated for clinical use with study demonstrating that it is 1) equivalent in the method to method correlation, precision, and LOD determination. 2)The validation of Alinity m, holds great promise with its optimized throughput for testing of large numbers of specimens with less technician handling and random access, is a valuable addition to the literature of test validations under the FDA EUA. 3)The validation of tests under the FDA EUA is unprecedented and provides an important way to improve patient care during this extraordinary pandemic.
Molecular Profiling in Thyroid cancer- Using next generation sequencing to differentiate rare cases of papillary thyroid hyperplasia from papillary thyroid carcinoma
Authors: Lazim A , Luceno S , Arriola A , Seth A , Jhala N 
Published: October 2021

Abstract

Introduction/Objective
Differentiating papillary thyroid hyperplasia from papillary thyroid carcinoma is made primarily on differences in key histologic and cytomorphologic features. These include architectural features such as invasion and nuclear changes such as chromatin pallor, nuclear grooves, and intranuclear pseudoinclusions. Distinguishing between these two diagnoses is not always straightforward in a minority of cases, as papillary thyroid hyperplasia nodules can be misinterpreted as papillary thyroid carcinoma and vice versa. This is because the nuclear changes can be subtle and be induced artificially by poor or inadequate formalin fixation. Immunostains such as cytokeratin 19 (CK19), galectin-3, and HBME1 may be used to distinguish between papillary thyroid hyperplastic nodules and papillary thyroid carcinoma; however, as immunostaining results are not always definitive, other more definitive ancillary tests are sometimes utilized such as molecular testing.

Methods/Case Report
Thyroid cases with indeterminate diagnoses (n=6) were obtained from the archives. Such cases included papillary thyroid hyperplasia and cases with descriptive diagnoses such as well-differentiated encapsulated and low-grade papillary carcinoma. Five cases of definitive papillary thyroid carcinoma and one case of follicular thyroid carcinoma (n=6) were used as a comparison group. Next generation sequencing (NGS) assays were performed using a custom SLIMamp targeted DNA solid tumor panel (Pillar Biosciences) and a targeted multi gene RNA fusion panel (Invitae).

Results (if a Case Study enter NA)
All of the definitive cases of papillary thyroid carcinoma showed characteristic mutations such as BRAF V600E as well as RNA fusions such as RET/PTC while all of the indeterminate cases did not show any detectable DNA mutations or RNA fusions, confirming their benign nature. A separate case that was signed out as non-invasive follicular thyroid neoplasm with papillary-like nuclear features showed an NRAS Q61R mutation and a novel ETV1-ERG fusion.

Conclusion
This study demonstrates the utility of molecular testing as an adjunct to histopathological evaluation in definitive diagnosis and differentiation of papillary thyroid hyperplasia from papillary carcinoma. Next generation sequencing with targeted DNA and RNA panels will be beneficial for both known and novel variant or fusion detection in suspect cases.
EGFR testing patterns and detection of EGFR exon 20 insertions among patients with NSCLC in the US
Authors: Lin H M , Yin Y , Curran E , Crossland V , Wu Y , Ou S 
Published: October 2021

Abstract

Introduction/Objective
Epidermal growth factor receptor (EGFR) mutations are common in non-small cell lung cancer (NSCLC). EGFR exon 20 insertions (EGFRex20ins), a rare subset of EGFR mutations, are refractory to tyrosine kinase inhibitors. With the development of targeted therapies for EGFRex20ins, such as mobocertinib, molecular testing is required to optimize treatment. A better understanding of real-world EGFR detection patterns is needed to maximize patient outcomes.

Methods/Case Report
This retrospective study describes EGFR testing and EGFRex20ins detection patterns in patients with NSCLC in the United States. The Flatiron Health electronic health record database was used to identify patients ≥18 years, with advanced NSCLC, and with ≥2 clinic visits between 01/01/2011 and 12/31/2020. Baseline demographics, clinical characteristics, EGFR testing, and EGFRex20ins detection rates by sex, race, and smoking history were summarized.

Results (if a Case Study enter NA)
A total of 67,281 patients with NSCLC were identified. EGFR testing increased from 44% in 2011 to 77% in 2020. Of all patients, 44,926 (66.8%) were tested: 50.8% female; 3.3% Asian; 16.0% never-smokers. Of all patients, 22,355 (33.2%) were not tested: 41.4% female; 1.2% Asian; 7.5% never-smokers. Of those tested, 6,245 (13.9%) patients had EGFR mutations: 65.9% female; 11.8% Asian; 48.4% never-smokers.
EGFRex20ins detection rates changed from 0.6% in 2011 to 1.0% in 2019 and 0.7% in 2020. Of those tested, 304 patients had EGFRex20ins: 58.2% female; 8.2% Asian; 50.3% never-smokers. EGFR testing was higher in females (71.2%) than males (62.8%), never-smokers (84.5%) than those with a smoking history (64.6%), and Asian patients (84.2%) than White (66.6%), Black (65.4%), or other patients (69.5%). Of those tested, EGFRex20ins mutations were detected in 0.8% of females (males: 0.6%), 2.2% of never-smokers (with smoking history: 0.4%), and 1.7% of Asians (White: 0.6%, Black: 0.6%, other patients: 0.7%) had EGFRex20ins. A similar trend was observed for EGFR mutations with higher proportions of females, never-smokers, and Asian patients affected.

Conclusion
EGFR testing and EGFRex20ins detection rates have increased. However, not all patient subgroups were tested at the same rate and undertesting occurred in all subgroups. Further education of specialists diagnosing NSCLC is warranted to ensure all patients receive biomarker testing and benefit from emerging EGFRex20ins- targeted therapies.
Complete response of a colonic high-grade neuroendocrine carcinoma to platinum-based therapy: Insights from comprehensive genomic profiling
Authors: Wood R , Arnason T , DeCoste R , Gaston D , Carter M D , Rayson D 
Published: October 2021

Abstract

Introduction/Objective
Comprehensive genomic profiling (CGP) is an essential tool in precision medicine, providing diagnostic, prognostic, and predictive (therapeutic) information to enable personalized and optimized care for cancer patients. We present the case of a patient with a metastatic high-grade tumor of the colon who showed an impressive response to systemic therapy and discuss the role of CGP in cancer management.

Methods/Case Report
A 54-year-old woman with was diagnosed with stage IV large-cell neuroendocrine carcinoma (LCNEC) of the colon with large volume liver and nodal metastases with imminent hepatic failure. CGP was performed on the resected tumor (TSO500 panel, 523 cancer-related genes, Illumina), showing pathogenic mutations in multiple oncogenes and tumor suppressor genes, including BRCA1, BAP1, and BRAF. Additionally, global parameters revealed a very high tumor mutation burden (TMB, 351 / Mb), and high-degree microsatellite instability (MSI-H). Treatment of the patient’s metastases with platinum-based systemic therapy resulted in a complete radiographic response, with no evidence of disease recurrence after 6.5 years. This type of complete response to therapy is rarely reported in colonic LCNEC. Assessment by Medical Genetics did not identify a germline mutation suggestive of hereditary breast/ovarian cancer or Lynch syndrome.

Results (if a Case Study enter NA)
NA

Conclusion
The patient’s extraordinary response to therapy is likely due to loss of BRCA1 and/or BAP1 function, as deleterious mutations in both genes predict sensitivity to platinum-based therapy through exploitation of deficient homologous recombination repair (HRR). The high TMB and MSI-H status suggest the immune system may have contributed to tumor clearance through neoantigen activation of T-cells. The information provided by CGP also suggested potential tumor sensitivity to poly(ADP-Ribose) polymerase inhibitors (PARPi), immunotherapy (IT), and BRAF/MEK inhibitor therapy, should the tumor recur. This case highlights the value of CGP in guiding management of rare and aggressive tumors.
The optimization of an ultra-sensitive single molecule assay for the multiplexed detection of SARS-CoV-2 antigens
Authors: Senussi Y , Swank Z N , Walt D R 
Published: October 2021

Abstract

Introduction/Objective
SARS-CoV-2 antigens, including the nucleocapsid (N) protein, spike protein, and its S1 subunit have served as key biomarkers for research and diagnostic purposes. We previously developed quantitative single molecule array (Simoa) assays to measure the concentration of spike, S1 subunit and N protein in plasma samples with femtomolar limits of detection. We aimed to test antibodies that were not available early in the pandemic, reduce assay cross-reactivity, develop a multiplexed assay for spike, S1, and N protein in order to minimize the sample volume needed.

Methods/Case Report
Using the Simoa platform, a bead-based digital enzyme-linked immunosorbent assay, we cross-tested 17 S1 subunit and spike antibodies for a total of 130 antibody-pair combinations, we performed dilution linearity experiments to determine the ideal dilution factor, spike and recovery experiments, tested the assay using S1 subunit from other human coronavirus HKV1, NL63, and 229E, pre-pandemic plasma samples from patients that were sick with viral or bacterial respiratory infections. We then used the best antibody pairs to measure S1 and spike in plasma samples collected from patients with severe SARS-CoV-2. Lastly, we conjugated the best-performing capture antibodies for spike, S1 and N to beads labeled with different fluorophores to test if the assay for all three antigens could be multiplexed.

Results (if a Case Study enter NA)
We observed no cross-reactivity with S1 from other coronavirus strains, no detection of S1 or spike in a cohort of 30 pre-pandemic samples and successfully developed a multiplexed assay for the detection of spike, S1, and N protein, enabling us to use 50% less sample volume.

Conclusion
Reduction of necessary sample volume is important for studies involving multisystem inflammatory syndrome in children (MIS-C), and possible adverse effects of SARS-CoV-2 vaccinations on children and young adults. An improved assay with minimal cross-reactivity will also be useful to study individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).
Bioinformatics and wet laboratory analysis of rs1800562 to predict genetic aetiology of iron overload in Nigeria
Authors: Bolarinwa A B , Onawoga F 
Published: October 2021

Abstract

Introduction/Objective
The most reported single nucleotide polymorphism (SNP) of the HFE gene is rs1800562, representing the substitution of Adenine for Guanine at position 847 of the HFE gene. This has been widely implicated in hereditary haemochromatosis and other conditions like altered cholesterol balance, Alzheimer’s disease and cutaneous photosensitivity. Abnormal HFE protein resulting from the mutant HFE gene leads to formation of excess iron which has been postulated as likely mechanism for these diseases. Although there is evidence of iron overload in Africans, only few studies have explored possible genetic causes, and prevalence of rs1800562 is not known in West African population. Hence the need to determine the prevalence of rs1800562 in Nigeria using computational and wet laboratory approach.

Methods/Case Report
Details of rs1800562 were retrieved from Ensembl Genome Browser version 99. Severity of the consequences of this SNP on protein product was determined using bioinformatics tools including SIFT, Polyphen, Mutation Assessor, HOPE, I-mutant and MutPred2. Genotyping of rs1800562 was done In silico using restriction fragment length polymorphism (RFLP). Primer3plus was used for primer design, NCBI BLAST and SMS were used for primer validation. We used Webcutter 2.0 to determine suitable restriction enzymes. The genotyping was simulated using USCS virtual PCR and RestrictionMapper. Whole blood samples were obtained from 200 participants selected randomly from a pool of blood donors. DNA was extracted and flanking region of rs1800562 was amplified. The amplified product was digested by RSA1and fragments examined on agarose gel electrophoresis.

Results (if a Case Study enter NA)
The MAF was found to be 0.01 globally and 0.02 in Africa. In the two Nigerian population examined (Yoruba and Esan population), MAF was 0.00. Mutation Assessor and SIFT Polyphen consistently predicted the mutation to be of severe consequences. Analysis on HOPE, I-mutant and Mutpred2 revealed loss of protein stability, change in net charges affecting the HFE protein localization and its interaction with other proteins. All the participants in the wet laboratory analysis were homozygous for the wild type allele of rs1800562 (MAF=0).

Conclusion
This study confirmed the In silico prediction of the absence of rs1800562 in Nigeria. Future studies should focus on other SNPs of the HFE gene as well as other gene involved in iron metabolism.
A rare case of hairy cell leukemia variant with ATM nonsense mutation and ATM deletion, resulting in complete loss of function
Authors: Wei Q , Harada S , Reddy V 
Published: October 2021

Abstract

Introduction/Objective
Hairy cell leukemia variant (HCL-v) is a rare B cell lymphoproliferative disorder. Although HCL- v shares some overlapping features with classic HCL, it lacks the characteristic immune-morphology and pathogenic BRAF V600E mutation seen in classic HCL and recognized as a distinct entity in the 2017 WHO classification. Approximately half of HCL-v harbors MAPK2 mutation and one third has TP53 mutation. Cytogenetic abnormalities include gain of chromosome 5, loss of chromosome 7q, and deletion of 17p13/TP53 and 11q/22 ATM gene

Methods/Case Report
We report a case of HCL-v with total loss of ATM gene function. A 71-year-old male with splenomegaly presented with an outside diagnosis of splenic marginal zone lymphoma and underwent splenectomy. Flow cytometry on spleen demonstrated mature clonal B lymphoid cells and was positive for CD11c and CD103. However, unlike classical HCL, it was CD25 negative, which supports the diagnosis of HCL-v. Sections of spleen revealed most of the red pulp replaced by hairy cell leukemic infiltrate with minimal preservation of the normal lymphoid stroma. Peripheral blood smear showed atypical lymphocytosis with prominent nucleoli but most lacking circumferential shaggy contours, seen in classic HCL. Cytogenetic analysis identified a deletion in chromosome 11(q13q23), which deletes the ATM gene. NGS analysis demonstrated a nonsense variant in ATM (p. E888*). No significant sequence variants were identified in BRAF, MAP2K1 or TP53. This is the first case report of HCL-v with a deletion as well as a non-sense mutation in the ATM gene. ATM gene belongs to the PI3/PI4-kinase family, and is an important cell cycle checkpoint kinase that phosphorylates downstream proteins, including TP53, BRCA1 etc. Although detection of the ATM has therapeutic application for prostate cancer patient for poly [ADP]-ribose polymerase inhibitor treatment, the significance of loss of ATM function in hairy cell leukemia variant is unknown.

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

Conclusion
In conclusion, our case demonstrates that molecular test in hairy cell leukemia variant can be helpful for confirming the diagnosis as well as providing predictive information for potential target therapy. In our case, lack of MAP2K1 mutation precludes the patient for targeted therapy. In addition, the finding of novel mutation might help to understand the molecular pathogenesis in this rare entity.
Non-IgG4-Related Fibrosing Mediastinitis Diagnosed on Needle Biopsy and Treated with Steroids
Authors: Wilhelm A , Muthukumarana P V , Uddin H , Okereke I 
Published: October 2021

Abstract

Introduction/Objective
Fibrosing mediastinitis (FM) is a rare and aggressive fibroinflammatory process of the mediastinum. It is a difficult diagnosis, especially on small biopsies as the presentation and the fibrosing background mimics malignancy. Although the exact etiology is unknown, prior fungal infections, certain medications and autoimmune conditions are documented. Significant histopathologic overlap with IgG4-related disease (IgG4-RD) can complicate the diagnosis. An accurate diagnosis is important for treatment as corticosteroids for IgG4-RD is proven to be effective; however, no effective treatment is described for FM. Additionally, immunosuppression would prove harmful in other conditions with fibrosing morphology. We report a very unique case of non-IgG4-related FM that was diagnosed on a needle biopsy and showed marked improvement with corticosteroids.

Methods/Case Report
A 65-year-old man with no significant medical history presented with syncope and recent weight loss. Imaging revealed a pericardial effusion and a heterogeneous 8.1 cm mediastinal mass encasing the great vessels and aortic arch. Needle biopsy showed fibrosis with keloid-type collagen, mixed inflammatory cells, and few benign lymphoid follicles. No evidence of hematolymphoid malignancy, carcinoma, or infection was seen. Serum and tissue IgG-4 studies were negative for IgG4-RD. A diagnosis of FM was made, and a trial of corticosteroids was initiated. Interestingly, the patient showed improvement with a 2.3 cm decrease in lesion size and near-complete resolution of pericardial effusion after one month of treatment.

Results (if a Case Study enter NA)
NA

Conclusion
FM should be included in the differential diagnosis of infiltrative mediastinal masses which presents a diagnostic challenge on limited needle biopsies. Although effective treatment for non-IgG4 related FM is not clearly established, corticosteroids may prove beneficial, as in this patient. Mortality from FM is directly related to the compressive effect on adjacent structures. Early diagnosis and treatment are therefore crucial. Further studies on the pathogenesis are necessary, as well as better directed therapeutic options.
Anaplastic lymphoma kinase rearrangements in non-small cell lung cancer in Jordan
Authors: Sughayer M A , Maraqa B , Al-Ashhab M 
Published: October 2021

Abstract

Introduction/Objective
ALK rearrangement is an important oncogenic driver in a substantial portion of non-small cell lung cancer (NSCLC) patients ranging from 2-7%. Treatment options such as ALK tyrosine kinase inhibitors (TKI) improve progression-free survival and overall survival. Candidates for such treatment are selected based on the identification of the ALK rearrangement. While fluorescence in situ hybridization (FISH) was considered the gold standard method, the availability of a robust FDA-approved companion diagnostic immunohistochemistry (IHC) assay has led to a paradigm shift in ALK testing. The purpose of this study is to determine the prevalence of ALK rearrangement in Jordanian NSCLC patients along with their clinicopathological characteristics and to compare the results of IHC and FISH methods for detecting ALK rearrangements.

Methods/Case Report
A retrospective study was conducted on 449 Jordanian King Hussein Cancer Center patients with NSCLC whose biopsy samples were tested for ALK rearrangement using FISH and or IHC (clone D5F3) in the period between 2018 and 2020.

Results (if a Case Study enter NA)
During the study period, the rate of ALK positivity by either IHC or FISH method was 4 percent (18 ALK positive cases out of 449 cases of non-small cell lung cancer). Seven cases were positive for both IHC and FISH, and nine cases were positive for IHC with no confirmation by FISH method; one case was ALK positive by IHC and negative by FISH with a significant response to ALK TKI; one case was IHC negative but FISH positive, with no ALK TKI therapy. The calculated sensitivity of ALK D5F3 immunostain compared to FISH results in the current study is 87.5% while the specificity is 96%.
ALK positive patients were significantly younger than those with negative results (p-value=0.051), and women were three times more likely than men to have the rearrangement (p-value=0.013). Rearrangement was more likely to be found in nonsmokers/light or ex-smokers (p-value= 0.013). All patients had clinical stage IV or III disease at presentation with stage IV found in tow thirds of the patients.

Conclusion
ALK rearrangement is found in 4% of all NSCLC in Jordan. Patients are more likely to be younger, females and light or nonsmokers with an advanced stage disease at presentation. IHC is an acceptable alternative to FISH for ALK testing with reasonable sensitivity and specificity in addition to its advantages in terms of robustness, turnaround time and cost savings