bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of Next Generation Sequencing in the Workup and Diagnosis of Myeloproliferative neoplasm in the Peripheral Blood: A single institution experience
Authors: Lynn T , Campbell A , Ding Y 
Published: October 2021

Abstract

Introduction/Objective
In patients with suspicion of Myeloproliferative neoplasm (MPN) and negative for BCR-ABL1, NCCN guideline currently recommends two molecular workup pathways in peripheral blood: 1) a multi-step reflex mutation testing algorithm including JAK2 V617F, CALR, MPL, JAK2 exon12 or 2) a multigene Next Generation Sequencing (NGS) panel that includes at least JAK2, CALR and MPL genes. Here we report the clinical utilization and impact of a NGS based MPN diagnosis assay.

Methods/Case Report
Total of 690 consecutive cases at Geisinger between 2019 and 2021 were included in this study. Patient’s CBC showed chronic cytosis in either single or multi-lineage myelopoiesis and was clinically suspicious for MPNs. For BCR-ABL1 negative cases, NGS based MPN diagnostic assay was performed, which include the four disease defining genes recommended by NCCN guideline: JAK2, CALR, MPL, CSF3R as well as three additional genes NRAS, PPM1D and TP53. Variants are classified in to four tiers based on their level of clinical significance.

Results (if a Case Study enter NA)
Among all cases tested, 25 out of 690 cases (3.6%) were positive for BCR-ABL1 transcript. 20.9% (139 out of 665 BCR-ABL1 negative cases) had at least one variant detected, which included 73 variants in Tier I category (11.0%), 6 variants in Tier II (0.9%), 57 variants in Tier III (8.6%) and 3 variants in Tier IV(0.5%). Among all disease defining mutations, JAK2 V617F was the most commonly detected mutation (59 cases and 8.8%), followed by CALR indel mutations (13 cases and 2.0%). In addition, double variants were detected in total 7 cases (1.0%).

Conclusion
Comparing to the conventional multi-step sequential workup for MPN diagnosis, the multi-gene NGS panel provides a cost-effective and time- saving solution. When detected concurrently with the disease defining mutations, NRAS, PPM1D and TP53 could provide not only additional prognostic information but also may suggest pending progression in myeloproliferative neoplasms.
In Egyptian Patients with Hepatocellular Carcinoma the role of MicroRNA-215
Authors: Ali H A 
Published: October 2021

Abstract

Introduction/Objective
MicroRNAs (miRNAs) are a class of evolutionarily conserved small non-coding RNAs which are make a contribution in the regulation of gene expression and protein translation, and they play vital roles in differentiation, cell growth, and the development of diverse types of cancers.

Methods/Case Report
Our research was done in hepatology and gastroenterology department at the National Liver Institute, Menoufia University. It included 135 patients and 60 healthy subjects serving as control group. We have 3 groups:
Group I (Control)
This group included 60 apparently healthy individuals. They were 32 males and 28 females, whose ages ranged from 39 to 67 years old (mean ±SD= 51.67 ± 6.40 years).
Group II (Cirrhosis)
This group included 75 patients with liver cirrhosis due to chronic HCV infection. They were 41 males and 34 females whose ages ranged from 41 to 68 years old (mean ±SD= 54±6.73 years).
Group III (HCC)
Sixty patients with HCC were included. They were 35 males and 25 females, whose ages ranged from 41 to 70 years old (mean ±SD= 53.97±6.15 years).

Laboratory Investigations
Complete blood count (CBC), Liver tests: aspartate transaminase (AST) and alanine transaminase (ALT), serum albumin, total and direct bilirubin, alkaline phosphatase and INR were measured. Serum creatinine was also measured. The analysis of serum alpha fetoprotein (AFP) (ng/ml) was done. Chronic HCV infection was diagnosed by detection of HCV antibody and HCV RNA by real time PCR. Anti-HCV antibody was detected by means of a third generation enzyme immunoassay. Quantification of HCV RNA level was performed by means of COBAS Taqman 84 (Roche) real time HCV RNA Assay with lower detection limit 15 IU/ml.

Results (if a Case Study enter NA)
In control group, miRNA-215 ranged from 1.60 to 21.30 with a median value of 6.89. In cirrhotic patients group, it ranged from 0.70 to 14.65 with a median value of 2.85. In patients with HCC group, it ranged from 0.03 to 10.95 with a median value of 0.52 (pg/ml). MiRNA-215 and AFA mean levels showed a statistically significant difference (p &lt;0.001) between the three studied groups.

Conclusion
In conclusion, MicroRNA-215 was proved to be significantly lower in HCC patients compared to cirrhotic patients and control group. This marker might be used as a potential serologic marker for HCC and a complementary diagnostic tool in monitoring cirrhotic patients for detection of HCC.
Co-treatment of Garlic-Oils Extract, Dially-thiosulphate, and Histone Deacetylases Inhibitors (HDACI) Synergistically Inhibited Cell Proliferation and induced Apoptosis in Hepatocellular carcinoma cell lines
Authors: Fyala A S , Sultan A S 
Published: October 2021

Abstract

Introduction/Objective
Hepatocellular carcinoma (HCC) is the most common cause of cancer-deaths worldwide. Garlic (Allium Sativum), is a natural-medicinal herb which has anti-fungal, anti-bacterial, anti-inflammatory, anti-virus, and antiproliferative activities. Garlic-oil soluble-sulfur-compounds, diallyl-thiosulphate, (DT) are more effective than water-soluble-compounds in protection against cancer due to its capacity to induce apoptosis and revise anti- multidrug-resistance. Histone deacetylases inhibitors (HDACIs) are inhibitors of anti-cancer agents that play a role in inducing death, differentiation, apoptosis induction, and cell-cycle arrest in different cancer-types. The present studying aims to investigate the anti-proliferative effect of organosulfur-oil DT extract of garlic by possible modulation of HDACIs role on HCC cell-lines.

Methods/Case Report
Two HDACIs, suberanilohydroxamic acid (SAHA) and trichostatinA (TSA), were used to investigate their role on proliferation of two HCC cell-lines, HepG2 and Hep3B, respectively. Cell proliferation was examined by Wst-1 assay, apoptosis induction signaling pathways, cell-cycle analysis, and western-blot analysis of the major oncogenic signaling pathways in the two tested cell-lines.

Results (if a Case Study enter NA)
Our data showed that DT significantly inhibited the cell-proliferation and induced cell-cycle arrest at G2/M phase in both HCC cell-lines. In addition, co-treatment of DT and HDACIs for 48h enhanced the cell inhibitory effect and induced apoptosis by up-regulation of p53, p21, and Bax protein expression and down- regulation of Bcl-2 and cyclin-D1 protein expression compared to control or each treatment alone. Furthermore, the data showed that DT significantly increased caspases-3 activity in Hep-G2 cell-line than that of Hep3B cell-line in a dose dependent-time compared to the control. Apoptosis induction was consistent with up-regulated caspase-3 activity, and HepG2 cells, but not Hep3B cells, showed a significant increase in response to co-treatment of DT with SAHA compared to co-treatment with TSA.

Conclusion
The data of the present study demonstrated that DT, non-toxicity compound, might be a new modulator for HDACIs effects, which in turn might be a promising prospective agent for HCC treatment.
Multiplex Fragment analysis detects all COVID-19 variants of concern
Authors: SoRelle J A , Clark A , Wang Z , Park J 
Published: October 2021

Abstract

Introduction/Objective
The majority of tracking methods have employed whole genome sequencing, which can be very expensive and time consuming. An alternative method has been to use genotyping of specific mutations to identify variants. However, tracking SARS-CoV-2 variants by targeted methods has been a moving target. Most methods only multiplex four targets per reaction, but we have multiplexed 8 targets in a single tube using fragment analysis.

Methods/Case Report
Fluorescently labeled primers targeted a combination of insertion/ deletion mutations and single nucleotide mutations. The PCR amplified products, amplicons, were separated by capillary electrophoresis. Primers were designed to detect changes in size indicative of insertion or deletion mutations including: ORF1A:Del3675_3677, S:Del69_70, S:Del144, S:Del157_158, S:Del242_244, ORF8:Del119_120, and ORF8:ins28269-28273. Allele-specific primers were designed to detect both the wild-type and mutated versions of S:N501Y, S:E484K, and S:L452R.
Residual nasopharyngeal and nasal specimens testing positive for SARS-CoV-2 by RT-PCR or isothermal amplification (IDnow) methods were selected from May 1- June 24, 2021. Variant analysis was performed by multiplex targeted PCR and whole genome sequencing in parallel on the same specimens to determine positive percent agreement.

Results (if a Case Study enter NA)
Variant analysis was performed on 250 specimens detecting each of the major variants of concern Alpha (B.1.1.7, U.K. origin, n= 108), Beta (B.1.351, South Africa origin, n=3), Gamma (P.1, Brazil origin, n=12), Delta (B.1.617.2, Indian origin, n=17), and Iota (B.1.526, New York, n=5). Some specimens with low viral load were detected by only PCR (n=18), only WGS (n=41), or neither (n=20). Overall positive percent agreement was 95% (163/171).

Conclusion
This adjustable method robustly and accurately identifies COVID-19 VOCs utilizing a platform amenable to multiple targets (20-40 targets ranging from 100-500b.p. across four fluorescent channels) using equipment commonly found in routine molecular pathology laboratories. Future directions include adjusting targets to detect new variants.
Molecular Detection of Adenovirus in Tap Water from Coastal Areas Of Karachi Pakistan:The Real-Time PCR Assay
Authors: Kalam A 
Published: October 2021

Abstract

Introduction/Objective
Diarrhea is a major source of morbidity and mortality in low-income and middle-income countries. In underdeveloped countries, diseases caused by viruses identified in environmental samples cause major health problems. Little knowledge about the frequency and pattern of viral contamination of drinking water sources in these resource-poor settings. Adenovirus which causes watery diarrhea, particular has been recognized as important causal pathogen. Adenovirus remains a global threat to public health and an indicator of inequity and lack of social development. Tap water samples from coastal sites in Karachi between 2019 and 2020 over a period of 11 months. The total of 40 tap water sample was examined for infectious Adenovirus by a real time polymerase chain reaction (PCR) amplification.

Methods/Case Report
This Pilot study is conducted on tap water samples from Karachi Pakistan, n=40 are processed. Extraction of nucleic acid from all filtered water samples collected with Sterivex filter units by using Qiagen DNeasy Power Water Sterivex Kit. As per the manufacturer’s instruction. Phocine herpesvirus(PhHV) is added as an external positive control to monitor the efficiency of nucleic acid extraction and amplification. TaqMan Universal PCR Master Mix (Thermo Fisher Scientific) is being used in probe based real time PCR assay,the below 35 Ct value is considered as a positive sample.

Results (if a Case Study enter NA)
Results showed the total of 37.7% of the sources were positive for adenovirus.The level of viral contamination was moderate to high.

Conclusion
The results has been showed that no seasonal pattern for viral contaminations was found after samples obtained during the dry and wet seasons were compared. Further the Real time PCR assay increases the sensitivity and provides the high resolution of pathogen detection.
TERT Immunohistochemistry Expression as a Surrogate of TERT Promoter Mutations in Infiltrating Gliomas
Authors: Moosvi A M , Dono A , Bellman A , Ballester L , Goli P , Esquenazi Y 
Published: October 2021

Abstract

Introduction/Objective
Genomic alterations are critical for the diagnosis of infiltrating gliomas. Mutations in the telomerase reverse transcriptase promoter (TERTp) are sufficient for a diagnosis of glioblastoma in some cases, independent of histologic features. Although DNA sequencing is the preferred method for evaluating TERTp mutations, there are limitations with regards to turn-around-time, accessibility, and cost. In this study, we evaluated the efficacy of using TERT immunohistochemistry (IHC) as a surrogate marker for the identification of TERTp mutations in infiltrating gliomas.

Methods/Case Report
The study cohort consisted of 31 infiltrating gliomas diagnosed following the 2016 WHO classification of CNS tumors by a board-certified neuropathologist. Each case was evaluated by immunohistochemistry (anti-TERT monoclonal antibody) and with a targeted next-generation sequencing (NGS) panel. A systemic literature search was conducted to examine reports of TERT antibody as a surrogate marker of TERTp mutations. TERTp mutation detected by sequencing was considered the gold standard.

Results (if a Case Study enter NA)
TERT immunohistochemistry demonstrated a sensitivity of 61.1% and specificity of 69.2%. Cases were divided into IDH-WT and IDH-mutant infiltrating gliomas. Among the IDH-WT group, 84% contained the TERTp mutation with a sensitivity of 62.5% and specificity of 33.3% for the TERTp IHC. IDH-mutant gliomas showed a 16.2% TERTp mutation rate, and immunohistochemistry had a sensitivity of 50% and 80% specificity. The probability of TERT immunohistochemistry in diagnosing TERTp mutations exhibited a poor likelihood ratio for both the positive and negative test. Literature review included 5 studies with an overall sensitivity and specificity remaining consistently low (&lt;80%), with 2 of these studies evaluating CNS related tumors giving rise to similar diagnostic performance.

Conclusion
TERT IHC has suboptimal sensitivity and specificity for identifying TERTp mutations in IDH-WT and IDH- mutant infiltrating gliomas.
A case of NTRK-rearranged Spindle cell tumor in a Pediatric patient
Authors: Reddy A C , Reddy K S 
Published: October 2021

Abstract

Introduction/Objective
Recent studies continue to demonstrate that NTRK fusions occur more frequently in pediatric than in adult patients involving a broader panel of fusion partners as well as a wider range of pediatric tumors than previously recognized. The identification of these NTRK fusions has facilitated precision cancer diagnosis and TRK inhibitor targeted therapy. With the recent FDA approval of larotrectinib and entrectinib for the treatment of adult and pediatric NTRK-positive, unresectable solid tumors, identification of these fusions directly impacts patient care.

Methods/Case Report
Our patient, a 10 year old female presented with a large right sided buttock mass and pressure effects from the tumor. An incisional biopsy showed a moderately moderately cellular tumor with a collagenous and partially myxoid stroma. The atypical cells had ovoid nuclei with vesicular chromatin, minimal to no atypia, and rare mitotic activity (&lt;2/30 high-power fields), as well as fibrous tissue that appeared as ropy collagen. Some of the blood vessels were rimmed by a hyalinized cuff. A mild inflammatory component, namely scattered lymphocytes and fewer plasma cells were noted. Immunohistochemistry showed: SMA(faint+), S100(+), CD34(+), CD31(+), FLI1(+), NTRK(+). Negative for ALK1, desmin, SOX10, EMA, keratin AE1/3, CAM5.2, D2-40, myogenin, MUC4, TLE1, STAT6, BCOR, ERG. Both INI1 and H3K27me3 were retained. Proliferative rate by Ki-67 was low, showing &lt;2% positivity.
Next generation sequencing revealed the following: LMNA-NTRK1 fusion; CD36 N53fs*24 and CDKN2A/B CDKN2A loss exon 1. Thus, the histologic, immunophenotypic, and molecular findings together supported a diagnosis of NTRK-rearranged spindle cell tumor. This entity has alternately been termed lipofibromatosis-like tumor. Following confirmation of NTRK fusion, she was treated with oral TRK inhibitor with near total response. With this NTRK-rearranged spindle cell tumor’s minimal mitotic activity, absence of necrosis, and low cellularity, the behavior of this tumor was expected to be indolent rather than aggressive. However, the patient was presented for assessment and management at a recent tumor board about 8 months after her initial diagnosis as she had residual/recurrent tumor.

Results (if a Case Study enter NA)
NA

Conclusion
Our case highlights the clinical utility of screening for NTRK fusions in all pediatric tumors.
Identifiable Mutations in Pancreatic Adenocarcinoma in the Veteran Population: Molecular Testing Guidelines by NCCN 2020
Authors: Petersen J M , Jhala D 
Published: October 2021

Abstract

Introduction/Objective
In 2019 and 2020, the National Comprehensive Cancer Network (NCCN) advanced a recommendation that all patients with metastatic, recurrent, or locally advanced pancreatic adenocarcinoma should undergo tumor gene profiling (TGP). Prior to these recommendations, TGP in targeted patients have demonstrated a high frequency of KRAS (&gt;90%), TP53 (60-70%), CDKN2A (&gt;50%), SMAD4, TGF- βR1, and TGF- βR2 mutations or alterations. Even less frequent mutations such as the homologous recombination repair (HRR) genes impact treatment by predicting tumor response to platinum-based therapies. However, the literature is sparse for the frequency of these mutations in patients with pancreatic adenocarcinoma undergoing generalized testing as part of the standard of care per NCCN guidance, particularly for veterans.

Methods/Case Report
For a quality assurance study, a retrospective review was performed to identify patients with pancreatic adenocarcinoma at a tertiary medical center serving veterans from January 2019 to February 2021 with TGP performed as part of their care. All of the TGP had been sent to Foundation Medicine (Cambridge MA), and the identifiable tumor mutations from the test reports were recorded to document the frequency of KRAS, TP53, CDKN2A, SMAD4, TGF- βR1, TGF- βR2 and HRR mutations or alterations.

Results (if a Case Study enter NA)
There were a total of 11 patients with pancreatic adenocarcinoma who had a tumor specimen for TGP during the study period. All 11 patient tumors had KRAS mutation. 10 out of 11 had a mutation or alteration in TP53. 8 of 11 patients had a CDKN2A mutation or alteration. 7 of 11 patients had a mutation or alteration of SMAD4 though none had TGF- βR1 or TGF- βR2. 2 of 11 patients had HRR mutations (1 with FANCA and 1 with ATM).

Conclusion
Tumor mutations on generalized gene profiling per NCCN guidelines continue to identify important mutations in pancreatic adenocarcinoma for veteran patients.
Pancreatic Gangliocytic Praganglioma: A Rare Case and Literature Review
Authors: Goyal G , Harris J 
Published: October 2021

Abstract

Introduction/Objective
Gangliocytic paraganglioma, GP is a morphologically distinct tumor first reported by Dahl in 1957, most often in second portion of duodenum near ampulla of Vater. GP mostly present as single tumors, but occasionally may be multiple, when seen in association with Von Recklinghausen disease and carcinoid tumors. Rare cases have been reported at other sites in gastrointestinal tract including esophagus, pylorus, jejunum and extra- gastrointestinal tract in the nasopharynx, thymus, lung and ovary. Pancreatic GP is extremely rare with five cases reported till date.

Methods/Case Report
A 42- year- old male presented with abdominal pain. Physical exam showed no abnormalities. The significant findings on labs were raised amylase levels in the range of 1262 U and mild hyperglycemia with blood glucose of 178mg/dl. CA 19-9 was found to be 8.0 U/ml. Coronal CT Abdomen showed hypodense well circumscribed nodule 1.5 cm in body of pancreas. Gross specimen of pancreas showed a circumscribed 1.5 cm nodule in body of Pancreas.The microscopic sections of pancreatic mass show epithelioid appearing neuroendocrine cells in nests, with spindle shaped schwann cells or sustentacular cells in periphery, and scattered ganglion cells. The immunohistochemical staining positive for synaptophysin in epithelioid cells, S100 in spindled schwann cells and CK in epithelioid cells and Ganglion cells. Based on the microscopic findings, a diagnosis of Gangliocytic Paraganglioma, GP arising in Pancreas was made.

Results (if a Case Study enter NA)
NA

Conclusion
Pancreatic GP, are often misdiagnosed as Pancreatic Neuro endocrine tumors, Grade1. The accurate differentiation and precise diagnosis is crucial for appropriate clinical management. WHO classification of 2010, classifies gangliocytic paragangliomas as benign. Duodenal GP has a benign behavior with lymph node metastasis in only 5-7% cases, and no evidence of distant metastasis. In comparison, Pancreatic GP show an more aggressive behavior with lymph node metastasis observed in 2/6 cases and one case with sternal bone metastasis, emphasizing the importance of the primary location of origin of GP as prognostic factor. Our understanding is limited due to the scarcity of literature; more published data shall be instrumental in further explaining the clinical behavior of this rare entity.
Chronic Histiocytic Intervillositis: A Placental Histopathologic Feature in Vertical Transmission of Maternal Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Authors: Oentoro J , Jalali-Farahani S , Davis J , Zee S 
Published: October 2021

Abstract

Introduction/Objective
Vertical transmission of severe acute respiratory syndrome associated with coronavirus-2 (SARS-CoV-2) infection has been reported as a rare occurrence. The purpose of this study is to identify any specific placental histopathologic abnormalities associated with SARS-CoV-2 infection, compare differences between mothers with symptomatic and asymptomatic coronavirus disease 2019 (COVID-19), and determine the frequency of vertical transmission.

Methods/Case Report
Placentas from mothers diagnosed with COVID-19 during pregnancy and delivered at Stony Brook University Hospital were identified. A control group of mothers with a negative COVID-19 test was selected from the same period. The frequency of histopathologic characteristics defined by the Amsterdam Placental Workshop Group Consensus was compared using chi-square tests between the following cohorts: COVID-19 positive mothers against COVID-19 negative mothers and symptomatic COVID-19 mothers against asymptomatic COVID-19 positive mothers.

Results (if a Case Study enter NA)
A retrospective study reviewed 23 placentas from mothers with COVID-19 for features of maternal vascular malperfusion, fetal vascular malperfusion, and inflammatory changes. 11 mothers displayed symptomatic COVID-19, and 12 mothers were asymptomatic. One neonate tested positive for SARS-CoV-2. No significant differences were identified in the frequency of the examined placental histopathologic characteristics between COVID-19 positive and negative mothers. The degree of COVID-19 severity did not significantly impact the frequency of examined histopathologic features. Interestingly, in the case with vertical transmission, the placenta demonstrated the only finding of chronic histiocytic intervillositis (CHI) with associated trophoblast necrosis.

Conclusion
Comparing across groups based on COVID-19 status, this study found no specific placental histopathologic features associated with maternal SARS-CoV-2 infection, regardless of symptom severity. However, in one case of vertical transmission, CHI was a unique histopathologic feature. These findings are consistent with the current literature. Further large-scale investigations are needed to establish additional patterns of specific placental histopathology, incidence and contributing factors of vertical transmission of COVID-19, and the impact of CHI in future pregnancies of affected women.