Use of next-generation sequencing (NGS) panels to predict recurrence in low-grade, early-stage endometrioid endometrial carcinoma.

2016 ◽  
Vol 34 (15_suppl) ◽  
pp. 5580-5580
Author(s):  
Katherine Kurnit ◽  
Bryan Fellman ◽  
Diana L Urbauer ◽  
Gordon B. Mills ◽  
Russell Broaddus
Keyword(s):  
Next Generation Sequencing ◽  
Endometrial Carcinoma ◽  
Early Stage ◽  
Low Grade ◽  
Next Generation ◽  
Endometrioid Endometrial Carcinoma ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique

Antibiotics ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 91 ◽  
Author(s):  
Akiko Ogawa ◽  
Keito Takakura ◽  
Katsuhiko Sano ◽  
Hideyuki Kanematsu ◽  
Takehiko Yamano ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Silver Nanoparticle ◽  
Biofilm Formation ◽  
Early Stage ◽  
Biofilm Reactor ◽  
Next Generation ◽  
Microbiome Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Closed Laboratory

Previously, we demonstrated that silver nanoparticle-dispersed silane-based coating could inhibit biofilm formation in conditions where seawater was used as a bacterial source and circulated in a closed laboratory biofilm reactor. However, it is still unclear whether the microbiome of a biofilm of silver nanoparticle-dispersed silane-based coating samples (Ag) differs from that of a biofilm of non-dispersed silane-based coating samples (Non-Ag). This study aimed to perform a microbiome analysis of the biofilms grown on the aforementioned coatings using a next-generation sequencing (NGS) technique. For this, a biofilm formation test was conducted by allowing seawater to flow through a closed laboratory biofilm reactor; subsequently, DNAs extracted from the biofilms of Ag and Non-Ag were used to prepare 16S rRNA amplicon libraries to analyze the microbiomes by NGS. Results of the operational taxonomy unit indicated that the biofilms of Non-Ag and Ag comprised one and no phyla of archaea, respectively, whereas Proteobacteria was the dominant phylum for both biofilms. Additionally, in both biofilms, Non-Ag and Ag, Marinomonas was the primary bacterial group involved in early stage biofilm formation, whereas Anaerospora was primarily involved in late-stage biofilm formation. These results indicate that silver nanoparticles will be unrelated to the bacterial composition of biofilms on the surface of silane-based coatings, while they control biofilm formation there.

The impact of next generation sequencing on sarcoma diagnosis.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e23528-e23528
Author(s):  
Gang Zhao ◽  
Lu Xie ◽  
Wei Guo ◽  
Yanfeng Xi ◽  
Yanzhi Cui ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Spindle Cell ◽  
Cell Tumor ◽  
Low Grade ◽  
Round Cell ◽  
Next Generation ◽  
Small Round Cell ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

e23528 Background: The rarity and heterogeneity of sarcoma has been complicating the diagnosis of sarcoma for years. Even expert pathologists of sarcoma could make mistakes in the diagnosis of this disease. The availability of Next Generation Sequencing (NGS) data enabled more accurate diagnosis of sarcoma. In this study, we systematically described the application of NGS on the diagnosis of sarcoma and the contribution of NGS to the diagnostic accuracy of sarcoma. Methods: A multi-center, retrospective study included 235 sarcoma patients’ tumor and paired normal samples that were sent from 56 hospitals to a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory, at Shanghai, China for Next Generation Sequencing (NGS) was performed. Using next generation sequencing based YS panel consisting 450 genes, these 235 sarcoma patients’ sample were sequenced and the NGS data was analyzed. The initial diagnosis without NGS information was reconsidered by expert pathologists. Results: Taking into consideration both the initial diagnosis and the NGS results, the final diagnosis of these 235 sarcoma cases included 8 low grade malignant fibromyxoid tumors, 11 dermatofibrosarcoma protuberans (DFSP), 38 myxoliposarcomas, 22 alveolar rhabdomyosarcomas, 11 alveolar soft tissue sarcoma, 2 desmoplastic small round cell tumors, 37 NTRK rearrangement spindle cell tumors, 40 Ewing’s sarcoma and 66 synoviosarcomas. In total, 29% initial diagnoses were changed according to NGS identified fusions, including 13% low grade malignant fibromyxoid tumors (1 FUS- CREB3L2 fusion), 27% DFSPs (3 COL1A1- PDGFB fusions), 11% myxoliposarcomas (3 FUS- DDIT3 fusions and 1 EWSR1- DDIT3 fusion), 14% alveolar rhabdomyosarcomas (2 PAX7- FOXO1 fusions and 1 FOXO1- LINC00598 fusion), 18% alveolar soft tissue sarcomas (2 ASPSCR1- TFE3 fusions), 50% desmoplastic small round cell tumor (1 EWSR1- WT1 fusion), 95% NTRK rearrangement spindle cell tumors, 13% Ewing’s sarcomas (3 EWSR1- FLI1 fusions and 2 EWSR1- ERG fusions) and 21% synoviosarcomas (9 SS18- SSX1 fusions and 5 SS18- SSX2 fusions). Conclusions: NGS would be highly recommended for accurate diagnosis of sarcoma, especially for NTRK rearrangement spindle cell tumor, the majority of which were confirmed according to NGS identified fusions.

scholarly journals Immunohistochemistry and Next Generation Sequencing are Complementary Tests in Identifying PTEN Abnormality in Endometrial Carcinoma Biopsies

2020 ◽  
Author(s):  
Linyuan Wang ◽  
Anna Piskorz ◽  
Tjalling Bosse ◽  
Mercedes Jimenez-Linan ◽  
Brian Rous ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Endometrial Carcinoma ◽  
Internal Control ◽  
Molecular Subtype ◽  
Serous Carcinoma ◽  
Next Generation ◽  
Loss Of Function ◽  
Sensitivity Specificity ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

PTEN plays a central role in the pathogenesis of endometrial carcinoma. Previous studies reported a high interobserver reproducibility for the interpretation of PTEN immunohistochemistry (IHC). However, PTEN IHC and its interpretation remain challenging during laboratory practice. The purpose of this study was to reevaluate PTEN IHC pattern in direct comparison to next generation sequencing (NGS) in identifying PTEN abnormality. IHC and tagged-amplicon NGS PTEN sequencing was performed on 182 endometrial carcinoma biopsy/curetting samples from five centers (Barts, Calgary, Cambridge, Leiden, and Vancouver). Sensitivity, specificity and accuracy of PTEN IHC to predict loss of function (LOF) PTEN mutations were calculated. Abnormalities of PTEN in association with histotype and molecular subtype were assessed. A total of five PTEN IHC patterns were recorded: absent, subclonal loss, equivocal, reduced (relative to internal control) and retained. The absence of PTEN IHC has a sensitivity of 75.4% (95% CI 62.7 to 85.5%), a specificity of 84.6% (95% CI 76.2 to 90.9%), and accuracy of 81.2% (95% CI 74.4 to 86.9%) in predicting LOF PTEN mutation. PTEN abnormality by complementary interpretation of both assays was present in 91.9% of endometrial endometrioid carcinoma, grade 1, and significantly higher in endometrial endometrioid carcinomas of all grades compared to endometrial serous carcinoma (80.0% versus 19.4%, p<0.0001). PTEN abnormalities are common across all molecular subtypes of endometrioid carcinomas. Our data support complementary testing of both IHC and sequencing of PTEN to assess the PTEN status in endometrial carcinomas.

scholarly journals Next generation sequencing in early diagnosis of pneumocystis jirovecii pneumonia after chemotherapy: a case report

2019 ◽  
Vol 7 (9) ◽  
pp. 3561
Author(s):  
Donghua Zheng ◽  
Kai Chen ◽  
Fang Xiao ◽  
Na Liu
Keyword(s):  
Case Report ◽  
Next Generation Sequencing ◽  
Early Stage ◽  
Severe Pneumonia ◽  
Pneumocystis Pneumonia ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Next Generation ◽  
Pneumocystis Jiroveci ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The incidence of Pneumocystis pneumonia is increasing in immunosuppressive patients. How to diagnose and treat Pneumocystis pneumonia in the early stage has become an important issue for clinicians. The development of Next-generation Sequencing (NGS) provides technical support for the diagnosis of Pneumocystis pneumonia. Case report: A 14-year-old male patient was diagnosed with T lymphoblastoma and treated with chemotherapy. After chemotherapy, the patient developed bone marrow suppression and was complicated with severe pneumonia. He was given endotracheal intubation and ventilator assisted respiration. Samples of patients' alveolar lavage fluid were obtained, and Next-generation Sequencing (NGS) was used for diagnosis, confirming the pathogen as Pneumocystis jiroveci, which was treated by TMP/SMX. The patient's condition gradually improved, and was finally removed from ventilator and endotracheal tube. Pneumocystis jiroveci is a common opportunistic pathogen in immunosuppressive patients, and Next-generation Sequencing (NGS) can be used for rapid diagnosis of Pneumocystis pneumonia, thus improving the clinical therapeutic effect. 

scholarly journals Aging, Bone Marrow and Next-Generation Sequencing (NGS): Recent Advances and Future Perspectives

2021 ◽  
Vol 22 (22) ◽  
pp. 12225
Author(s):  
Payal Ganguly ◽  
Bradley Toghill ◽  
Shelly Pathak
Keyword(s):  
Bone Marrow ◽  
Next Generation Sequencing ◽  
Protein Interactions ◽  
Genetic Alterations ◽  
Low Grade ◽  
Next Generation ◽  
High Throughput Analysis ◽  
Age Related ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The aging of bone marrow (BM) remains a very imperative and alluring subject, with an ever-increasing interest among fellow scientists. A considerable amount of progress has been made in this field with the established ‘hallmarks of aging’ and continued efforts to investigate the age-related changes observed within the BM. Inflammaging is considered as a low-grade state of inflammation associated with aging, and whilst the possible mechanisms by which aging occurs are now largely understood, the processes leading to the underlying changes within aged BM remain elusive. The ability to identify these changes and detect such alterations at the genetic level are key to broadening the knowledgebase of aging BM. Next-generation sequencing (NGS) is an important molecular-level application presenting the ability to not only determine genomic base changes but provide transcriptional profiling (RNA-seq), as well as a high-throughput analysis of DNA–protein interactions (ChIP-seq). Utilising NGS to explore the genetic alterations occurring over the aging process within alterative cell types facilitates the comprehension of the molecular and cellular changes influencing the dynamics of aging BM. Thus, this review prospects the current landscape of BM aging and explores how NGS technology is currently being applied within this ever-expanding field of research.

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