scholarly journals Seminal Vesicle Involvement by Carcinoma In Situ of the Bladder: Clonal Analysis Using Next-Generation Sequencing to Elucidate the Mechanism of Tumor Spread

2020 ◽  
Author(s):  
Hyun Sik Park ◽  
Hyunbin Shin ◽  
Myung-Shin Lee ◽  
Joo Heon Kim ◽  
Seon-Young Kim ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Seminal Vesicle ◽  
Clonal Analysis ◽  
Next Generation ◽  
Tumor Spread ◽  
Seminal Vesicle Involvement ◽  
Generation Sequencing

Novel and established EWSR1 gene fusions and associations identified by next-generation sequencing and fluorescence in-situ hybridization

2019 ◽  
Vol 93 ◽  
pp. 65-73 ◽  
Author(s):  
Melissa Krystel-Whittemore ◽  
Martin S. Taylor ◽  
Miguel Rivera ◽  
Jochen K. Lennerz ◽  
Long P. Le ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Next Generation Sequencing ◽  
Fluorescence In Situ Hybridization ◽  
Gene Fusions ◽  
Next Generation ◽  
Ewsr1 Gene ◽  
Generation Sequencing

scholarly journals Next generation sequencing of the clonal IGH rearrangement detects ongoing mutations and interfollicular trafficking in in situ follicular neoplasia

PLoS ONE ◽  
2017 ◽  
Vol 12 (6) ◽  
pp. e0178503 ◽  
Author(s):  
Perikles Kosmidis ◽  
Irina Bonzheim ◽  
Claudia Dufke ◽  
Sema Colak ◽  
Thomas Hentrich ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Igh Rearrangement ◽  
Generation Sequencing

scholarly journals CellectSeq: In silico discovery of antibodies targeting integral membrane proteins combining in situ selections and next-generation sequencing

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Abdellali Kelil ◽  
Eugenio Gallo ◽  
Sunandan Banerjee ◽  
Jarrett J. Adams ◽  
Sachdev S. Sidhu
Keyword(s):  
Next Generation Sequencing ◽  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Cost Effective ◽  
Integral Membrane Proteins ◽  
Sequencing Error ◽  
Next Generation ◽  
Synthetic Antibody ◽  
Generation Sequencing

AbstractSynthetic antibody (Ab) technologies are efficient and cost-effective platforms for the generation of monoclonal Abs against human antigens. Yet, they typically depend on purified proteins, which exclude integral membrane proteins that require the lipid bilayers to support their native structure and function. Here, we present an Ab discovery strategy, termed CellectSeq, for targeting integral membrane proteins on native cells in complex environment. As proof of concept, we targeted three transmembrane proteins linked to cancer, tetraspanin CD151, carbonic anhydrase 9, and integrin-α11. First, we performed in situ cell-based selections to enrich phage-displayed synthetic Ab pools for antigen-specific binders. Then, we designed next-generation sequencing procedures to explore Ab diversities and abundances. Finally, we developed motif-based scoring and sequencing error-filtering algorithms for the comprehensive interrogation of next-generation sequencing pools to identify Abs with high diversities and specificities, even at extremely low abundances, which are very difficult to identify using manual sampling or sequence abundances.

scholarly journals In vivo optical imaging-guided targeted sampling for precise diagnosis and molecular pathology

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aditi Sahu ◽  
Yuna Oh ◽  
Gary Peterson ◽  
Miguel Cordova ◽  
Cristian Navarrete-Dechent ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Pathology ◽  
Ex Vivo ◽  
Molecular Profiling ◽  
Next Generation ◽  
Spatial Targeting ◽  
Mutational Profiling ◽  
Generation Sequencing

AbstractConventional tissue sampling can lead to misdiagnoses and repeated biopsies. Additionally, tissue processed for histopathology suffers from poor nucleic acid quality and/or quantity for downstream molecular profiling. Targeted micro-sampling of tissue can ensure accurate diagnosis and molecular profiling in the presence of spatial heterogeneity, especially in tumors, and facilitate acquisition of fresh tissue for molecular analysis. In this study, we explored the feasibility of performing 1–2 mm precision biopsies guided by high-resolution reflectance confocal microscopy (RCM) and optical coherence tomography (OCT), and reflective metallic grids for accurate spatial targeting. Accurate sampling was confirmed with either histopathology or molecular profiling through next generation sequencing (NGS) in 9 skin cancers in 7 patients. Imaging-guided 1–2 mm biopsies enabled spatial targeting for in vivo diagnosis, feature correlation and depth assessment, which were confirmed with histopathology. In vivo 1-mm targeted biopsies achieved adequate quantity and high quality of DNA for next-generation sequencing. Subsequent mutational profiling was confirmed on 1 melanoma in situ and 2 invasive melanomas, using a 505-gene mutational panel called Memorial Sloan Kettering-Integrated mutational profiling of actionable cancer targets (MSK-IMPACT). Differential mutational landscapes, in terms of number and types of mutations, were found between invasive and in situ melanomas in a single patient. Our findings demonstrate feasibility of accurate sampling of regions of interest for downstream histopathological diagnoses and molecular pathology in both in vivo and ex vivo settings with broad diagnostic, therapeutic and research potential in cutaneous diseases accessible by RCM-OCT imaging.

scholarly journals Comparison of MET gene amplification analysis by next-generation sequencing and fluorescence in situ hybridization

Oncotarget ◽  
2021 ◽  
Vol 12 (22) ◽  
pp. 2273-2282
Author(s):  
Christina Schmitt ◽  
Anna-Alice Schulz ◽  
Ria Winkelmann ◽  
Kevin Smith ◽  
Peter J. Wild ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Next Generation Sequencing ◽  
Fluorescence In Situ Hybridization ◽  
Gene Amplification ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Primary renal NUT carcinoma identified by next-generation sequencing: A case report and literature review

2020 ◽  
Author(s):  
Fei Yang ◽  
Danhua Shen ◽  
Junping Shi
Keyword(s):  
Next Generation Sequencing ◽  
Ewing Sarcoma ◽  
Undifferentiated Carcinoma ◽  
Next Generation ◽  
Advanced Neoplasm ◽  
Poorly Differentiated ◽  
Nut Carcinoma ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background NUT carcinoma is a rare aggressive squamous cell carcinoma subtype genetically defined by NUTM1 rearrangements. NUT carcinoma usually has a primitive differentiation state and can be easily misdiagnosed as an undifferentiated carcinoma or Ewing sarcoma. Case presentation We report a case of NUT carcinoma of renal origin initially diagnosed as a malignant small round-cell tumor, likely to be Ewing sarcoma/primitive neuroectodermal tumor. Based on next-generation sequencing (NGS), the diagnosis was revised to NUT carcinoma with a characteristic NUTM1 rearrangement. The patient relapsed after surgery and received a standard NUT carcinoma treatment. However, due to advanced neoplasm progression, first-line chemotherapy failed and the patient died. Conclusion Routine NUT immunohistochemistry staining, NGS, and/or fluorescent in situ hybridization for poorly differentiated carcinoma and sarcoma tumors can help avoid misdiagnosis of NUT carcinoma-related tumors, allowing patients to benefit from bromodomain and extra-terminal motif inhibitor therapy.

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