Next-generation sequencing of single-stranded DNA (ssDNA) is attracting increased attention from a wide variety of research fields. Accordingly, various methods are actively being tested for the efficient adaptor-tagging of ssDNA. We conceived a novel chemo-enzymatic method termed terminal deoxynucleotidyl transferase (TdT)-assisted, copper-catalyzed azide-alkyne cycloaddition (CuAAC)-mediated ssDNA ligation (TCS ligation). In this method, TdT is used to incorporate a single 3'-azide-modified dideoxyribonucleotide onto the 3'-end of target ssDNA, followed by CuAAC-mediated click ligation of the azide-incorporated 3'-end to a 5'-ethynylated synthetic adaptor. This report presents the first proof-of-principle application of TCS ligation with its use in the preparation of a next-generation sequencing library.
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http://dx.doi.org/10.1093/nar/gky452 | DOI Listing |
Jpn J Clin Oncol
January 2025
Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, 47-1 Nodayama, Medeshima-Shiode, Natori, Miyagi 981-1293, Japan.
A Japanese woman with Li-Fraumeni syndrome in her 40s underwent comprehensive genetic profiling accompanied by germline data using the Oncoguide NCC Oncopanel, but no germline pathogenic variants in the tumor suppressor gene TP53 were detected. However, careful examination of additional data in the report suggested the presence of a large TP53 deletion. Custom targeting next-generation sequencing and nanopore sequencing revealed a 3.
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January 2025
Institute of Technology and Life Sciences-National Research Institute, Falenty, 3 Hrabska Avenue, 05-090, Raszyn, Poland.
Plant growth-promoting bacteria (PGPB) are considered an effective eco-friendly biostimulator. However, relatively few studies have examined how PGPB affect the native bacterial community of major crops. Thus, this study investigates the impact of a PGPB consortium, comprising Pseudomonas sp.
View Article and Find Full Text PDFZhonghua Bing Li Xue Za Zhi
February 2025
Department of Pathology, Foshan Traditional Chinese Medicine Hospital, Foshan 528000, China.
To investigate the clinicopathological and genetic features of infantile rhabdomyofibrosarcoma (IRFS) with EGFR kinase domain duplication (EGFR-KDD). The clinical, morphological and immunohistochemical features of three IRFS with EGFR-KDD diagnosed from January 2022 to January 2024 at Department of Pathology, Foshan Traditional Chinese Medicine Hospital, Foshan, China were retrospectively analyzed using PCR or next generation sequencing technique; and related literature was reviewed. There were 1 male and 2 females, aged at presentation ranging from 1 to 4 years.
View Article and Find Full Text PDFZhonghua Bing Li Xue Za Zhi
February 2025
Department of Pathology, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China.
To investigate the clinicopathological characteristics of solid, endometrial-like and transitional (SET) cell growth subtype in high-grade serous ovarian carcinoma (HGSC). Clinical data of 25 cases of HGSC-SET were collected from January 2020 to March 2024 at the Affiliated Suzhou Hospital of Nanjing Medical University, and their histological features were analyzed. Immunohistochemical stains were used to analyze the expression of ER, PR, PAX8, WT-1, p16, p53 and Ki-67.
View Article and Find Full Text PDFZhonghua Bing Li Xue Za Zhi
February 2025
Department of Pathology, People's Hospital of Zhengzhou University/People's Hospital of Henan University, Zhengzhou 450043, China.
To investigate the expression pattern of pan-TRK protein in colorectal cancers with NTRK gene fusion and mismatch repair deficient (dMMR) and to analyze its molecular pathological characteristics. A total of 117 dMMR colorectal cancers diagnosed in the Department of Pathology of Henan Provincial People's Hospital, Zhengzhou, China from 2020 to 2023 were collected. Immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) and DNA/RNA-based next-generation sequencing (NGS) were used to detect pan-TRK protein expression and fusion partner genes in tumors, and to further explore the correlation between pan-TRK staining patterns and partner genes.
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