Identifying the function of novel cross-species microRNAs from the excretory-secretory products of Angiostrongylus cantonensis fifth-stage larvae by Kuang-Yao Chen, Yi-Hsuan Lin, Chien-Ju Cheng, Yi-Hao Huang, Sheng-Yu Lin, Chyi-Liang Chen, Cheng-Hsun Chiu

“…Methods: Here, we employed next-generation sequencing (NGS) to establish the secreted microRNAs dataset. …”
Get full text

A Novel CRYBB2 Stopgain Mutation Causing Congenital Autosomal Dominant Cataract in a Chinese Family by Yu Zhou, Yaru Zhai, Lulin Huang, Bo Gong, Jie Li, Fang Hao, Zhengzheng Wu, Yi Shi, Yin Yang

“…This study aimed to identify gene mutations responsible for autosomal dominant congenital cataract (ADCC) in a Chinese family using next-generation sequencing technology. This family included eight unaffected and five affected individuals. …”
Get full text

Rumen DNA virome and its relationship with feed efficiency in dairy cows by Xiaohan Liu, Yifan Tang, Hongyi Chen, Jian-Xin Liu, Hui-Zeng Sun

“…In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE. …”
Get full text

Rare Somatic MEN1 Gene Pathogenic Variant in a Patient Affected by Atypical Parathyroid Adenoma by Luigia Cinque, Flavia Pugliese, Celeste Clemente, Stefano Castellana, Maria Pia Leone, Danilo de Martino, Teresa Balsamo, Claudia Battista, Tommaso Biagini, Paolo Graziano, Marco Castori, Alfredo Scillitani, Vito Guarnieri

“…We suggest that MEN1 gene could be an underestimate genetic determinant of these rare histological entities, and we highlight the utility of a complete genetic screening protocol, by the use of next-generation sequencing technology in such undetermined clinical cases with no frank clinical presentation.…”
Get full text

Mutation in the COL2A1 gene is associated with acetabular dysplasia by Miaomiao Xin, Xin Guan, Xin Guan, Jiangfei Yang, Yi Li, Zhentao Man, Hongsheng Sun, Min Fu

“…Clinical whole-exome sequencing (WES) using next-generation sequencing (NGS) was conducted to identify potential mutation sites, which were then validated through Sanger sequencing. …”
Get full text

Association of tumour mutation burden with prognosis and its clinical significance in stage III gastric cancer by Ya-Lin Han, Li Chen, Xu-Ning Wang, Mao-Lin Xu, Rui Qin, Fang-Ming Gong, Peng Sun, Hong-Yi Liu, Zhi-Peng Teng, Zhao-Xia Li, Guang-Hai Dai

“…In the study cohort, next-generation sequencing was used to detect mutated GC genes and obtain TMB data. …”
Get full text

An Unusually Short Latent Period of Therapy-Related Myeloid Neoplasm Harboring a Rare MLL-EP300 Rearrangement: Case Report and Literature Review by Reina Takeda, Kazuaki Yokoyama, Seiichiro Kobayashi, Toyotaka Kawamata, Sousuke Nakamura, Tomofusa Fukuyama, Mika Ito, Nozomi Yusa, Eigo Shimizu, Nobuhiro Ohno, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Kaoru Uchimaru, Arinobu Tojo

“…Bone marrow examinations revealed chronic myelomonocytic leukemia-like disease with a chromosomal translocation of t(11;22)(q23;q13) as a solo cytogenetic abnormality, resulting in the diagnosis of t-MN. Next-generation sequencing analysis identified a rare chimeric transcript, MLL-EP300, without any additional somatic mutations. …”
Get full text

mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms by Barnabé, Christian, Sempéré, Guilhem, Manzanilla, Vincent, Millan, Joel Moo, Amblard-Rambert, Antoine, Waleckx, Etienne

“…In our workflow, VSEARCH is utilized for processing fastq files derived from amplicon-based Next-Generation Sequencing data. This software is a versatile open-source tool for processing amplicon sequences, offering advantages such as high speed, efficient memory usage, and the ability to handle large datasets. …”
Get full text

Investigating the potential immunomodulatory effects of commercial oral probiotic supplements on equine gastrointestinal tract barrier function by Agnieszka Żak-Bochenek, Paulina Żebrowska-Różańska, Joanna Bajzert, Łukasz Łaczmański, Bogumiła Szponar, Natalia Siwińska, Klaudia Gładysz, Katarzyna Sikorska, Anna Chełmońska-Soyta

“…The samples were subjected to microbiome analysis via next-generation sequencing of hypervariable regions V3-V4 and V7-V9 of the 16S rRNA gene for analysis of short-chain fatty acids via HPLC analysis and fecal secretory immunoglobulin A (SIgA) quantification via ELISA.ResultsMicrobiome analysis revealed no significant differences in either alpha or beta diversity parameters between the groups. …”
Get full text

An exploratory study on the differential diagnostic indicators between adult systemic EBV-positive T-cell lymphoproliferative disorders and angioimmunoblastic T-cell lymphoma with... by Xiaodan Zheng, Yuanyuan Zheng, Yanlin Zhang, Jianlan Xie, Xiaojing Teng, Kuo Bi, Lan Sun, Xiaowen Huang, Mulan Jin, Xiaoge Zhou

“…Differences in immunophenotype, type of EBV-infected cells, clonality and gene mutations between the two groups of cases were compared by immunohistochemical staining, double-label staining, TCR gene rearrangement and next-generation sequencing analysis. Results 7 cases of adult EBV+ T-LPD: all cases had no more than 1 T follicular helper (THF) marker was expressed, and there were significantly more EBER+/CD3 + cells than EBER+/CD20 + cells; 5 cases had mutation detection results, in which only 1 had the characteristic KMT2D mutation, 2 had TET2 mutations, and no common mutations such as DDX3X were detected.16 cases of AITL with multiple EBV infections: all cases were found to express at least 2 TFH markers, with 87% of them expressing at least 3 TFH markers., and had significantly more EBER+/CD20 + cells than EBER+/CD3 + cells; 4 cases had mutation test results, with mutated high-frequency genes being TET2 (100%, and all of them had 2 or more TET2 mutations) and RHOA G17V (100%), DNMT3A mutation occurred in 2 cases (50%), and IDH2 R172 mutation occurred in 1 case (25%). …”
Get full text

Clinical and molecular characteristics and long-term outcomes of pediatric intracranial meningiomas: a comprehensive analysis from a single neurosurgical center by Leihao Ren, Jiaojiao Deng, Hiroaki Wakimoto, Qing Xie, Ye Gong, Lingyang Hua

“…Method We enrolled 74 patients with intracranial PMs and analyzed their clinicopathological characteristics. Targeted next generation sequencing was used to detect alterations in meningioma relevant genes. …”
Get full text

Tp53 determines the spatial dynamics of M1/M2 tumor-associated macrophages and M1-driven tumoricidal effects by Yi-Jing Hsiao, Min-Shu Hsieh, Gee-Chen Chang, Yin-Chen Hsu, Chia-Yu Wang, Yan-Ming Chen, Yi-Ling Chen, Pan-Chyr Yang, Sung-Liang Yu

“…We characterized the mutation status and density of M1/M2 TAMs within tumor islets and stroma in 117 lung adenocarcinomas using next-generation sequencing and immunohistochemistry, respectively. …”
Get full text

Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis by E. V. Antontseva, A. O. Degtyareva, E. E. Korbolina, I. S. Damarov, T. I. Merkulova

“…The development of the NGS (next-generation sequencing) technology has contributed not only to the identification of a huge number of SNPs and to the search for their association (genome-wide association studies, GWASs) with certain diseases or phenotypic manifestations, but also to the development of more productive approaches to their functional annotation. …”
Get full text

Korean patients with hereditary cancer: a prospective multicentre cohort study protocol exploring psychosocial and health outcomes by Boyoung Park, Sun-young Kong, Dongju Won, Jong Eun Park, Jun-Kyu Kim, Mi-Ae Jang, Jung-Sook Ha, Kyoung-Bo Kim

“…This study evaluates changes in participant quality of life (QoL), unmet needs and mental health over time based on their genetic variant status.Methods and analysis This prospective cohort study will recruit 1435 patients with suspected hereditary cancer who have undergone BRCA1/2 or next-generation sequencing (NGS) testing. The study began in July 2023 and will continue until December 2027. …”
Get full text

Detecting gene copy number alterations by Oncomine Comprehensive genomic profiling in a comparative study on FFPE tumor samples by Fabio Bozzi, Elena Conca, Marco Silvestri, Gianpaolo Dagrada, Alice Ardore, Donata Penso, Daniele Lorenzini, Chiara Costanza Volpi, Desirè Viola Trupia, Adele Busico, Iolanda Capone, Federica Perrone, Elena Tamborini, Andrea Vingiani, Luca Agnelli, Giancarlo Pruneri

“…The introduction of other procedures, such as Next-Generation Sequencing has dramatically improved CNAs discovery at genome-wide level. …”
Get full text

The application of Vavilov’s approaches to the phylogeny and evolution of cultivated species of the genus <i>Avena</i> L. by I. G. Loskutov, A. A. Gnutikov, E. V. Blinova, A. V. Rodionov

“…The phylogenetic analysis of the representative intraspecific diversity of cultivated and wild Avena species carried out using next generation sequencing (NGS) showed that diploid species with A-genome variants are in fact not primary diploids, but a peculiar Mediterranean introgressive hybridization complex of species that sporadically enter into interspecific hybridization. …”
Get full text

Bacteriophage Treatment Induces Phenotype Switching and Alters Antibiotic Resistance of ESBL <i>Escherichia coli</i> by Árpád Rózsa, László Orosz, Nikoletta Szemerédi, Gabriella Spengler, Gábor Kecskeméti, Otília Vágó, Károly Péter Sárvári, Diana Szabó, Zoltán Szabó, Katalin Burián, Dezső Péter Virok

“…<b>Methods:</b> We used next generation sequencing, proteomics and phenotypic screens to investigate the effect of bacteriophage infections on <i>E. coli</i> metabolism and resistance phenotypes. …”
Get full text

High Frequency of AIFM1 Variants and Phenotype Progression of Auditory Neuropathy in a Chinese Population by Hongyang Wang, Dan Bing, Jin Li, Linyi Xie, Fen Xiong, Lan Lan, Dayong Wang, Jing Guan, Qiuju Wang

“…A total of 36 families of individuals with AN (50 cases) with AIFM1 variations were recruited and identified by Sanger sequencing or next-generation sequencing; the participants included 30 patients from 16 reported families and 20 new cases. …”
Get full text

Gastric Cancer Cell Lines Have Different MYC-Regulated Expression Patterns but Share a Common Core of Altered Genes by Jersey Heitor da S. Maués, Helem Ferreira Ribeiro, Giovanny R. Pinto, Luana de Oliveira Lopes, Letícia M. Lamarão, Carla Mariana F. Pessoa, Caroline de Fátima Aquino Moreira-Nunes, Raimundo Miranda de Carvalho, Paulo P. Assumpção, Juan A. Rey, Rommel M. Rodríguez Burbano

“…By using siRNA and Next-Generation Sequencing (NGS), we identified MYC-regulated differentially expressed Genes (DEGs) in three Brazilian gastric cancer cell lines representing the histological subtypes of GC (diffuse, intestinal, and metastasis). …”
Get full text

Cryptic transmission of a SARS-CoV-2 variant detected by wastewater surveillance in Panama by Melissa Gaitán, Yamitzel Zaldivar, Michelle Hernandez, Jessica Góndola, Oris Chavarría, Brechla Moreno, Danilo Franco, Rodrigo DeAntonio, Santiago Mirazo, Florencia Cancela, Maria Eugenia Barnett, Alexander A. Martinez, Juan Miguel Pascale, Sandra López-Vergès

“…Wastewater samples were collected monthly in duplicate at two collection points from three districts of Panama city metropolitan area for testing by SARS-CoV-2 RT-qPCR, and positive samples were analyzed by next-generation sequencing to identify sublineages. A total of 36 wastewater samples and 822 samples obtained through the clinical surveillance were analyzed for molecular detection and sequencing. …”
Get full text