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

Molecular and immune landscape of tumours in geriatric patients with non-small cell lung cancer, melanoma and renal cell carcinoma by Abdul Rafeh Naqash, April K Salama, Emil Lou, Andrew Elliott, Wafik S El-Deiry, Chul Kim, Stephen V Liu, Anwaar Saeed, Hirva Mamdani, Khalil Choucair, Dipesh Uprety, Phillip Walker, Himisha Beltran, Matthew James Oberley, Azhar Saeed, Lujia Chen

“…Then, using next-generation sequencing and programmed death-ligand 1 (PD-L1) assessment, we evaluated gene expression differences between age groups and across tumour types, with a focus on ageing-related processes such as DNA damage response (DDR), immune checkpoint (IC) and metabolism-related genes. …”
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

Antimicrobial Resistance Genes in Clinical <i>Escherichia coli</i> Strains from Livestock and Poultry in Shandong Province, China During 2015–2020 by Miaoli Wang, Shaopeng Wu, Yao Wang, Feng Chen, Zhangqi Shen, Zouran Lan

“…<b>Methods:</b> A total of 158 <i>E. coli</i> strains were collected and subjected to antimicrobial susceptibility testing and sequencing by whole-genome Next Generation Sequencing (NGS). <b>Results:</b> MDR strains accounted for 46.20% of the 158 <i>E. coli</i> strains with the highest resistant rate of ciprofloxacin (71.52%). …”
Get full text

Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol by Alexandra Wharton-Smith, Caterina Guinovart, Pedro Aide, Francisco Saute, Alfredo Mayor, Bryan Greenhouse, Baltazar Candrinho, Joshua L Proctor, Arantxa Roca-Feltrer, Clemente da Silva, Eduard Rovira-Vallbona, Craig Bonnington, Caitlin Bever, Arlindo Chidimatembue, Maria Rodrigues, Neide Canana, Paulo Arnaldo, Simone Boene, Sonia Enosse

“…We will use a multiplex amplicon-based next-generation sequencing approach targeting informative single nucleotide polymorphisms, gene deletions and microhaplotypes. …”
Get full text

Clinicopathological analysis of adrenal intravascular large B-cell lymphoma by LIN Jiaxin, WEI Ran, SHUI Ruohong, LU Hongfen, LI Xiaoqiu, YU Baohua

“…The molecular genetic characteristics were detected using next-generation sequencing (NGS). This study was approved by the Ethics Committee of Fudan University Shanghai Cancer Center (Ethics number: 050432-4-2307E). …”
Get full text

Bioinformatics services for analyzing massive genomic datasets by Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Ho-Yeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byunghee Kang, Sunguk Shin, Lian Kim, Seung-Won Lee, Dougu Nam, Jihyun F. Kim, Namshin Kim, Seon-Young Kim, Sanghyuk Lee, Tae-Young Roh, Byungwook Lee

“…The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. …”
Get full text

A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa by Deon deJager, Marlo Möller, Eileen Hoal, Paul vanHelden, Brigitte Glanzmann, Cindy Harper, Paulette Bloomer

“…ABSTRACT The reduced cost of next‐generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non‐model species. …”
Get full text

Antibiotic susceptibility and molecular characterization based on whole-genome sequencing of Staphylococcus aureus causing invasive infection in children and women living in Southw... by Li Liu, Ziyi Yan, Fumei He, Jie Chen, Linghan Kuang, Xingxin Liu, Yali Cui, Xia Wang, Chenglin Miao, Hong Li, Yongmei Jiang

“…Methods The demographic and clinical characteristics of patients with invasive S. aureus infection were collected and analyzed. Next-generation sequencing (NGS) and sequence analysis techniques were used to determine the molecular epidemiological characteristics of the S. aureus isolates, and the microdilution broth method was used for antimicrobial susceptibility testing. …”
Get full text

Association of pituitary neuroendocrine tumors and neurofibromatosis type 1: assessing causation versus coincidence. Case report by Mercedes Aguilar-Soto, Julia M. Zuarth-Vázquez, Laura Leyva-Figueroa, Karla Zarco-Ávila, Armando Gamboa-Domínguez, Aldo Eguiluz-Melendez, Laura C. Hernández-Ramírez

“…Genetic testing was carried out by means of targeted next generation sequencing (NGS) and Sanger sequencing in blood and tumor DNA, respectively. …”
Get full text

Relationship between bacteria and nitrogen dynamics in wastewater treatment oxidation ponds by S. Saneha, T. Pattamapitoon, S. Bualert, O. Phewnil, W. Wararam, N. Semvimol, K. Chunkao, C. Tudsanaton, M. Srichomphu, U. Nachaiboon, O. Wongsrikaew, P. Wichittrakarn, C. Chanthasoon

“…This study was carried out in the oxidation wastewater treatment at the King’s Royally Initiated Laem Phak Bia Environmental Research and Development or LERD Project, in Phetchaburi, Thailand.METHODS: Wastewater samples were collected from the 1st–5th oxidation ponds at a depth of 30 centimeter from the water surface and analyzed for various quality parameters including temperature, dissolved oxygen, potential of hydrogen, biochemical oxygen demand, nitrates, ammonia, and total kjeldahl nitrogen. Next-generation sequencing by Illumina Miseq was used to examine the 16S ribosomal ribonucleic acid of bacteria in the collected samples. …”
Get full text

Genome-Wide Profiling of Human Papillomavirus DNA Integration into Human Genome and Its Influence on PD-L1 Expression in Chinese Uygur Cervical Cancer Women by Feng Yang-chun, Wang Sen-yu, Zhang Yuan, Huang Yan-chun

“…The integration situation of HPV gene into host cell genome was detected by Agilent SureSelect™ Target Enrichment Chip and Next-Generation Sequencing. The related genes were analyzed by GO functional annotation and KEGG pathway enrichment. …”
Get full text