Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods by Rué, Olivier, Coton, Monika, Dugat-Bony, Eric, Howell, Kate, Irlinger, Françoise, Legras, Jean-Luc, Loux, Valentin, Michel, Elisa, Mounier, Jérôme, Neuvéglise, Cécile, Sicard, Delphine

“…Next generation sequencing offers several ways to study microbial communities. …”
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Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population by Marie-Ming Aynaud, Lauren Caldwell, Khalid N. Al-Zahrani, Seda Barutcu, Kin Chan, Andreea Obersterescu, Abiodun A. Ogunjimi, Min Jin, Kathleen-Rose Zakoor, Shyam Patel, Ron Padilla, Mark C. C. Jen, Princess Mae Veniegas, Nursrin Dewsi, Filiam Yonathan, Lucy Zhang, Amelia Ayson-Fortunato, Analiza Aquino, Paul Krzyzanowski, Jared Simpson, John Bartlett, Ilinca Lungu, Bradly G. Wouters, James M. Rini, Michael Gekas, Susan Poutanen, Laurence Pelletier, Tony Mazzulli, Jeffrey L. Wrana

“…We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we here deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). …”
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Molecular testing stratifies the risk of structural recurrence in high risk differentiated thyroid cancer: a retrospective cohort study by Jie Liu, Wensi Gao, Xiong Zheng, Shuping Wu, Yi Shi, Feng Wang, Yu Wu

“…Molecular characterize groups were conducted using an 18-gene next-generation sequencing assay. Patients harboring mutations in the TERT promoter, TP53, or PIK3CA genes were categorized as the high molecular risk group, while all others were assigned to the non-high molecular risk group.ResultsAmong the 108 cases, 32 (29.6%) fell into the high molecular risk group, characterized by a significantly older mean age (57.8 vs. 42.6 years, p < 0.001), larger tumor size (3.1 cm vs. 2.0 cm, p = 0.003), a higher incidence of aggressive pathological subtypes (43.8% vs. 7.9%, p < 0.001), and an increased occurrence of distant metastasis (34.4% vs. 7.9%, p = 0.001). …”
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Integrating genetic subtypes with PET scan monitoring to predict outcome in diffuse large B-cell lymphoma by Matías S. Mendeville, Jurriaan Janssen, G. Tjitske Los-de Vries, Erik van Dijk, Julia Richter, Marcel Nijland, Margaretha G. M. Roemer, Phylicia Stathi, Nathalie J. Hijmering, Reno Bladergroen, Diego A. Pelaz, Arjan Diepstra, Corinne J. Eertink, Coreline N. Burggraaff, Yongsoo Kim, Pieternella J. Lugtenburg, Anke van den Berg, Alexandar Tzankov, Stefan Dirnhofer, Ulrich Dührsen, Andreas Hüttmann, Wolfram Klapper, Josée M. Zijlstra, Bauke Ylstra, Daphne de Jong

“…Abstract Next Generation Sequencing-based subtyping and interim- and end of treatment positron emission tomography (i/eot-PET) monitoring have high potential for upfront and on-treatment risk assessment of diffuse large B-cell lymphoma patients. …”
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Utilization of primary tumor samples for cancer neoantigen discovery by Yong Li, Steven A Rosenberg, Paul Robbins, Billel Gasmi, Todd D Prickett, Jared J Gartner, Devikala Gurusamy, Stephanie L Goff, Vid Leko, Victoria Hill, Frank J Lowery, Bradley Sinclair White, Sivasish Sindiri, Maria Parkhust, Noam Levin, Eric Groh, Shoshana T Levi, Amy R Copeland, Sanghyun Peter Kim

“…For the treatment of the latter, selecting cells for therapy typically involves laborious screening of TIL for recognition of autologous tumor-specific mutations, detected through next-generation sequencing of freshly resected metastatic tumors. …”
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Detection of low frequency artemisinin resistance mutations, C469Y, P553L and A675V, and fixed antifolate resistance mutations in asymptomatic primary school children in Kenya by Victor Osoti, Kevin Wamae, Leonard Ndwiga, Paul M. Gichuki, Collins Okoyo, Stella Kepha, Kibor Keitany, Regina Kandie, Stephen Aricha, Rosebella Kiplagat, Charles Mwandawiro, Philip Bejon, Robert W. Snow, Lynette Isabella Ochola-Oyier

“…Recent advances in next-generation sequencing (NGS) technologies have enabled the tracking of drug-resistant malaria parasites. …”
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Circulating tumor DNA for surveillance in high-risk melanoma patients: a study protocol by Magnús P.B. Obinah, Sarah A. Al-Halafi, Karin Dreisig, Tim S. Poulsen, Christoffer Johansen, Thomas Litman, Stig E. Bojesen, Estrid Høgdall, Annette H. Chakera, Lisbet R. Hölmich

“…In case of recurrence, patient-specific mutations are identified through next-generation sequencing (NGS) of formalin and paraffin embedded tissue from diagnostic routine. …”
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Prokaryotic diversity of the rhizosphere from Argentinean wine-producing regions by Andres Martin Toscani, Monica Oyuela Aguilar, Constanza Rey, Ramiro Eugenio Rocco Welsh, Alex Gobbi, Maria Florencia del Papa, Liliana Carmen Semorile, Lars Hestbjerg Hansen, Mariano Pistorio

“…In this work, we conducted a comprehensive examination of the diversity of prokaryotic microorganisms in the rhizosphere of vineyards located in three wine regions of Argentina. We used next-generation sequencing methods, concentrating the analysis on two relevant cultivars, Malbec and Cabernet Sauvignon. …”
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Optical genome mapping: Unraveling complex variations and enabling precise diagnosis in dystrophinopathy by Jiahui Mai, Jing Duan, Xiaoyu Chen, Liqin Liu, Dachao Liang, Tao Fu, Gang Lu, Wai Yee Chan, Xufeng Luo, Feiqiu Wen, Jianxiang Liao, Zhuo Li, Xinguo Lu

“…Abstract Objective Approximately 7% of individuals with dystrophinopathy remain undiagnosed at the genetic level using conventional genetic tests like multiplex ligation‐dependent probe amplification (MLPA) and next‐generation sequencing (NGS). We used the optical genome mapping (OGM) technology to detect and analyze uncommon mutations or structural variations (SVs) within the DMD gene, thus contributing to more precise clinical diagnoses. …”
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Prevalence and molecular characterization of human bocavirus-1 in children and adults with influenza-like illness from Kunming, Southwest China by Yanhong Sun, Lili Jiang, Yaoyao Chen, Zhaosheng Liu, Meiling Zhang, Xiaonan Zhao, Xiaoyu Han, Lifen Zhang, Xiaoqing Fu, Jienan Zhou

“…Amplification of the near-complete HBoV genome was achieved through three overlapping fragments, followed by next-generation sequencing (NGS) and phylogenetic analysis. …”
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Neuropilin1-dependent paracrine signaling of cancer cells mediated by miRNA exosomal cargo by Claudia Palazzo, Roberta Mastrantonio, Noemi Gioelli, Erika Testa, Francesco Recco, Donatella Lucchetti, Giulia Villari, Alessio D’Alessio, Alessandro Sgambato, Flavio Mignone, Guido Serini, Maria Teresa Viscomi, Luca Tamagnone

“…The micro-RNA profile carried by exosomes was investigated by Next Generation Sequencing. miRNA-Scope in situ hybridization was used to assess the transfer of miRNA exosome cargo to target cells, and immunofluorescence analysis revealed expression regulation of targeted proteins. miRNA activity was blocked by the use of specific antago-miRs. …”
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Telomere Length Is Associated With Adverse Atrial Remodeling in Patients With Atrial Fibrillation by Kabita Pradhan, Balram Neupane, Paul Niehues, Martin Kirschner, Fabian Beier, Chao‐Chung Kuo, Erika Anneliese Hilbold, Christian Bär, Oana‐Maria Thoma, Maximilian Waldner, Margherita Vieri, Tim H. Brümmendorf, Vithurithra Tharmapalan, Wolfgang Wagner, Michael Kleines, Mahdi Emrani, Matthias Daniel Zink, Andreas Napp, Nikolaus Marx, Michael Gramlich

“…Clonal hematopoiesis of indeterminate potential was assessed by next generation sequencing. Telomerase reverse transcriptase knockout (Tert−/−) and telomerase RNA component knockout (Terc−/−) mice were used to investigate the mechanistic impact of telomere shortening on atrial remodeling. …”
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Clinical utility and predictive value of cerebrospinal fluid cell-free DNA profiling in non-small cell lung cancer patients with leptomeningeal metastasis by Sheng-Kai Liang, Wei-Yu Liao, Jin-Yuan Shih, Chia-Lin Hsu, Ching-Yao Yang, Shang-Gin Wu, Yen-Ting Lin, Yueh-Feng Wen, Lun-Che Chen, Yen-Fu Chen, Ya-Fang Chen, Yen-Heng Lin, Chong-Jen Yu

“…Cerebrospinal fluid (CSF) cell-free DNA (cfDNA) analysis using next-generation sequencing (NGS) offers insights into resistance mechanisms and potential treatment strategies. …”
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Low & Anaplastic Grade Glioma Umbrella Study of MOlecular Guided TherapieS (LUMOS-2): study protocol for a phase 2, prospective, multicentre, open-label, multiarm, biomarker-direct... by Marshall Pitz, Eng-Siew Koh, Elizabeth H Barnes, Lucille Sebastian, Mandy L Ballinger, David M Thomas, Christopher O'Callaghan, John Simes, Hui K Gan, Sonia Yip, Hao-Wen Sim, Desma Spyridopoulos, Richard De Abreu Lourenco, Cynthia Hawkins, Kristen McParland, Benjamin Kong, Subotheni Thavaneswaran, Patrick J Wheeler

“…Investigational treatment will be assigned based on molecular profiling of contemporaneous tissue obtained at disease relapse using next-generation sequencing. LUMOS-2 will begin with three therapeutic treatment arms: paxalisib, cadonilimab and selinexor. …”
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Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors by Kristopher Amirault, Michael Collins, Luca Beker, Brandon Mills, Martina Werner, Jonathan Andreas, Daniel Hartman, Jordan Dargert, Vanessa Process, Sean Cederlund, Thuy Dao, Linnea Menin, Molly Ferrara, Andrew Briggs, Joshua Shreve, Daniel Metzger, Angela Stout, Erin Deblasi, Jie An, Taylor Jensen, Shengle Zhang, Vinesh Rana, Bryn Burlingame, Ulrich Thomann, Durga Prasad Dash, Sha Liao, Jeffrey M. Conroy, Eugenio Daviso

“…By identifying actionable mutations through next-generation sequencing of solid tumors CGP enables targeted therapy decisions. …”
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Kuiyangling Enema Alleviates Ulcerative Colitis Mice by Reducing Levels of Intestinal NETs and Promoting HuR/VDR Signaling by Zhang D, Zhu Z, He Z, Duan S, Yi Q, Qiu M, Dai X, Su G, Li K, Xu L, Liu D, Wu Y, Gao Y, Li R, Guo S

“…An ELISA kit was utilized to determine cytokine levels, LC-MS was performed to analyze the composition of Kuiyangling, and next-generation sequencing was conducted for detection of the intestinal mucosal transcriptome.Results: Kuiyangling reduced DAI, splenic index, and ROS content; maintained mucosal structure; decreased inflammation; and increased colon length and body mass index. …”
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Vertical bacterial variability in oxidation ponds in the tropical zone by C. Tudsanaton, T. Pattamapitoon, O. Phewnil, W. Wararam, K. Chunkao, P. Maskulrath, M. Srichomphu

“…The purpose of this study is to examine the vertical variability of bacteria in natural treatment oxidation ponds in tropical zones.METHODS: Wastewater samples were collected from an oxidation pond at 3 different depths (0–0.6, 0.6–1.5 and more than 1.5 meter), and their chemical, physical and biological qualities were analysed. Next-generation sequencing techniques were used to identify bacterial diversity, and the water quality at each depth was applied as an indicator of bacterial degradation activities.FINDINGS: Community domestic wastewater contained 10 major bacterial phyla that differed at different depths. …”
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Impacts of genomic alterations on the efficacy of HER2-targeted antibody–drug conjugates in patients with metastatic breast cancer by Riqing Huang, Anqi Hu, Qixiang Rong, Ditian Shu, Meiting Chen, Wei Yang, Yue Zhang, Qiufan Zheng, Xin An, Cong Xue, Haifeng Li, Yanxia Shi

“…Methods This comprehensive real-world retrospective study collected clinical data from patients diagnosed with metastatic breast cancer and performed genomic profiling using targeted next-generation sequencing. The study analyzed the associations between genomic alterations and clinical outcomes of HER2 ADC treatment. …”
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The role of mNGS in the diagnosis of talaromycosis and case series by Jing Zhao, Hui-Ting Su, Dong Zhang, Xue-Tong Li, Min-Ya Lu, Juan Du, Jia-Yu Guo, Yi Gao, Xin-Fei Chen, Dong-Hua Wen, Shi-Yu Jia, Yao Wang, Qi-Wen Yang

“…This study aimed to analyze four classic cases of Talaromyces marneffei infection diagnosed using metagenomic next-generation sequencing (mNGS) to improve understanding of its diagnosis and treatment. …”
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Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing by Ting-Yu Yen, Ching Hsu, Ni-Chung Lee, Chao-Szu Wu, Hsin Wang, Kuan-Yi Lee, Chia-Ray Lin, Chun-Yi Lu, Mo-Li Tsai, Tzu-Yu Liu, Che Lin, Chien-Yu Chen, Luan-Yin Chang, Feipei Lai, Li-Min Huang

“…However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures. …”
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