High and Low Taxa Specificity of Rhizosphere Bacteria Communities of Mangrove (Rhizophora mucronata) from Kuala Langsa and Telaga Tujuh Island, East Aceh by Siti Maysaroh, Meutia Samira Ismet, Rita Andini, Nurlita Anggraini, Beginer Subhan

“…This research examines sediment from rehabilitated and natural areas to understand how human and natural factors shape bacterial communities.The DNA sequence was analyzed using Next-Generation Sequencing (NGS), which targeted the 16S bacterial region in the V3-V4 rDNA. …”
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Genetic Testing Distinguishes Multiple Chondroid Chordomas with Neuraxial Bone Metastases from Multicentric Tumors by Hiroshi Kobayashi, Masahiro Shin, Naohiro Makise, Aya Shinozaki-Ushiku, Masachika Ikegami, Yuki Taniguchi, Yusuke Shinoda, Shinji Kohsaka, Tetsuo Ushiku, Katsutoshi Oda, Kiyoshi Miyagawa, Hiroyuki Aburatani, Hiroyuki Mano, Sakae Tanaka

“…Sequential surgeries and radiotherapy were performed for these lesions, and postoperative histological diagnosis revealed that all lesions were chondroid chordomas. Next-generation sequencing revealed that these lesions harbored a common somatic mutation in epidermal growth factor receptor (EGFR), c.3617A>C, which is not considered a pathogenic chordoma mutation, thus indicating that these lesions were not multicentric but rather multiple metastatic tumors. …”
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Case report: Chemotherapy plus sintilimab for the treatment of gastroesophageal junction hepatoid adenocarcinoma with liver metastasis: a case study with literature review by Genlin Lu, Jiarui Tu, Jinming Tu, Renya Jiang

“…ObjectiveTo elucidate the clinicopathological features and treatment of metastatic gastroesophageal junction hepatoid adenocarcinoma (GEJ HAC)using a case study and literature review.MethodsClinical presentation, results of histology and immunohistochemistry, and next-generation sequencing(NGS) in a patient with GEJ HAC metastasizing to the liver were reviewed. …”
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Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens by Nicola Z. Angel, Mitchell J. Sullivan, Areej Alsheikh-Hussain, Liang Fang, Samantha MacDonald, Alena Pribyl, Blake Wills, Gene W. Tyson, Philip Hugenholtz, Donovan H. Parks, Paul Griffin, David L. A. Wood

“…Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. …”
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Metagenomic analysis post thermal stress in buffalo sludge and tomato pomace anaerobic digestion: a case study by Maria Chiara La Mantia

“…The bacterial and archaeal communities were an-alyzed using next-generation sequencing of 16S rRNA gene amplicons. After seven days of fermentation, due to the high volatile solid content in TP (77 g/L), the pH dropped to a value of 5, and the methane production reached a plateau (860 Nml of cumulative CH4 production). …”
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Genomic characterization and molecular predictive biomarkers for chemotherapy in patients with metastatic triple-negative breast cancer treated in a real-world setting by Erik Olsson, Henrik Lindman, Evangelos Digkas, Viktoria Thurfjell, Haidar Mir Ali, Ute Krüger, Anna-Karin Wennstig, Marie Sundqvist, Antonios Valachis

“…Patients and methods: Next-generation sequencing with FoundationOne® CDx was conducted primarily on primary tumor tissue from 112 consecutive patients with mTNBC. …”
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Streptococcus suis-associated neonatal meningitis and sepsis: characterization, antimicrobial resistance, and public health implications by Giovanna Fusco, Rubina Paradiso, Lorena Cardillo, Maria Antonia Salvia, Saveria Dodaro, Veronica Del Monaco, Gianfranco Scarpelli, Francesca Greco, Antonio Rinaldi, Lorella Barca, Stefania Ambrogio, Antonio Limone, Esterina De Carlo, Giorgia Borriello

“…Streptococcus (S.) suis was isolated from cerebrospinal fluid and blood. Next-generation sequencing revealed that the strain was serotype 2 sequence type 1, and contained the ermB and tet(W) genes, which are responsible for resistance to macrolides and tetracycline, along with several pilus-associated genes and 20 virulence factors. …”
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Sequencing Analysis of Invasive Carbapenem-Resistant <i>Klebsiella pneumoniae</i> Isolates Secondary to Gastrointestinal Colonization by Gaetano Maugeri, Maddalena Calvo, Dafne Bongiorno, Dalida Bivona, Giuseppe Migliorisi, Grete Francesca Privitera, Guido Scalia, Stefania Stefani

“…All the patients who had dissemination episodes were furtherly investigated through next-generation sequencing, analyzing both colonizing and disseminating strains. …”
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Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data by Caitlin Guccione, Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio Gonzalez, Gregory D. Sepich-Poore, Kyuto Sonehara, Mohsen Zakeri, Yang Chen, Amanda Hazel Dilmore, Neil Damle, Sergio E. Baranzini, George Hightower, Teruaki Nakatsuji, Richard L. Gallo, Ben Langmead, Yukinori Okada, Kit Curtius, Rob Knight

“…Abstract As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. …”
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Efficient Dual Cas9 Nickase Correction of a Prevalent Pathogenic LAMB3 Variant for Junctional Epidermolysis Bullosa by Alex du Rand, John Hunt, Daniel Verdon, Ben Buttle, P. Rod Dunbar, Diana Purvis, Vaughan Feisst, Hilary Sheppard

“…Targeting a hotspot pathogenic variant (c.1903C>T, p.R635∗), we report perfect correction efficiencies of up to 54% based on standard next-generation sequencing. Using a high-fidelity Cas9 nuclease, we also report perfect repair of up to 74% when using a small-molecule modulator of DNA repair. …”
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Magnetic resonance imaging does not distinguish Kallmann syndrome from normosmic isolated hypogonadotropic hypogonadism by Małgorzata Kałużna, Katarzyna Katulska, Katarzyna Ziemnicka, Pola Kompf, Bartłomiej Budny, Paweł Komarnicki, Michał Rabijewski, Jerzy Moczko, Jarosław Kałużny, Marek Ruchała

“…Genetic diagnosis was conducted in all IHH patients based on next-generation sequencing. Results: Almost 70% prevalence of pituitary hypoplasia was observed in IHH subjects. …”
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Diagnosis and treatment of thyroblastoma: a case report and review of literature by Xiting Chen, Xiting Chen, Lijuan Xiong, Lijuan Xiong, Hongling Liu, Haoqiang Wang, Donghai Cheng, Wei Wang, Wenyuan He, Bo Xie, Juan Zhou

“…This classification was based on the observation that the tumor presents with independent primitive multilineage elements and is frequently associated with DICER1 hotspot mutations.The objective of this study was to explore and investigate the clinicopathologic characteristics, molecular features and treatment strategies of patients with thyroblastoma, followed by a review of the previous relevant literature.MethodsThe clinical manifestations, pathological characteristics, molecular features and treatment strategies of the initial case of thyroblastoma pathologically confirmed in China were analyzed.ResultsThe tumor was revealed to have high invasive potential, rapid disease progression, and primitive multilineage elements of pathology, including immature thyroid epithelium, spindled mesenchymal proliferations, and neuroepithelial blastema. Next-generation sequencing (NGS) confirmed the presence of germline DICER1 heterozygous pathogenic mutation at p.G1784* in patient, accompanied by the somatic hotspot mutation at p.E1813D of the RNase IIIb domain. …”
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Splenic B-Cell Lymphomas with Diffuse Cyclin D1 Protein Expression and Increased Prolymphocytic Cells: A Previously Unrecognized Diagnostic Pitfall by Khaled Algashaamy, Yaohong Tan, Nicolas Mackrides, Alvaro Alencar, Jing-Hong Peng, Joseph Rosenblatt, Juan P Alderuccio, Izidore S. Lossos, Francisco Vega, Jennifer Chapman

“…Both lymphomas were very unusual because the tumor cells diffusely and strongly expressed cyclin D1 despite lacking the t(11; 14)(q13; q32) as detected by several approaches including next-generation sequencing, fluorescence in situ hybridization using CCND1 break apart probe and fusion probes for t(11; 14)(q13; q32), and conventional karyotyping. …”
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Diagnostic performance of the DISQVER metagenomic sequencing tool for the identification of pathogens in febrile neutropenic patients: the ADNEMIA trial by Geneviève Héry-Arnaud, Christophe Burucoa, Marie Kempf, David Boutoille, Yohann Foucher, Philippe Lanotte, Maxime Pichon, Stéphane Corvec, Cécile Le Brun, Helene Pailhories

“…This study will aim to assess the clinical utility of metagenomic next-generation sequencing (mNGS)-DISQVER technology in detecting pathogenic microorganisms from blood samples of patients undergoing high-risk FN treatment.Methods and analysis This nationwide, prospective, multicentre, interventional, proof-of-concept clinical trial will enrol 200 patients. …”
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The search for microRNAs potentially involved in the selfrenewal maintaining of laboratory rat pluripotent stem cells by V. V. Sherstyuk, S. P. Medvedev, M. T. Ri, Y. V. Vyatkin, O. V. Saik, D. N. Shtokalo, S. M. Zakian

“…We analyzed the expression of miRNAs in rat embryonic stem cells, induced pluripotent stem cells and embryonic fibroblasts using bioinformatic methods and data obtained with next generation sequencing. The analysis of differential expression between groups of rat pluripotent cells and fibroblasts, and the analysis of experimentally confirmed target genes of differentially expressed known rat miRNAs revealed novel potential players of pluripotency maintaining and reprogramming processes. …”
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Microbiome of <i>Hyalomma dromedarii</i> (Ixodida: Ixodidae) Ticks: Variation in Community Structure with Regard to Sex and Host Habitat by Nighat Perveen, Alejandro Cabezas-Cruz, Daniil Iliashevich, Lianet Abuin-Denis, Olivier Andre Sparagano, Arve Lee Willingham

“…A total of 40 ticks (male (15), female (15), and nymph (10)) were selected from tick samples collected from camels and processed for genomic DNA and next-generation sequencing using the Illumina MiSeq platform. …”
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The Search of miRNA Related to Invasive Growth of Nonfunctioning Gonadotropic Pituitary Tumors by Joanna Boresowicz, Paulina Kober, Natalia Rusetska, Maria Maksymowicz, Agnieszka Paziewska, Michalina Dąbrowska, Natalia Zeber-Lubecka, Jacek Kunicki, Wiesław Bonicki, Jerzy Ostrowski, Janusz A. Siedlecki, Mateusz Bujko

“…Methods. miRNA profiles were determined in 20 patients (11 invasive and 9 noninvasive tumors) using next-generation sequencing. The expression of selected miRNAs was assessed in the independent cohort of 80 patients with qRT-PCR. …”
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Detection of I491F and V170F rpoB mutations associated with misdiagnosis of rifampicin resistance among patients with drug-susceptible tuberculosis treatment failure, Myanmar, 2022 by Phyu Win Ei, Mi Mi Htwe, Myat Htut Nyunt, Aye Su Mon, Zaw Myint, Wint Wint Nyunt, Su Mon Win, Sandar Aung, Wai Myat Thwe, Wah Wah Aung

“…Whole genome or Deeplex-targeted next-generation sequencing was performed using Illumina Miseq. …”
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From Natural Hosts to Agricultural Threats: The Evolutionary Journey of Phytopathogenic Fungi by Asanka Madhushan, Dulan Bhanuka Weerasingha, Evgeny Ilyukhin, Paul W. J. Taylor, Amila Sandaruwan Ratnayake, Jian-Kui Liu, Sajeewa S. N. Maharachchikumbura

“…The study of pathogen evolution has been transformed by advancements in molecular biology, genomics, and bioinformatics, utilizing methods like next-generation sequencing, comparative genomics, transcriptomics and population genomics. …”
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A case of de novo neuroendocrine prostate cancer presented with elevated level of serum CEA carrying BRCA2 mutation: case report and literature review by Weizhe Han, Nihati Rexiati, Fang Yu, Yongzhi Wang, Yueli Tian, Jianyuan Wu, Gang Wang, Tao Liu, Zhonghua Yang

“…Immunohistochemistry (IHC) staining and next generation sequencing demonstrated a strong expression of chromogranin A (CgA), synaptophysin (SYN) and CEA, and a germline mutation in BRCA2, respectively. …”
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