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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Complex immunohistochemical and molecular study on 5 cases of ovarian juvenile granulosa cell tumors reveals a consistent alteration in the PI3K/AKT/mTOR signaling pathway by Adam Šafanda, Nikola Hájková, Michaela Kendall Bártů, Marián Švajdler, Radoslav Matěj, Jitka Hausnerová, Tomáš Zima, Pavel Dundr, Kristýna Němejcová

“…Moreover, DNA next-generation sequencing (NGS) and PTEN methylation analysis was performed. …”
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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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Characterization and genome analysis of lytic Vibrio phage VPK8 with potential in lysing Vibrio parahaemolyticus isolates from clinical and seafood sources by Valalak Jintasakul, Jiranan Pattano, Sutima Preeprem, Pimonsri Mittraparp-arthorn

“…Phage morphology was characterized by transmission electron microscopy (TEM), while genomic features were analyzed using next-generation sequencing. Lytic characteristics, including latent period and burst size, were determined through one-step growth curves, and bacterial growth reduction was evaluated over a 24-h. …”
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Nanopore-based random genomic sampling for intraoperative molecular diagnosis by Francesco E. Emiliani, Abdol Aziz Ould Ismail, Edward G. Hughes, Gregory J. Tsongalis, George J. Zanazzi, Chun-Chieh Lin

“…Results In our retrospective cohort of 26 malignant brain tumors, iSCORED demonstrated 100% concordance in CNV detection, including chromosomal alterations and oncogene amplifications, when compared to clinically validated assays such as Next-Generation Sequencing and Chromosomal Microarray. Furthermore, we validated iSCORED’s real-time applicability in 15 diagnostically challenging primary brain tumors, achieving 100% concordance in detecting aberrant CNV detection, including diagnostic chromosomal gains/losses and oncogene amplifications (10/10). …”
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Mutations in the ARAP3 Gene in Three Families with Primary Lymphedema Negative for Mutations in Known Lymphedema-Associated Genes by Maurizio Ricci, Rita Compagna, Bruno Amato, Sercan Kenanoglu, Dominika Veselenyiova, Danjela Kurti, Mirko Baglivo, Syed Hussain Basha, Roberta Serrani, Giacinto Abele Donato Miggiano, Barbara Aquilanti, Giuseppina Matera, Giuseppe Marceddu, Valeria Velluti, Lucilla Gagliardi, Munis Dundar, Juraj Krajcovic, Matteo Bertelli

“…We applied next-generation sequencing to DNA samples of a cohort of 246 Italian patients with lymphatic malformations. …”
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Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity by Eamonn MM Quigley, Thomas J Borody, Sabine Hazan, Neil Stollman, Huseyin S Bozkurt, Sonya Dave, Andreas J Papoutsis, Jordan Daniels, Brad D Barrows

“…Objective The study objective was to compare gut microbiome diversity and composition in SARS-CoV-2 PCR-positive patients whose symptoms ranged from asymptomatic to severe versus PCR-negative exposed controls.Design Using a cross-sectional design, we performed shotgun next-generation sequencing on stool samples to evaluate gut microbiome composition and diversity in both patients with SARS-CoV-2 PCR-confirmed infections, which had presented to Ventura Clinical Trials for care from March 2020 through October 2021 and SARS-CoV-2 PCR-negative exposed controls. …”
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Proximal bronchiolar adenoma with malignant transformation to invasive mucinous adenocarcinoma with 4 years follow-up: a case report and literature review by Yuan-Hui Yang, Ke Yin, Jia-Qi Xu, Xiao-Ying Xu, Jun-Lei Zhang, Ji-Xuan Liu, Xin-Zhi Feng, Xiao-Yan Lin, Xiao-Yan Lin

“…Hybridization Capture-based next-generation sequencing (NGS) analysis detected driver gene mutations in Kirsten Rat Sarcoma viral oncogene homolog (KRAS) and Cyclin-Dependent Kinases (CDK) 6 in the case, thereby inferring the malignant transformation of BA into IMA.ConclusionIn this case, the detection of driver gene KRAS mutation and loss of continuity in the basal cell layer within the mucous glandular structures of the nodule suggests the malignant transformation of BA into IMA, inferring the malignant potential of BA.…”
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Enhanced membrane protein production in HEK293T cells via ATF4 gene knockout: A CRISPR-Cas9 mediated approach by Byung-Jo Choi, Ba Reum Kim, Ho Joong Choi, Ok-Hee Kim, Say-June Kim

“…Genome sequencing and membrane protein productivity of ATF4-KO cells were compared to wild-type cells using next-generation sequencing (NGS) and a membrane protein isolation kit, respectively. …”
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Targeted detection of sequence variants in cell-free DNA from cerebrospinal fluid in pediatric central nervous system tumors by Katrina O’Halloran, Katrina O’Halloran, Erin E. Crotty, Eirini Christodoulou, Sarah E. Leary, Alexandra Miller, Alexandra Miller, Vera A. Paulson, Christina M. Lockwood, Ashley S. Margol, Ashley S. Margol, Jaclyn A. Biegel, Jaclyn A. Biegel

“…These include polymerase chain reaction (PCR), both droplet digital PCR and reverse transcription-based PCR, Sanger sequencing, and next-generation sequencing approaches that incorporate amplicon- and hybrid capture-based methods. …”
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Unusual hypertrophic cardiomyopathy: case report of an early onset wild-type ATTR amyloidosis accompanied by a chromosomal duplication involving the MYH6 and MYH7 gene by Jassin Hamidi, Yvonne Hanel, Sven Dittmann, Wanda Maria Gerding, Huu Phuc Nguyen, Karin Klingel, Eric Schulze-Bahr

“…Therefore, next-generation sequencing (NGS) analysis revealed a rare chromosomal duplication in both cardiac myosin genes, MYH6 and MYH7. …”
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RAS/BRAF Circulating Tumor DNA Mutations as a Predictor of Response to First-Line Chemotherapy in Metastatic Colorectal Cancer Patients by Jiannan Yao, Wanchun Zang, Yang Ge, Nathaniel Weygant, Pan Yu, Lei Li, Guanhua Rao, Zhi Jiang, Rui Yan, Linjia He, Yang Yu, Mulan Jin, Gang Cheng, Guangyu An

“…Since circulating tumor DNA (ctDNA) offers clear advantages as a minimally invasive method for tumor monitoring compared with tumor tissue, we aimed to evaluate genotyping ctDNA using a next-generation sequencing- (NGS-) based panel to identify the prognostic value of mutation status in metastatic colorectal cancer (mCRC) patients with primary tumor resected and with subsequent lines of treatment in this study. …”
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Human blood cell transcriptomics unveils dynamic systemic immune modulation along colorectal cancer progression by Pedro J Romero, Mauro Delorenzi, Amaia Martínez-Usatorre, Laura Ciarloni, Noushin Hadadi, Eric Durandau, Sylvain Monnier-Benoit, Paolo Angelino, Victoria Wosika, Alessandra Jordano Conforte, Sara S Fonseca Costa, Hector Fabio Satizabal, Jérémie Despraz, Andres Perez-Uribe, Stephan Morgenthaler, Brian Hashemi, Sahar Hosseinian-Ehrensberger

“…Here we propose the host immune response to the onset of cancer as an alternative approach for early detection of CRC.Methods We perform whole transcriptome analysis of peripheral blood mononuclear cells (PBMCs) isolated from individuals with CRC, precancerous lesions or negative colonoscopy in two independent cohorts using next-generation sequencing.Results We discover and validate novel early CRC RNA biomarkers. …”
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Biochemical Pattern of Methylmalonyl-CoA Epimerase Deficiency Identified in Newborn Screening: A Case Report by Evelina Maines, Roberto Franceschi, Francesca Rivieri, Giovanni Piccoli, Björn Schulte, Jessica Hoffmann, Andrea Bordugo, Giulia Rodella, Francesca Teofoli, Monica Vincenzi, Massimo Soffiati, Marta Camilot

“…The analysis of methylmalonic pathway genes by next-generation sequencing (NGS) allowed the identification of the known homozygous nonsense variation c.139C>T (p.R47X) in exon 2 of the MCE gene. …”
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Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling by David Kim, Chad M. Vanderbilt, Soo-Ryum Yang, Subhiksha Nandakumar, Khedoudja Nafa, Rusmir Feratovic, Natasha Rekhtman, Ivelise Rijo, Jacklyn Casanova, Anita Yun, A. Rose Brannon, Michael F. Berger, Marc Ladanyi, Oscar Lin, Maria E. Arcila

“…Abstract Comprehensive molecular profiling by next-generation sequencing has revolutionized tumor classification and biomarker evaluation. …”
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Crispant analysis in zebrafish as a tool for rapid functional screening of disease-causing genes for bone fragility by Sophie Debaenst, Tamara Jarayseh, Hanna De Saffel, Jan Willem Bek, Matthieu Boone, Ivan Josipovic, Pierre Kibleur, Ronald Y Kwon, Paul J Coucke, Andy Willaert

“…Six genes linked to severe recessive osteogenesis imperfecta (OI) and four associated with bone mineral density (BMD) from genome-wide association studies were analyzed using CRISPR/Cas9-based crispant screening in F0 mosaic founder zebrafish. Next-generation sequencing confirmed high indel efficiency (mean 88%), mimicking stable knock-out models. …”
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Prediction of Blood Lipid Phenotypes Using Obesity-Related Genetic Polymorphisms and Lifestyle Data in Subjects with Excessive Body Weight by Omar Ramos-Lopez, Jose I. Riezu-Boj, Fermin I. Milagro, Marta Cuervo, Leticia Goni, J. A. Martinez

“…A total of 95 single nucleotide polymorphisms (SNPs) related to obesity and weight loss were analyzed by a targeted next-generation sequencing system. Relevant genotypes of each SNP were coded as 0 (nonrisk) and 1 (risk). …”
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Protocol for faecal microbiota transplantation in irritable bowel syndrome: the MISCEAT study – a randomised, double-blind cross-over study using mixed microbiota from healthy dono... by Lenka Kramna, Ondrej Cinek, Jakub Hurych, Jiri Vejmelka, Lucie Hlinakova, Vladyslav Larionov, Michal Kulich, Pavel Kohout

“…Faecal bacteriome will be profiled before and regularly after interventions using 16S rDNA next-generation sequencing. Food records, dietary questionnaires, anthropometry, bioimpedance, biochemistry and haematology workup will be obtained at study visits during the follow-up period. …”
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Malignant phyllodes tumors with sarcomatous components: A histopathologic and molecular study by Ting Lei, Yunjie Song, Zhiyi Shen, Yongqiang Shi, Cunyan Xia, Xu Deng, Wenyue Da, Yan Peng, Qing Li

“…Methods: A total of ten cases were collected with eight cases undergoing DNA next-generation sequencing (NGS). The clinicopathological characteristics, prognostic information, and genomic profiles were compared to those of MPTs without sarcomatous components. …”
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Genetic Profile and Associated Characteristics of 150 Korean Patients with Retinitis Pigmentosa by You Na Kim, Yoon Jeon Kim, Chang Ahn Seol, Eul-Ju Seo, Joo Yong Lee, Young Hee Yoon

“…All the genetic variants in patients with RP, identified using targeted next-generation sequencing (NGS) with a panel of 88 RP-related genes between November 2018 and November 2019, were retrospectively reviewed. …”
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