Application of metagenomic next-generation sequencing in the diagnosis of post-stroke infections: a case series study using multiple sample types by Xiaopu Chen, Yong Liang, Wei Yang, Wenzhen He, Zhiqiang Xing, Shunxian Li, Shaoyu Cai, Jiping Fu, Xiaotang Peng, Manli Chen, Jiaming Wu

“…Additionally, while mNGS offers promising potential, it facts limitations related to sensitivity, specificity, cost, and standardization, which could influence its integration into routine clinical practice.MethodsWe retrospectively analyzed 18 stroke patients admitted to the First Affiliated Hospital of Medical College of Shantou University from January to February 2023, comparing culture-based methods with mNGS detection, and assessing its significance in etiological diagnosis. Additionally, we evaluated the performance differences among various sequencing platforms.ResultsAmong the 18 stroke patients enrolled, pulmonary infections were identified in 7 cases, urinary tract infections in 1 case, central nervous system infections in 10 cases, and combined pulmonary and central nervous system infections in 2 cases, with 2 cases yielding negative results. mNGS detected pathogens in 13 cases, aligning with clinical diagnoses (75% concordance), whereas culture-based methods yielded positive results in only 6 cases (22% concordance). …”
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Optimal surgery sequence in the treatment of degenerative hip-spine syndrome: a propensity score-based inverse probability of treatment weighting analysis by Yiming Fan, Yi Huang, Tianhao Wang, Qi Wang, Han yu, Chao Xue, Guoquan Zheng, Yan Wang

“…The impact of surgical sequence on clinical function scores, radiological parameters, and long-term complications was evaluated before and after conducting IPTW. …”
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The importance of targeted next-generation sequencing based genomic profiling in the diagnosis of childhood acute myeloid leukemia: a single center experience by Dilek Kaçar, Büşranur Çavdarlı, Ayça Koca Yozgat, Melek Işık, Fatma Burçin Kurtipek, Fatma Tuba Yıldırım, Turan Bayhan, Dilek Gürlek Gökçebay, Namık Yaşar Özbek, Neşe Yaralı

“…Targeted next-generation sequencing (NGS) is a reliable method used to identify recurrently mutated genes of pediatric AML and associated prognosis. …”
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Distinct microbial signatures and their predictive value in recurrent acute pancreatitis: insights from 5-region 16S rRNA gene sequencing by Qi-Wen Wang, Haorui Zheng, Yang Yang, Xinyao Chang, Zengkan Du, Zi-ning Hang, Zhao-Shen Li, Zhuan Liao

“…Microbial composition of blood samples is analyzed using 5-region (5R) 16S rRNA gene sequencing. Key microbial taxa and functional predictions are made. …”
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Solar and Wind 24 H Sequenced Prediction Using L-Transform Component and Deep LSTM Learning in Representation of Spatial Pattern Correlation by Ladislav Zjavka

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Targeted deep sequencing of plasma circulating cell-free DNA reveals Vimentin and Fibulin 1 as potential epigenetic biomarkers for hepatocellular carcinoma. by Reetta Holmila, Athena Sklias, David C Muller, Davide Degli Esposti, Paule Guilloreau, James Mckay, Suleeporn Sangrajrang, Petcharin Srivatanakul, Pierre Hainaut, Philippe Merle, Zdenko Herceg, Andre Nogueira da Costa

“…In this study, we applied targeted massively parallel semiconductor sequencing to assess methylation on a panel of genes (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM and YWHAZ) in plasma circulating cell-free DNA (cfDNA) and to evaluate the potential of these genes as HCC biomarkers in two different series, one from France (42 HCC cases and 42 controls) and one from Thailand (42 HCC cases, 26 chronic liver disease cases and 42 controls). …”
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Application of targeted high-throughput sequencing as a diagnostic tool for neonatal genetic metabolic diseases following tandem mass spectrometry screening by Guihua Lai, Qiying Gu, Zhiyong Lai, Haijun Chen, Xiangwen Tu, Junkun Chen, Jungao Huang

“…Therefore, this study aimed to evaluate the role of targeted next-generation sequencing (NGS) in the accurate diagnosis of positive samples identified through MS/MS screening.MethodsA cohort study of 260,915 newborns was conducted from January 2018 to June 2023 in Ganzhou City, southern China. …”
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Single-Cell Sequencing and Transcriptome Analysis Explored Changes in Midnolin-Related Immune Microenvironment and Constructed Combined Prognostic Model for Pancreatic Cancer by Guan X, Xu L, Liu J, Fei H, Wang C

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Identification and validation of m6A RNA methylation and ferroptosis-related biomarkers in sepsis: transcriptome combined with single-cell RNA sequencing by Jinshuai Lu, Jianhao Wang, Kun Han, Yuxia Tao, Jiyi Dong, Xiaoyu Pan, Xiaolan Wen

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Applying metagenomic next-generation sequencing to analyze infections in immunosuppressed patients with chronic kidney disease: A single-center retrospective study by Zhe Li, Shuhua Zhu, Jing Jiang, Yang Wang, Yuchao Zhou, Lixuan Lou, Shutian Xu, Shijun Li

“… Introduction: This retrospective study evaluated the diagnostic value and clinical application of metagenomic next-generation sequencing (mNGS) for detecting infections in immunosuppressed CKD patients. …”
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Genome-wide association studies and genetic architecture of carcass traits in Angus beef cattle using imputed whole-genome sequences data by Hasan Baneh, Nikolay Elatkin, Laurent Gentzbittel

“…Genome-wide association studies (GWAS) were performed using linear mixed models on 6,511,978 imputed whole genome sequence (WGS) variants in a population of 13,241 Angus beef cattle. …”
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Whole genome sequencing and functional annotation of Fusarium oxysporum f. sp. lentis to unravel virulence and secondary metabolite biosynthesis gene clusters by Sanjay Kharte, Ashish Kumar, Priyamvada Mishra, R. S. Ramakrishnan, Stuti Sharma, Nishi Mishra, Puneet Singh Chauhan, Radheshyam Sharma, Vedant Gautam, Shweta Tiwari, Vinod Goyal, Sonu Sharma, G. K. Koutu, N. K. Joshi

“…Despite its importance, the genetic underpinnings of this pathogen remain poorly understood.MethodsWe performed whole-genome sequencing of F. oxysporum f. sp. lentis using the Illumina Shotgun Sequencing platform. …”
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Assessment of MGMT promoter methylation status in glioblastoma using deep learning features from multi-sequence MRI of intratumoral and peritumoral regions by Xuan Yu, Jing Zhou, Yaping Wu, Yan Bai, Nan Meng, Qingxia Wu, Shuting Jin, Huanhuan Liu, Panlong Li, Meiyun Wang

“…Abstract Objective This study aims to evaluate the effectiveness of deep learning features derived from multi-sequence magnetic resonance imaging (MRI) in determining the O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status among glioblastoma patients. …”
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Single nucleus RNA sequencing profile analysis to reveal cell type specific common molecular drivers of Parkinson’s disease and therapeutic agents by Md. Al Amin Pappu, Md. Alamin, Most. Humaira Sultana, AKM Azad, Md. Rabiul Auwul, Sabkat Mahmud, Alvira Ajadee, Arnob Sarker, Salem A. Alyami, Md. Nurul Haque Mollah

“…In-silico ADME/T analyses were conducted using pkCSM and SwissADME to evaluate the pharmacokinetic properties of these compounds. …”
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Brain short T2 component imaging using double adiabatic inversion recovery prepared ultrashort Echo time (DIR-UTE) sequence by Jiyo S. Athertya, Mahyar Daskareh, Soo Hyun Shin, Jiaji Wang, James Lo, Yajun Ma

“…Technical feasibility was evaluated using phantoms, six healthy volunteers, and five patients with multiple sclerosis (MS) on a 3T MRI scanner. …”
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Comparison of clinical performance of MeltPro hearing loss assay and targeted next generation sequencing assay for genetic screening of hearing loss by Xudong Wang, Jiafei Chen, Meijiao Cai, Liping Zhang, Chaoyi Tian, Yunsheng Ge, Guowang Zhang, Yulin Zhou

“…Wide-spread genetic screening is important for early diagnosis and intervention. We aimed to evaluate and compare the clinical performance of the MeltPro HL assay and a targeted next-generation sequencing assay for genetic screening of HL and to explore the relationship between the c.109G > A genotype and the HL phenotype. …”
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The emerging role of next-generation sequencing in minimal residual disease assessment in acute lymphoblastic leukemia: a systematic review of current literature by Andreea-Iulia Ștefan, Andreea-Iulia Ștefan, Letiția-Elena Radu, Letiția-Elena Radu, Dumitru Jardan, Anca Coliță, Anca Coliță

“…The well studied and used MRD detection methods, multiparametric flow cytometry (MFC) and real-time quantitative polymerase chain reaction (qRT-PCR) for fusion genes and receptor gene rearrangements have significantly improved risk stratification, but have limitations in sensitivity and applicability. Next-generation sequencing (NGS) has emerged as a promising approach for MRD assessment, offering better sensitivity and the ability to track clonal evolution.ObjectivesThis systematic review evaluates the clinical utility and prognostic value of NGS for MRD detection in ALL, comparing its performance with conventional methods and exploring its potential role in therapeutic guidance.MethodsA comprehensive literature search was conducted across PubMed and Web of Science following PRISMA guidelines. …”
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Molecular Characterization of Vancomycin-Resistant <i>Enterococcus</i> spp. from Clinical Samples and Identification of a Novel Sequence Type in Mexico by Raúl Alejandro Atriano Briano, Nallely S. Badillo-Larios, Perla Niño-Moreno, Luis Fernando Pérez-González, Edgar A. Turrubiartes-Martínez

“…This study intends to evaluate the prevalence of glycopeptide-resistant genotypes and virulence factors in <i>Enterococcus</i> spp. strains. …”
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5-hydroxymethylcytosine sequencing of plasma cell-free DNA identifies epigenomic features in prostate cancer patients receiving androgen deprivation therapies by Qianxia Li, Chiang-Ching Huang, Shane Huang, Yijun Tian, Jinyong Huang, Amirreza Bitaraf, Xiaowei Dong, Marja T. Nevalainen, Manishkumar Patel, Jodie Wong, Jingsong Zhang, Brandon J. Manley, Jong Y. Park, Manish Kohli, Elizabeth M. Gore, Deepak Kilari, Liang Wang

“…Abstract Background We evaluated whether 5hmC signatures in cell-free DNA (cfDNA) are associated with treatment failure to androgen-deprivation therapies (ADT) among men with hormone-naive prostate cancer. …”
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Identification and validation of glycolysis-related diagnostic signatures in diabetic nephropathy: a study based on integrative machine learning and single-cell sequence by Xiaoyin Wu, Xiaoyin Wu, Buyu Guo, Buyu Guo, Xingyu Chang, Xingyu Chang, Yuxuan Yang, Yuxuan Yang, Qianqian Liu, Qianqian Liu, Jiahui Liu, Jiahui Liu, Yichen Yang, Yichen Yang, Kang Zhang, Yumei Ma, Songbo Fu, Songbo Fu, Songbo Fu

“…The diagnostic efficacy was evaluated by decision curve and calibration curve. …”
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