Results of <em>UGT1A1</em> gene sequencing in individuals with the Gilbert syndrome phenotype by A. A. Ivanova, N. E. Apartseva, A. P. Kashirina, E. G. Nemcova, Ju. V. Ivanova, M. V. Kruchinina, S. A. Kurilovich, V. N. Maksimov

“…Aim. To evaluate the effectiveness of automated Sanger sequencing of the UGT1A1 gene to search for pathogenic mutations in individuals with the Gilbert syndrome phenotype. …”
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Detection and functional assessment of structural variants using whole-genome re-sequencing data in Nellore cattle by Natalia A. Marín-Garzón, Lucio F. M. Mota, Giovana Vargas, Leonardo M. Arikawa, Larissa F. S. Fonseca, Gerardo A. Fernandes Júnior, Roberto Carvalheiro, Lucia G. Albuquerque

“…Abstract Ongoing advances in genome sequencing technologies have enabled the identification of numerous structural variants (SVs) in livestock genomes, which are the main determinants of complex traits due to their impact on gene expression. …”
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Optimizing Cost-Effective gene expression phenotyping approaches in cattle using 3′ mRNA sequencing by Ruwaa I. Mohamed, Taylor B. Ault-Seay, Sonia J. Moisá, Jonathan E. Beever, Agustín G. Ríus, Troy N. Rowan

“…While the cost of whole transcriptome sequencing has declined recently, its required sequencing depth still makes it an expensive choice for wide-scale molecular phenotyping. …”
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Optimizing radiomics for prostate cancer diagnosis: feature selection strategies, machine learning classifiers, and MRI sequences by Eugenia Mylona, Dimitrios I. Zaridis, Charalampos Ν. Kalantzopoulos, Nikolaos S. Tachos, Daniele Regge, Nikolaos Papanikolaou, Manolis Tsiknakis, Kostas Marias, ProCAncer-I Consortium, Dimitrios I. Fotiadis

“…Their performance was evaluated in a nested cross-validation and externally, using seven performance metrics. …”
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Long-read sequencing transforms the diagnosis of congenital adrenal hyperplasia: resolving pseudogene interference and structural variations by Junfeng Zeng, Junfeng Zeng, Xiaoling Huang, Xiaoling Huang, Yanwei Li, Tizhen Yan, Jiwu Lou, Guizhen Lyu, Yanjin Li, Yanjin Li

“…Conventional genetic methods struggle to resolve complex structural variations and pseudogene interference in key genes like CYP21A2. Our study will evaluate the efficacy of Long-Read Sequencing (LRS) as a comprehensive diagnostic tool for CAH, demonstrating its ability to simultaneously detect large structural variations, single nucleotide variants (SNVs), and small insertions or deletions.MethodsFour probands with clinically diagnosed CAH underwent detailed biochemical profiling, including serum 17-hydroxyprogesterone, serum sodium and serum potassium. …”
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Exome sequencing reveals low-frequency and rare variant contributions to multiple sclerosis susceptibility in Turkish families by Furkan Büyükgöl, Berk Gürdamar, Mehmet Ufuk Aluçlu, Yeşim Beckmann, Kaya Bilguvar, Cavit Boz, Alper Bülbül, Sena Destan Bünül, Özge Çetin, Caner Feyzi Demir, Serkan Demir, Taşkın Duman, Hüsnü Efendi, Özgül Ekmekçi, Utku Ertetik, Özlem Ethemoğlu, Elif Everest, Haluk Gümüş, Tuncay Gündüz, Rana Karabudak, Bedriye Karaman, Murat Kürtüncü, Muzaffer Mutluer, Meziyet Dilara Reda, Sabahattin Saip, Meral Seferoğlu, Elif Sever, Osman Ugur Sezerman, Sedat Şen, Beril Taşdelen, Mehmet Tecellioğlu, Murat Terzi, Aslı Tuncer, Ömer Faruk Turan, Melih Tütüncü, Gülgün Uncu, Uğur Uygunoğlu, Cihat Uzunköprü, Umut Voyvoda, Mehmet Fatih Yetkin, Nur Yüceyar, Aksel Siva, Eda Tahir Turanlı

“…Whole exome sequencing was conducted on all samples including affected and unaffected members, followed by investigation of the effect of well-established human leukocyte antigen loci for MS on the elevated MS risk observed in our families. …”
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Single-cell RNA sequencing reveals palmitoylation-driven cellular heterogeneity and prognostic biomarkers in lung adenocarcinoma by Taibo Huang, Lijie Kou, Qianqian Zhang, Xueya Liu, Xingang Hu

“…Methods: We examined single-cell RNA sequencing datasets from LUAD samples to identify distinct malignant cell groups. …”
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Time-Domain Versus Frequency-Embedded EEG Sequences for Sensorimotor BCI Using 1D-CNN by Simanto Saha, Mathias Baumert, Alistair Mcewan

“…Thus, the number of input channels for 1D-CNN was N, N or <inline-formula> <tex-math notation="LaTeX">$N\times N$ </tex-math></inline-formula> for EEG signals, PSD or CPSD sequences. We used dataset IVa from BCI Competition III in 5&#x2212;fold cross-validation settings to evaluate intra-subject, inter-subject (pairwise) and inter-subject (pooled) BCI classification accuracies. …”
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Clinical Characteristics and Predicting Disease Severity in Chlamydia psittaci Infection Based on Metagenomic Next-Generation Sequencing by Huang M, Wang Y, Lu Y, Qu W, Zou Q, Zhang D, Shen Y, Han D, Yu F, Zheng S

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ANALYSIS OF GENETIC SEQUENCING DATA IN PATIENTS WITH AML AND MDS: WHAT IS ITS IMPACT ON BONE MARROW TRANSPLANTATION by CASA Dalva, JVA Duarte, FBD Filho

“…Introduction: Next-generation sequencing (NGS) has rapidly evolved in recent years as an efficientalternative for the genetic analysis of patients with Acute Myeloid Leukemia (AML) andMyelodysplastic Syndrome (MDS). …”
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The 3′ region of the ZPA regulatory sequence (ZRS) is required for activity and contains a critical E-box by Kathryn F. Ball, Kathryn F. Ball, Stephen Manu, Abbie K. Underhill, Jeanyoung Kim, Jessica C. Britton, Sarah R. Rudd, Madison M. Malone, Japhet Amoah, Allen Cooper, Charmaine Pira, Kerby C. Oberg

“…BackgroundDuring development, Hand2 and Hoxd13 transcription factors (TFs) regulate Sonic hedgehog (Shh) expression in the zone of polarizing activity (ZPA) in the distal posterior limb mesoderm. The ZPA regulatory sequence (ZRS) is a conserved, limb-specific enhancer that controls Shh expression. …”
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Can whole genome sequencing resolve taxonomic ambiguities in fungi? The case study of Colletotrichum associated with ferns by Andrea Menicucci, Salvatore Iacono, Madalena Ramos, Madalena Ramos, Chiara Fiorenzani, Natalia Aparecida Peres, Lavern Wayne Timmer, Antonio Prodi, Riccardo Baroncelli, Riccardo Baroncelli

“…Whole-genome sequencing (WGS) offers a promising alternative by providing genome-wide resolution for phylogenetic analysis. …”
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Bronchoalveolar lavage fluid and lung biopsy tissue metagenomic next-generation sequencing in the diagnosis of pulmonary cryptococcosis by Jinbao Huang, Heng Weng, Ling Ye, Meiqin Jiang, Lulu Chen, Yangyu Li, Hongyan Li

“…ObjectiveTo evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens.MethodsIn this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. …”
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Whole-genome sequencing reveals transmission pattern and drug resistance of Mycobacterium tuberculosis intra- or inter-hosts by Feng Ding, Wanfei Liu, Chi Wu, Chi Wu, Wensi Zhang, Shuyan Chen, Shuyan Chen, Wenjie Lai, Wenjie Lai, Jiayao Qu, Jiayao Qu, Qiang Lin, Shuihua Lu, Jiuxin Qu, Jiuxin Qu

“…Sample diversity was evaluated by SNPs and transmission clusters were identified based on SNP differences of 12 or fewer in genetic clusters.ResultsExcept four samples identified as non-tuberculous mycobacteria, 282 MTB samples (181 patients) underwent mDST, with 244 samples (162 patients) undergoing pDST. …”
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Transcriptome sequencing and Mendelian randomization analysis identified biomarkers related to neutrophil extracellular traps in diabetic retinopathy by Linlin Hao, Songhong Wang, Lian Zhang, Lian Zhang, Jie Huang, Yue Zhang, Xuejiao Qin

“…To explore the mechanism of NETs-related genes in DR, the transcriptome of NETs from normal and DR individuals were analyzed with gene sequencing and mendelian randomization (MR) analysis. …”
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Impact of cytomegalovirus DNAemia detected by next-generation sequencing on short-term prognosis after lung transplantation by Zhongping Xu, Yujiao Zhang, Dapeng Wang, Chenhao Xuan, Zhiyu Li, Hongyang Xu

“…Background: Cytomegalovirus (CMV) is a common opportunistic pathogen following lung transplantation, associated with post-transplant complications and adverse outcomes. This study aims to evaluate the incidence of CMV DNAemia identified through metagenomic next-generation sequencing (mNGS) during the early postoperative phase of lung transplantation and assess its effects on the short-term outcomes for recipients. …”
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Household clusters of SARS-CoV-2 Omicron subvariants contemporaneously sequenced from dogs and their owners by Francisco C. Ferreira, Lisa D. Auckland, Rachel E. Busselman, Edward Davila, Wendy Tang, Ailam Lim, Nathan Sarbo, Hayley D. Yaglom, Heather Centner, Heather L. Mead, Ying Tao, Juan Castro, Yan Li, Jing Zhang, Haibin Wang, Lakshmi Malapati, Peter Cook, Adam Retchless, Suxiang Tong, Italo B. Zecca, Ria R. Ghai, Casey Barton Behravesh, Rebecca S. B. Fischer, Gabriel L. Hamer, Sarah A. Hamer

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Inflammatory profiling and immune cell infiltration in dysthyroid optic neuropathy: insights from bulk RNA sequencing by Qintao Ma, Yuanping Hai, Yongbo Duan, Genfeng Yu, Cheng Song, ShengAi Huang, Anqi Huang, Yan Zhu, Yongzhi Shen, Zimeng Huang, Xiao Wang, Lan Liu, Thomas Efferth, Huiyu Guo, Yi Wang, Yi Wang, Jie Shen

“…ROC analysis and single-gene GSEA were used to evaluate the diagnostic potential and functional relevance of core genes. …”
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Decoding the m6A epitranscriptomic landscape for biotechnological applications using a direct RNA sequencing approach by Chuwei Liu, Heng Liang, Arabella H. Wan, Min Xiao, Lei Sun, Yiling Yu, Shijia Yan, Yuan Deng, Ruonian Liu, Juan Fang, Zhi Wang, Weiling He, Guohui Wan

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Refinement of the Reference Viral Database (RVDB) for improving bioinformatics analysis of virus detection by high-throughput sequencing (HTS) by Pei-Ju Chin, Jaysheel D. Bhavsar, Trent J. Bosma, Madolyn L. MacDonald, Shawn W. Polson, Arifa S. Khan

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