Scapular Angiomatoid Fibrous Histiocytoma with EWSR1-CREB1 Fusion in an Adult Patient by Hiroshi Kobayashi, Naohiro Makise, Aya Shinozaki-Ushiku, Yuki Ishibashi, Masachika Ikegami, Shinji Kohsaka, Tetsuo Ushiku, Katsutoshi Oda, Kiyoshi Miyagawa, Hiroyuki Aburatani, Hiroyuki Mano, Sakae Tanaka

“…The final postresection histopathological diagnosis was the same as the preoperative diagnosis, and no obvious chemotherapeutic effect was observed. Next-generation sequencing of RNA isolated from paraffin-embedded tumor tissue revealed that these lesions harbored the EWSR1-CREB1 fusion gene, and the tumor was diagnosed as AFH. …”
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Identification and Characterization of a Cryptic Genomic Deletion-Insertion in EYA1 Associated with Branchio-Otic Syndrome by Hao Zheng, Jun Xu, Yu Wang, Yun Lin, Qingqiang Hu, Xing Li, Jiusheng Chu, Changling Sun, Yongchuan Chai, Xiuhong Pang

“…In a sporadic deaf patient diagnosed as BOS, we identified an apparent heterozygous genomic deletion spanning the first four coding exons and one 5′ noncoding exon of EYA1 by targeted next-generation sequencing of 406 known deafness genes. Real-time PCR at multiple regions of EYA1 confirmed the existence of this genomic deletion and extended its 5′ boundary beyond the 5′-UTR. …”
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Clinical features and prognostic predictors of C. Psittaci Pneumonia: a systematic review and individual patient meta-analysis by Qingqing Jia, Jibo Sun, Dongguang Wang, Jiao Xu, Xiu Li, Shijie Zhang, Lian Wang, Sitong Liu, Xiang Tong, Hong Fan

“…The presence of dyspnea, neuropsychiatric symptoms, gastrointestinal symptoms, and multilobar infiltrates upon admission merits clinicians’ attention, advocating for timely sample submission for metagenomic next-generation sequencing (mNGS) to ascertain the etiology.…”
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Comparing acute versus AIDS ART initiation on HIV-1 integration sites and clonal expansion by Jun Wang, Nan Xiao, Zhengnong Zhu, Haiyan Qiao, Fang Zhao, Lukun Zhang, Jizhou Gou, Mengji Lu, Yun He, Hongzhou Lu, Qian Li

“…In this study, we used Linear Target Amplification-PCR (LTA-PCR) and Next Generation Sequencing to compare unique integration site (UIS) clonal counts between individuals who initiated ART during acute HIV infection stage (Acute-ART group) and those in the AIDS stage (AIDS-ART group). …”
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Exome Sequencing Identified a Recessive RDH12 Mutation in a Family with Severe Early-Onset Retinitis Pigmentosa by Bo Gong, Bo Wei, Lulin Huang, Jilong Hao, Xiulan Li, Yin Yang, Yu Zhou, Fang Hao, Zhihua Cui, Dingding Zhang, Le Wang, Houbin Zhang

“…This study is to identify gene mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in a Chinese family using next-generation sequencing technology. A Chinese family with 7 members including two individuals affected with severe early-onset RP was studied. …”
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The Identification of Molecular Ploidy Status of Abnormal Pronuclear Zygotes Reveals a Significant Number of Euploid Blastocysts Available for Conception by Blair R. McCallie, Mary E. Haywood, Lauren N. Henry, Rachel M. Lee, William B. Schoolcraft, Mandy G. Katz-Jaffe

“…Biopsied trophectoderm cells were then lysed, and the isolated DNA was whole-genome amplified followed by library preparation. Next-generation sequencing was performed for PGT-A, and excess whole-genome amplified DNA was utilized for single nucleotide polymorphism beadchip array analysis. …”
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Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis by Peter T. Bell, Timothy Baird, John Goddard, Olusola S. Olagoke, Andrew Burke, Shradha Subedi, Tiana R. Davey, James Anderson, Derek S. Sarovich, Erin P. Price

“…These data will help to inform the design of larger prospective clinical trials and identify potential obstacles to be overcome before next-generation sequencing technologies can be integrated into routine clinical practice.…”
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Identifying the function of novel cross-species microRNAs from the excretory-secretory products of Angiostrongylus cantonensis fifth-stage larvae by Kuang-Yao Chen, Yi-Hsuan Lin, Chien-Ju Cheng, Yi-Hao Huang, Sheng-Yu Lin, Chyi-Liang Chen, Cheng-Hsun Chiu

“…Methods: Here, we employed next-generation sequencing (NGS) to establish the secreted microRNAs dataset. …”
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Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat by Duo Su, Tingting Jiang, Yulong Song, Die Li, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Li Li, Hongping Zhang, Linjie Wang

“…Here, we employed circularized chromosome conformation capture coupled with next-generation sequencing (4C-seq) to generate high-resolution chromatin interaction profiles of Ucp1 in interscapular brown adipose tissue (iBAT) and epididymal white adipose tissue (eWAT) and revealed marked changes in Ucp1 chromatin interaction between iBAT and eWAT. …”
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A Novel CRYBB2 Stopgain Mutation Causing Congenital Autosomal Dominant Cataract in a Chinese Family by Yu Zhou, Yaru Zhai, Lulin Huang, Bo Gong, Jie Li, Fang Hao, Zhengzheng Wu, Yi Shi, Yin Yang

“…This study aimed to identify gene mutations responsible for autosomal dominant congenital cataract (ADCC) in a Chinese family using next-generation sequencing technology. This family included eight unaffected and five affected individuals. …”
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Rumen DNA virome and its relationship with feed efficiency in dairy cows by Xiaohan Liu, Yifan Tang, Hongyi Chen, Jian-Xin Liu, Hui-Zeng Sun

“…In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE. …”
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Rare Somatic MEN1 Gene Pathogenic Variant in a Patient Affected by Atypical Parathyroid Adenoma by Luigia Cinque, Flavia Pugliese, Celeste Clemente, Stefano Castellana, Maria Pia Leone, Danilo de Martino, Teresa Balsamo, Claudia Battista, Tommaso Biagini, Paolo Graziano, Marco Castori, Alfredo Scillitani, Vito Guarnieri

“…We suggest that MEN1 gene could be an underestimate genetic determinant of these rare histological entities, and we highlight the utility of a complete genetic screening protocol, by the use of next-generation sequencing technology in such undetermined clinical cases with no frank clinical presentation.…”
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Mutation in the COL2A1 gene is associated with acetabular dysplasia by Miaomiao Xin, Xin Guan, Xin Guan, Jiangfei Yang, Yi Li, Zhentao Man, Hongsheng Sun, Min Fu

“…Clinical whole-exome sequencing (WES) using next-generation sequencing (NGS) was conducted to identify potential mutation sites, which were then validated through Sanger sequencing. …”
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Association of tumour mutation burden with prognosis and its clinical significance in stage III gastric cancer by Ya-Lin Han, Li Chen, Xu-Ning Wang, Mao-Lin Xu, Rui Qin, Fang-Ming Gong, Peng Sun, Hong-Yi Liu, Zhi-Peng Teng, Zhao-Xia Li, Guang-Hai Dai

“…In the study cohort, next-generation sequencing was used to detect mutated GC genes and obtain TMB data. …”
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An Unusually Short Latent Period of Therapy-Related Myeloid Neoplasm Harboring a Rare MLL-EP300 Rearrangement: Case Report and Literature Review by Reina Takeda, Kazuaki Yokoyama, Seiichiro Kobayashi, Toyotaka Kawamata, Sousuke Nakamura, Tomofusa Fukuyama, Mika Ito, Nozomi Yusa, Eigo Shimizu, Nobuhiro Ohno, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Kaoru Uchimaru, Arinobu Tojo

“…Bone marrow examinations revealed chronic myelomonocytic leukemia-like disease with a chromosomal translocation of t(11;22)(q23;q13) as a solo cytogenetic abnormality, resulting in the diagnosis of t-MN. Next-generation sequencing analysis identified a rare chimeric transcript, MLL-EP300, without any additional somatic mutations. …”
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mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms by Barnabé, Christian, Sempéré, Guilhem, Manzanilla, Vincent, Millan, Joel Moo, Amblard-Rambert, Antoine, Waleckx, Etienne

“…In our workflow, VSEARCH is utilized for processing fastq files derived from amplicon-based Next-Generation Sequencing data. This software is a versatile open-source tool for processing amplicon sequences, offering advantages such as high speed, efficient memory usage, and the ability to handle large datasets. …”
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Investigating the potential immunomodulatory effects of commercial oral probiotic supplements on equine gastrointestinal tract barrier function by Agnieszka Żak-Bochenek, Paulina Żebrowska-Różańska, Joanna Bajzert, Łukasz Łaczmański, Bogumiła Szponar, Natalia Siwińska, Klaudia Gładysz, Katarzyna Sikorska, Anna Chełmońska-Soyta

“…The samples were subjected to microbiome analysis via next-generation sequencing of hypervariable regions V3-V4 and V7-V9 of the 16S rRNA gene for analysis of short-chain fatty acids via HPLC analysis and fecal secretory immunoglobulin A (SIgA) quantification via ELISA.ResultsMicrobiome analysis revealed no significant differences in either alpha or beta diversity parameters between the groups. …”
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Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits by Sukoluhle Dube, Sharefa Al-Mannai, Li Liu, Sara Tomei, Satanay Hubrack, Shimaa Sherif, Ayesha Jabeen, Eiman I. Ahmed, Apryl Sanchez, William Mifsud, Davide Bedognetti, Wouter Hendrickx, Christophe M. Raynaud

“…Abstract Background FFPE tissue samples are commonly used in biomedical research and are a valuable source for next-generation sequencing in oncology, however, extracting RNA from these samples can be difficult the quantity and quality achieved can impact the downstream analysis. …”
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An exploratory study on the differential diagnostic indicators between adult systemic EBV-positive T-cell lymphoproliferative disorders and angioimmunoblastic T-cell lymphoma with... by Xiaodan Zheng, Yuanyuan Zheng, Yanlin Zhang, Jianlan Xie, Xiaojing Teng, Kuo Bi, Lan Sun, Xiaowen Huang, Mulan Jin, Xiaoge Zhou

“…Differences in immunophenotype, type of EBV-infected cells, clonality and gene mutations between the two groups of cases were compared by immunohistochemical staining, double-label staining, TCR gene rearrangement and next-generation sequencing analysis. Results 7 cases of adult EBV+ T-LPD: all cases had no more than 1 T follicular helper (THF) marker was expressed, and there were significantly more EBER+/CD3 + cells than EBER+/CD20 + cells; 5 cases had mutation detection results, in which only 1 had the characteristic KMT2D mutation, 2 had TET2 mutations, and no common mutations such as DDX3X were detected.16 cases of AITL with multiple EBV infections: all cases were found to express at least 2 TFH markers, with 87% of them expressing at least 3 TFH markers., and had significantly more EBER+/CD20 + cells than EBER+/CD3 + cells; 4 cases had mutation test results, with mutated high-frequency genes being TET2 (100%, and all of them had 2 or more TET2 mutations) and RHOA G17V (100%), DNMT3A mutation occurred in 2 cases (50%), and IDH2 R172 mutation occurred in 1 case (25%). …”
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Enhancing newborn screening sensitivity and specificity for missed NICCD using selected amino acids and acylcarnitines by Peiyao Wang, Lingwei Hu, Yuhe Chen, Duo Zhou, Shasha Zhu, Ting Zhang, Ziyan Cen, Qimin He, Benqing Wu, Xinwen Huang

“…Metabolic profiles were analyzed using the non-derivatized MS/MS Kit, and genetic mutations were identified via next-generation sequencing and confirmed by Sanger sequencing. …”
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