Impacts of genomic alterations on the efficacy of HER2-targeted antibody–drug conjugates in patients with metastatic breast cancer by Riqing Huang, Anqi Hu, Qixiang Rong, Ditian Shu, Meiting Chen, Wei Yang, Yue Zhang, Qiufan Zheng, Xin An, Cong Xue, Haifeng Li, Yanxia Shi

“…Methods This comprehensive real-world retrospective study collected clinical data from patients diagnosed with metastatic breast cancer and performed genomic profiling using targeted next-generation sequencing. The study analyzed the associations between genomic alterations and clinical outcomes of HER2 ADC treatment. …”
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The role of mNGS in the diagnosis of talaromycosis and case series by Jing Zhao, Hui-Ting Su, Dong Zhang, Xue-Tong Li, Min-Ya Lu, Juan Du, Jia-Yu Guo, Yi Gao, Xin-Fei Chen, Dong-Hua Wen, Shi-Yu Jia, Yao Wang, Qi-Wen Yang

“…This study aimed to analyze four classic cases of Talaromyces marneffei infection diagnosed using metagenomic next-generation sequencing (mNGS) to improve understanding of its diagnosis and treatment. …”
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Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing by Ting-Yu Yen, Ching Hsu, Ni-Chung Lee, Chao-Szu Wu, Hsin Wang, Kuan-Yi Lee, Chia-Ray Lin, Chun-Yi Lu, Mo-Li Tsai, Tzu-Yu Liu, Che Lin, Chien-Yu Chen, Luan-Yin Chang, Feipei Lai, Li-Min Huang

“…However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures. …”
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Clinical Significance of Perioperative Minimal Residual Disease Detected by Circulating Tumor DNA in Patients With Lung Cancer With a Long Follow-up Data: An Exploratory Study by Shuta Ohara, MD, PhD, Kenichi Suda, MD, PhD, Sumedha Sudhaman, PhD, Akira Hamada, MD, PhD, Masato Chiba, MD, PhD, Masaki Shimoji, MD, PhD, Toshiki Takemoto, MD, PhD, Ekaterina Kalashnikova, PhD, Samantha K. Cheung, PhD, Michael Krainock, MD, PhD, Jordan Feeney, BS, Himanshu Sethi, MPH, Minetta C. Liu, MD, Junichi Soh, MD, PhD, Yasuhiro Tsutani, MD, PhD, Tetsuya Mitsudomi, MD, PhD

“…A clinically validated, personalized, tumor-informed 16-plex polymerase chain reaction–next-generation sequencing assay was used for the detection and quantification of ctDNA in retrospectively analyzed plasma samples. …”
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A novel high-throughput screen identifies phenazine-1-carboxylic acid as an inhibitor of African swine fever virus replication in primary porcine alveolar macrophages by Jing Lan, Rui Luo, Di Liu, Changxing Qi, Xin Song, Zhanhao Lu, Ruojia Huang, Yuying Yang, Yuan Sun, Yonghui Zhang, Tao Wang, Hua-Ji Qiu

“…Furthermore, analysis of Gluc activities, fluorescence, and next-generation sequencing indicated that rASFV-Gluc/EGFP maintains good genetic stability after 20 consecutive passages in PAMs. …”
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Construction of feature selection and efficacy prediction model for transformation therapy of locally advanced pancreatic cancer based on CT, 18F-FDG PET/CT, DNA mutation, and CA19... by Liang Qi, Xiang Li, Jiayao Ni, Yali Du, Qing Gu, Baorui Liu, Jian He, Juan Du

“…With the rapid development of radiomics, next-generation sequencing, and machine learning, there is hope to identify biomarkers that can predict the efficacy of transformative treatment for locally advanced pancreatic cancer through simple and non-invasive clinical methods. …”
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Impact of Ketogenic and Mediterranean Diets on Gut Microbiota Profile and Clinical Outcomes in Drug-Naïve Patients with Diabesity: A 12-Month Pilot Study by Vanessa Palmas, Andrea Deledda, Vitor Heidrich, Giuseppina Sanna, Giulia Cambarau, Michele Fosci, Lorenzo Puglia, Enrico Antonio Cappai, Alessio Lai, Andrea Loviselli, Aldo Manzin, Fernanda Velluzzi

“…The GM analysis was performed through next-generation sequencing. <b>Results</b>: Improvements in anthropometric and metabolic parameters were more pronounced in the KETO group at T6, particularly for body mass index (−5.8 vs. −1.7 kg/m²; <i>p</i> = 0.006) and waist circumference (−15.9 vs. −5.2 cm; <i>p</i> = 0.011). …”
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A new pathogen pattern of acute respiratory tract infections in primary care after COVID-19 pandemic: a multi-center study in southern China by Heng Zhang, Deqi Meng, Hao Huang, Longhao Feng, Yushao Li, Yong Jiang, Ling Wang, Ruoyu Deng, Yuchun Sun, Binqin Chen, Fuzhao Liao, Yumei Wu, Huancai Zheng, Junling Ding, Maokun Chen, Cui Zeng, Wanting Zhao, Meng Hou, Yinyan Li, Zhishen Li, Haibo Xia, Kai Yang, Lingwei Wang

“…Methods 1958 adult patients with ARTIs from 17 primary care clinics were recruited prospectively from January 2024 to March 2024. 17 and 62 pathogens in throat swab samples were tested using polymerase chain reaction (PCR) and targeted next-generation sequencing (tNGS), respectively. We analyzed the pathogen spectrum and co-infectious pattern of viral, bacterial or atypical pathogens. …”
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STR profiling in a cohort of Saudi patients with acute leukemia by Husein A. Alhatim, PhD Student, Muhammad NH Abdullah, PhD, Suhaili A. Jamaludin, PhD, Armania B. Nurdin, PhD, Sayed A. Amer, PhD

“…Further study applying next generation sequencing technology is necessary to validate these findings and explore the clinical applications of forensically used STRs as diagnostic tools for leukemia.…”
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Clonal hematopoiesis in patients with autoimmune thrombocytopenia: an international multicenter study by Bruno Fattizzo, Alfredo Marchetti, Alessandro Bosi, Carmelo Gurnari, Juri Alessandro Giannotta, Giacinto Luca Pedone, Elena Rossi, Valentina Carrai, Andrea Guido, Filippo Brioschi, Monica Carpenedo, Monica Crugnola, Domenica Caramazza, Livia Leuzzi, Monia Marchetti, Gabriele Merati, Simona Malato, Fabrizio Vianello, Andrea Patriarca, Hussein Awada, Marta Bortolotti, Marta Canzi, Niccolò Bolli, Marco Capecchi, Frederick Chen, Andrea Artoni, Jaroslaw P. Maciejewski, Wilma Barcellini

“…Abstract: Diagnostic boundaries between immune thrombocytopenia (ITP) and other thrombocytopenic states, such as thrombocytopenic myelodysplastic syndromes, may be difficult to establish, and the detection of somatic mutations by next-generation sequencing (NGS) may be of aid. Here, we aimed at characterizing the prevalence and clinical significance of clonal hematopoiesis in ITP. …”
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MRD-driven phase 2 study of daratumumab, carfilzomib, lenalidomide, and dexamethasone in newly diagnosed multiple myeloma by Manisha Bhutani, Myra Robinson, David Foureau, Shebli Atrash, Barry Paul, Fei Guo, Jason M. Grayson, Anna Ivanina-Foureau, Mauricio Pineda-Roman, Cindy Varga, Reed Friend, Christopher J. Ferreri, Xhevahire Begic, Sarah Norek, Tiffany Drennan, Michelle B. Anderson, James T. Symanowski, Peter M. Voorhees, Saad Z. Usmani

“…In a phase 2 trial, we assessed daratumumab, carfilzomib, lenalidomide, and dexamethasone (Dara-KRd) induction followed by a next-generation sequencing–based MRD-adapted strategy. The primary outcome was complete response (CR) and stringent CR (≥CR) after induction. …”
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Diagnostics of lung cancer by fragmentated blood circulating cell-free DNA based on machine learning methods by Ivan O. Meshkov, Alexander P. Koturgin, Pavel V. Ershov, Liubov A. Safonova, Julia A. Remizova, Valentina V. Maksyutina, Ekaterina D. Maralova, Vasilisa A. Astafieva, Alexey A. Ivashechkin, Boris D. Ignatiev, Antonida V. Makhotenko, Ekaterina A. Snigir, Valentin V. Makarov, Vladimir S. Yudin, Anton A. Keskinov, Sergey M. Yudin, Anna S. Makarova, Veronika I. Skvortsova

“…The aim of this work is to create a method for processing next-generation sequencing (NGS) data and an interpretable binary classification model (CM), which analyzed cfDNA fragmentation features for distinguishing healthy subjects and subjects with LC.Methods148 healthy subjects and 138 subjects with LC were included in the study. cfDNA fractions, isolated from blood plasma biospecimens, were used for DNA libraries preparations and NGS on the NovaSeq 6,000 Illumina system with a coverage of 100 million reads/sample. …”
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Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours by Surbhi Mishra, Mysore Vishakantegowda Tejesvi, Jenni Hekkala, Jenni Turunen, Niyati Kandikanti, Anna Kaisanlahti, Marko Suokas, Sirpa Leppä, Pia Vihinen, Hanne Kuitunen, Kaisa Sunela, Jussi Koivunen, Arja Jukkola, Ilja Kalashnikov, Päivi Auvinen, Okko-Sakari Kääriäinen, T. Peñate Medina, O. Peñate Medina, Juha Saarnio, Sanna Meriläinen, Tero Rautio, Raila Aro, Reetta Häivälä, Juho Suojanen, Mikael Laine, Pande Putu Erawijattari, Leo Lahti, Peeter Karihtala, Terhi S. Ruuska, Justus Reunanen

“…Methods: After isolating bEVs from the feces of solid tumor patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of feces from patients and controls using 16S sequencing and used machine learning to classify the samples into patients and controls based on their bEVs and fecal microbiomes. …”
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Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis by Salsabeel Yousuf, Hao Luo, Meiyin Zeng, Lei Chen, Tengfei Ma, Xiaofang Li, Maosheng Zheng, Xin Zhou, Liang Chen, Jiao Xi, Hongye Lu, Huiluo Cao, Xiaoya Ma, Bian Bian, Pengfan Zhang, Jiqiu Wu, Renyou Gan, Baolei Jia, Linyang Sun, Zhicheng Ju, Yunyun Gao, Waqar Afzal Malik, Chuang Ma, Hujie Lyu, Yahui Li, Huiyu Hou, Yuanping Zhou, Defeng Bai, Yao Wang, Haifei Yang, Jiani Xun, Shengda Du, Tianyuan Zhang, Xiulin Wan, Kai Peng, Shanshan Xu, Tao Wen, Tong Chen, Yong‐Xin Liu

“…Abstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration of microbial communities through amplicon sequencing. …”
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IMA Genome – F19 by Janneke Aylward, Andi M. Wilson, Cobus M. Visagie, Joseph Spraker, Irene Barnes, Carla Buitendag, Callin Ceriani, Lina Del Mar Angel, Deanné du Plessis, Taygen Fuchs, Katharina Gasser, Daniella Krämer, WenWen Li, Kiara Munsamy, Anja Piso, Jenna-Lee Price, Byron Sonnekus, Chanel Thomas, Ariska van der Nest, Alida van Dijk, Alishia van Heerden, Nicole van Vuuren, Neriman Yilmaz, Tuan A. Duong, Nicolaas A. van der Merwe, Michael J. Wingfield, Brenda D. Wingfield

“…Abstract The pace at which Next Generation Sequence data is being produced continues to accelerate as technology improves. …”
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A Homozygous CASQ2 Mutation in a Japanese Patient with Catecholaminergic Polymorphic Ventricular Tachycardia by Taishi Fujisawa, Yoshiyasu Aizawa, Yoshinori Katsumata, Akihiro Udo, Shogo Ito, Kazumasa Hatakeyama, Makoto Hirose, Hiroshi Miyama, Kazuaki Nakajima, Takahiko Nishiyama, Takehiro Kimura, Masamitsu Nitta, Kazuo Misumi, Seiji Takatsuki, Kenjiro Kosaki, Keiichi Fukuda

“…A genetic analysis with a next generation sequencer identified a homozygous W361X mutation in the CASQ2 gene. …”
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Pathogenesis of Helicobacter pylori-Related Gastroduodenal Diseases from Molecular Epidemiological Studies by Yoshio Yamaoka

“…Because genome wide analyses using whole-genome sequencing technology give a broad view of the genome of H. pylori, we hope that next-generation sequencers will enable us to efficiently investigate novel virulence factors.…”
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Access to Diagnostics and Treatment for People With Metastatic EGFR-Positive NSCLC: Lessons From Project PRIORITY by Jill Feldman, MA, Ivy Elkins, MBA, Zofia Piotrowska, MD, Bellinda L. King-Kallimanis, PhD, Tendai Chihuri, MD, Carly Johnson, BS, Alecia Clary, PhD, Teri Kennedy, MA, Upal Basu Roy, PhD, MPH

“…Participants residing in the United States were more likely to have access to advanced diagnostic (next-generating sequencing) and newer treatments such as osimertinib. …”
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Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding by I. V. Bykova, N. A. Shmakov, D. A. Afonnikov, A. V. Kochetov, E. K. Khlestkina

“…Large-scale studies of the potato genome and genes exploiting next-generation sequence (NGS) approaches are required for broad application of MAS, genomic selection as well as genomic editing (the newest approach for creating potato with desired properties). …”
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