Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Chemistry, Multidisciplinary
Jina Ko, Yongcheng Wang, Kuanwei Sheng, David A. Weitz, Ralph Weissleder
Summary: Circulating extracellular vesicles (EVs) are promising biomarkers and drug delivery vehicles, but human EVs exhibit significant heterogeneity even in homogeneous cell populations. An antibody-based immunosequencing method enables multiplex measurement of protein molecules from individual EVs, providing a way to detect specific proteins at the single EV level. This technology has the potential to be adapted for multiplexed protein analysis of any nanoparticle.
Review
Agronomy
Balakrishnan Marudamuthu, Tamanna Sharma, Supriya Purru, S. K. Soam, Ch. Srinivasa Rao
Summary: Next-generation sequencing (NGS) is a game-changing technology in genomic research, enabling massively parallel sequencing. In agriculture, NGS has transformed enhancement strategies and simplified genetic modification approaches. This review highlights the available NGS platforms and their applications in agricultural genomics.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biology
Maria Guarnaccia, Laura Guarnaccia, Valentina La Cognata, Stefania Elena Navone, Rolando Campanella, Antonella Ampollini, Marco Locatelli, Monica Miozzo, Giovanni Marfia, Sebastiano Cavallaro
Summary: The study developed a targeted next-generation sequencing approach for analyzing genetic variations and chromosomal aberrations in gliomas, which can provide accurate and specific assessment of tumor pathogenesis, prognosis, and treatment response. This has important implications for the diagnosis and treatment of gliomas.
Article
Chemistry, Analytical
Junyi Chen, Shaoqi Huang, Yan Long, Kan Wang, Yangtai Guan, Lianping Hou, Bo Dai, Songlin Zhuang, Dawei Zhang
Summary: Droplet-based microfluidics has great potential in various applications, and this paper introduces a modular microfluidic system using 3D printing technology for droplet generation. The system allows flexible control of droplet size and generation rate by adjusting flow rates. It is a promising candidate for chemical and biological applications.
Article
Chemistry, Analytical
Kailiang Zhang, Fangyuan Xing, Jiuqing Liu, Zhijie Xie
Summary: This paper presents a method for effective on-chip droplet generation, splitting, and switching using controllable hydrodynamics. A two-dimensional simulation model based on the phase-field method is established to analyze the hydrodynamic droplet manipulation behaviors. The numerical results show that the droplets can be generated with controlled sizes and can realize on-demand splitting and switching.
ANALYTICA CHIMICA ACTA
(2022)
Review
Immunology
Tapoka T. Mkandawire, Adam Sateriale
Summary: This review discusses the significance of using long read DNA and RNA sequencing technologies to provide novel insights into the biology of Cryptosporidium, and highlights that the widespread adoption of these technologies will help fill key gaps in the understanding of Cryptosporidium biology.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medicine, General & Internal
Cienne Morton, Debashis Sarker, Paul Ross
Summary: Cancers contain numerous mutations, but only a few are critical for malignancy. Targeted therapies and immunotherapy have shown great success in various cancer types. Next-generation sequencing enables the detection of potentially actionable mutations and contributes to the identification of new biomarkers. However, technical challenges and the development of targeted therapies against common genomic aberrations need to be overcome for personalized medicine to become more widely available.
Article
Biophysics
Run Xie, Yang Liu, Shiyu Wang, Xuyang Shi, Zhantao Zhao, Longqi Liu, Ya Liu, Zida Li
Summary: Combinatorial perturbation sequencing (CP-seq) is a high-throughput and comprehensive technology for screening combinatorial drug treatments on single cells. It utilizes the advantages of droplet microfluidics to enable efficient and multiplexed drug perturbation and transcriptome analysis.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Physical
Jingyu Qi, Haibin Zhu, Yijian Li, Xiangyu Guan, Ying He, Guanhua Ren, Qiang Guo, Longqi Liu, Ying Gu, Xuan Dong, Ya Liu
Summary: Cell-cell interaction is an important way for transmitting information and activating the effects of functional cells. Researchers propose a droplet-based microfluidic platform for cell-cell interaction sequencing and screening, which allows for efficient analysis and interpretation of single-cell transcriptomes in cell interactions. This work fills a gap in the current experimental platform for cell-cell interaction research and has significant practical implications in biomedicine.
Article
Oncology
Arnaud Bayle, Debora Basile, Simon Garinet, Bastien Rance, Pierre Laurent-Puig, Helene Blons, Julien Taieb, Geraldine Perkins
Summary: This study evaluated the role of NGS targeted panels in digestive oncology, showing that it allows for an exhaustive search for molecular abnormalities and provides patients with more opportunities for targeted therapies. Regular updates and further studies are needed for better analysis of prognostic factors.
Review
Biochemistry & Molecular Biology
Adrian Dockery, Laura Whelan, Pete Humphries, G. Jane Farrar
Summary: Inherited retinal diseases (IRDs) encompass a variety of genetically diverse conditions with phenotypic variations, researchers utilize cutting-edge sequencing techniques to identify elusive causes, providing accurate diagnoses and informed prognoses for family planning and medical interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Dario Kringel, Sebastian Malkusch, Eija Kalso, Jorn Lotsch
Summary: The genetic background of pain is being increasingly well understood, leading to the development of a cost-effective next generation sequencing-based pain-genotyping assay that identifies the most representative genes associated with pain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Chunyu Li, Yanhai Gong, Xixian Wang, Jian Xu, Bo Ma
Summary: An addressable dynamic droplet array (aDDA) integrates the advantages of static droplet arrays and continuous-flow droplet platforms, allowing all sample preparation steps to be performed within a sub-nanoliter droplet. Validation studies show that aDDA reduces amplification bias and increases genome recovery efficiency, making it a valuable tool for high-genome-coverage sequencing of single microbial cells.
Article
Biochemical Research Methods
Christopher Paul Wardell, Cody Ashby, Michael Anton Bauer
Summary: FiNGS is a software developed to improve the precision of variant caller outputs for somatic variants, with demonstrated reliability and better performance than other tools for the same task. It provides researchers with a simple, configurable, and reproducible tool for filtering somatic variants in sequencing data.
BMC BIOINFORMATICS
(2021)