Review
Medicine, General & Internal
Rajesh R. Singh
Summary: Screening for genomic sequence variants is crucial in precision medicine and next-generation sequencing technologies have become the preferred platforms due to their capacity for massively parallel sequencing. Targeted NGS workflow involves enrichment of the regions of interest, improving the accuracy and cost-effectiveness of screening.
Review
Microbiology
Amy H. Fitzpatrick, Agnieszka Rupnik, Helen O'Shea, Fiona Crispie, Sinead Keaveney, Paul Cotter
Summary: This review assesses and recommends approaches for targeted and agnostic High Throughput Sequencing of RNA viruses, highlighting the challenges and biases that method choice can impart to sequencing results. Methodology choices from RNA extraction to library preparation have a significant impact on the detection or characterization of RNA viruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Food Science & Technology
Lijin Duan, Shasha Zhang, Yingxia Yang, Qian Wang, Qingkuo Lan, Yong Wang, Wentao Xu, Wujun Jin, Liang Li, Rui Chen
Summary: This study introduces a novel GMO testing method, "SSH-seq", based on suppressive subtractive hybridization and next-generation sequencing, which can be used to detect unknown GMOs and has shown promising results in experiments. Although the method may be influenced by multiple factors, further optimizations could make SSH-seq a powerful tool in the field of GMO testing.
Review
Biochemistry & Molecular Biology
Alissa Drees, Markus Fischer
Summary: The HiTS-FLIP technology improves the efficiency of aptamer selection, providing insights into the relationship between sequence, structure, and function, which supports the evolution of aptamers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Valeria Trivellone, Yanghui Cao, Christopher H. Dietrich
Summary: This study compared traditional methods with a new method based on next-generation DNA sequencing for detecting and identifying phytoplasmas in DNA extracted from plant-feeding insects. The results showed that the next-generation method performed as well, if not better, for identifying phytoplasmas. Several new records and associations for known phytoplasmas were reported, as well as new subgroups and possible new groups. The findings suggest that using next-generation sequencing to screen phloem-feeding insects may be the most efficient method for discovering new phytoplasmas.
Article
Immunology
Lauren M. Walker, Andrea R. Shiakolas, Rohit Venkat, Zhaojing Ariel Liu, Steven Wall, Nagarajan Raju, Kelsey A. Pilewski, Ian Setliff, Amyn A. Murji, Rebecca Gillespie, Nigel A. Makoah, Masaru Kanekiyo, Mark Connors, Lynn Morris, Ivelin S. Georgiev
Summary: The development of novel technologies for discovering human monoclonal antibodies has been extremely valuable in combating infectious diseases. LIBRA-seq with epitope mapping is a next-generation sequencing technology that can determine residue-level epitopes for thousands of single B cells simultaneously, making it an efficient tool for high-throughput identification of antibodies against specific antigen epitopes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Jorge Alejandro Basiletti, Joan Valls, Tomas Poklepovich, Maria Dolores Fellner, Maryluz Rol, Rafael Alonso, Rita Mariel Correa, Maria Celeste Colucci, Mercedes Rodriguez de la Pena, Paula Gabriela Falabella, Agustina Saino, Josefina Campos, Rolando Herrero, Maribel Almonte, Maria Alejandra Picconi
Summary: Sensitive and specific genotyping of HPV is crucial for vaccine surveillance. This study used Nested-PCR and NGS to identify HPV genotypes in cervical samples, and found that multiple infections were more common in ≤CIN1 cases, while high-risk HPV genotypes were predominant in CIN3+ cases.
Article
Microbiology
Alexandra Rehn, Peter Braun, Mandy Knuepfer, Roman Woelfel, Markus H. Antwerpen, Mathias C. Walter
Summary: This study evaluated five commercially available sequence capture panels targeting SARS-CoV-2 and found that the specific panel from Twist Bioscience was the most efficient. The research provides a decision basis for the sequencing community and potential improvements for manufacturers.
Article
Biochemical Research Methods
Ze-Gang Wei, Xu Chen, Xiao-Dan Zhang, Hao Zhang, Xing-Guo Fan, Hong-Yan Gao, Fei Liu, Yu Qian
Summary: Recent advances in sequencing technology have led to a large amount of sequencing data, and clustering analysis is a powerful tool to study this data. However, comparison studies of clustering methods have limitations, and this study aims to provide a comprehensive benchmark for sequence clustering methods, helping biological analyzers choose appropriate algorithms and motivating algorithm designers to develop more efficient approaches.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Thorarinn Blondal, Cristina Gamba, Lea Moller Jagd, Ling Su, Dimiter Demirov, Shuang Guo, Camille M. Johnston, Eva M. Riising, Xiaolin Wu, Marie J. Mikkelsen, Ludmila Szabova, Peter Mouritzen
Summary: Validation of CRISPR-Cas9 editing typically focuses on the immediate vicinity and distal off-target sequences, concluding that editing is specific. However, studies show that unintended editing events like deletions and insertions are frequent but often missed. The Xdrop(TM) technology allows for targeted enrichment of long regions, identifying unknown and unintended genome editing events.
Article
Biochemical Research Methods
Eric de Bony, Fien Gysens, Nurten Yigit, Jasper Anckaert, Celine Everaert, Eveline Vanden Eynde, Kimberly Verniers, Willem van Snippenberg, Wim Trypsteen, Pieter Mestdagh
Summary: The molecular phenotyping method involving shallow 3'-end RNA-sequencing workflows is becoming more commonly used in large-scale chemical or genetic perturbation screens for studying disease biology or supporting drug discovery. This workflow combines 3'-end library preparation with 3'-end hybrid capture probes and shallow RNA-sequencing to target quantification of subsets of genes with low abundance, resulting in over 200-fold enrichment of target gene abundance compared to standard 3'-end RNA-sequencing, while preserving intergene and intersample abundances.
BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Natalie J. Wu-Woods, Jacob T. Barlow, Florian Trigodet, Dustin G. Shaw, Anna E. Romano, Bana Jabri, A. Murat Eren, Rustem F. Ismagilov
Summary: This study introduces a microbial-enrichment method (MEM) that enables the removal of host DNA in human intestinal biopsies and allows for the characterization of low-abundance microbial taxa. The method provides deeper insights into the high-throughput characterization of the gut microbiome and demonstrates the construction of metagenome-assembled genomes from human intestinal biopsies.
Article
Infectious Diseases
Ana Paula Muterle Varela, Marcia Regina Loiko, Juliana da Silva Andrade, Caroline Tochetto, Samuel Paulo Cibulski, Diane Alves Lima, Matheus Nunes Weber, Paulo Michel Roehe, Fabiana Quoos Mayer
Summary: The study described the complete nucleotide sequence of PCV3 recovered from wild boars lymph nodes, identifying the PCV3-wb/Br/RS genome as PCV3b subtype closely related to genomes recovered in Spain, China, Germany, and Denmark. The investigation in Southern Brazil found a high prevalence of PCV3 infection in wild boars, indicating that PCV3 is circulating in the wild boar population in that region.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Biochemical Research Methods
Makiko N. Hatori, Cyrus Modavi, Peng Xu, Daniel Weisgerber, Adam R. Abate
Summary: This article describes a modified workflow using particle-templated emulsification and flow cytometry to achieve cell detection and sorting, providing a powerful enrichment approach for targeted sequencing applications.
BIOTECHNOLOGY JOURNAL
(2022)
Article
Medical Laboratory Technology
Yoonjung Kim, Kyung-Hee Kim, Boyeon Kim, Saeam Shin, Kyung-A Lee
Summary: This study compared the analytical performance of the Ion S5 XL and NextSeq NGS systems using a hybridization capture-based panel, showing comparable results in terms of sequencing run metrics and accuracy. Both systems demonstrated high sensitivity, specificity, and accuracy in single-nucleotide variant and indel calling, indicating the successful implementation of a hybrid capture panel for genetic analysis.
CLINICA CHIMICA ACTA
(2021)
