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.
Article
Medicine, General & Internal
Paul Hofman, Olivier Bordone, Emmanuel Chamorey, Jonathan Benzaquen, Renaud Schiappa, Virginie Lespinet-Fabre, Elisabeth Lanteri, Patrick Brest, Baharia Mograbi, Charlotte Maniel, Virginie Tanga, Maryline Allegra, Myriam Salah, Julien Fayada, Jacques Boutros, Sylvie Leroy, Simon Heeke, Veronique Hofman, Charles-Hugo Marquette, Marius Ilie
Summary: This study aimed to develop a full genome sequencing method for SARS-CoV-2 in an academic hospital. Using Ion Ampliseq SARS-CoV-2 Assay, SARS-CoV-2 genome sequencing was found to be rapid and efficient not only in nasopharyngeal swab samples but also in saliva samples with a low viral load. The study identified multiple variants of SARS-CoV-2.
FRONTIERS IN MEDICINE
(2022)
Review
Medicine, General & Internal
Syahzuwan Hassan, Rosnah Bahar, Muhammad Farid Johan, Ezzeddin Kamil Mohamed Hashim, Wan Zaidah Abdullah, Ezalia Esa, Faidatul Syazlin Abdul Hamid, Zefarina Zulkafli
Summary: Thalassemia is a highly heterogeneous disease with over a thousand recorded mutation types worldwide. Conventional PCR-based DNA analysis for thalassemia diagnosis is time-consuming and resource-intensive due to phenotype variability, disease complexity, and test limitations. Advanced molecular techniques such as next-generation sequencing (NGS) and third-generation sequencing (TGS) offer more suitable and valuable options for DNA analysis of thalassemia. The continuous improvement of sequencing methods and bioinformatics tools, particularly for identifying copy number variations and homologous genes, will lead to more accurate thalassemia detection.
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
Oncology
Juan A. Santamaria-Barria, Chikako Matsuba, Adam Khader, Anthony J. Scholar, Mary Garland-Kledzik, Trevan D. Fischer, Richard Essner, Matthew P. Salomon, Joshua M. V. Mammen, Melanie Goldfarb
Summary: This study analyzed melanoma samples and identified age-related mutational differences, as well as potential targetable mutations for personalized therapies.
JOURNAL OF SURGICAL ONCOLOGY
(2023)
Article
Biochemical Research Methods
Muhammad Tahir, Muhammad Sardaraz, Zahid Mehmood, Muhammad Saud Khan
Summary: This paper proposed an efficient error estimation computational model ESREEM to assess error rates in NGS data. The model is based on a probabilistic error model integrated with Hidden Markov Model, and experimental results show that it efficiently estimates errors compared to state-of-the-art algorithms.
CURRENT BIOINFORMATICS
(2021)
Article
Nutrition & Dietetics
Dominika Salamon, Agnieszka Sroka-Oleksiak, Artur Gurgul, Zbigniew Arent, Magdalena Szopa, Malgorzata Bulanda, Maciej T. Malecki, Tomasz Gosiewski
Summary: The study suggests that the composition of fungi in the human colon may be associated with the development of diabetes. Differences were found in the types and quantities of fungi in the T1D group compared to the T2D and control groups, which may be linked to cholesterol levels.
Article
Oncology
Christian Rolfo, Alexander Drilon, David Hong, Caroline McCoach, Afshin Dowlati, Jessica J. Lin, Alessandro Russo, Alison M. Schram, Stephen Liu, Jorge J. Nieva, Timmy Nguyen, Shahrooz Eshaghian, Michael Morse, Scott Gettinger, Mohammad Mobayed, Sarah Goldberg, Emilio Araujo-Mino, Neelima Vidula, Aditya Bardia, Janakiraman Subramanian, Deepa Sashital, Thomas Stinchcombe, Lesli Kiedrowski, Kristin Price, David R. Gandara
Summary: This study retrospectively reviewed a ctDNA database in advanced stage solid tumors to identify NTRK1 fusions, and found NTRK1 fusion events in 37 patients with nine unique fusion partners. 44% of cases had tissue testing for NTRK1 fusions, and the NTRK1 fusions detected by ctDNA were confirmed in tissue in 88% of cases. This study reports for the first time that minimally-invasive plasma NGS can detect NTRK fusions with a high positive predictive value.
BRITISH JOURNAL OF CANCER
(2022)
Article
Virology
Laila Sara Arroyo Muhr, Daniel Guerendiain, Kate Cuschieri, Karin Sundstrom
Summary: NGS technology provides powerful opportunities for HPV genomics research, but rigorous validation and quality assurance procedures are essential to ensure reliable interpretation of results. Recommendations for optimizing sequencing data yield and curated bioinformatical procedures are crucial for robust analysis of HPV genotypes and mutations. International standards for quality assurance in HPV NGS should be developed to enhance testing and diagnostics in global efforts.
Article
Genetics & Heredity
Xiangyin Liu, Han Zhang, Xinyue Zhang, Hongguo Zhang, Yuting Jiang, Ruizhi Liu, Jia Fei, Ying Wang, Yang Yu
Summary: The NGS method was validated as an alternative to traditional STS-PCR method for detecting Y chromosome microdeletions in infertile men. It not only detects CNV like partial deletion or duplication, but also provides detailed information on the abnormal range and size of variations.
JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
(2021)
Review
Genetics & Heredity
Ziga I. Remec, Katarina Trebusak Podkrajsek, Barbka Repic Lampret, Jernej Kovac, Urh Groselj, Tine Tesovnik, Tadej Battelino, Marusa Debeljak
Summary: Newborn screening was introduced in the 1960s, and has expanded over time with the advancement of technology, particularly high-throughput sequencing. Genomic sequencing is now widely used in clinical applications, including newborn screening, but has also raised various concerns and challenges.
FRONTIERS IN GENETICS
(2021)
Article
Immunology
Ferhat Guzel, Micol Romano, Erdi Keles, David Piskin, Seza Ozen, Hakan Poyrazoglu, Ozgur Kasapcopur, Erkan Demirkaya
Summary: This study describes the development and validation of an NGS-based multiplex array for targeted sequencing of nine genes associated with common AIDs, offering a cost-effective, comprehensive, and informative screening tool compared to other methods.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jose Vicente Gil, Esperanza Such, Claudia Sargas, Javier Simarro, Alberto Miralles, Gema Perez, Inmaculada de Juan, Sarai Palanca, Gayane Avetisyan, Marta Santiago, Carolina Fuentes, Jose Maria Fernandez, Ana Isabel Vicente, Samuel Romero, Marta Llop, Eva Barragan
Summary: The molecular landscape of acute lymphoblastic leukemia (ALL) is highly heterogeneous, and genetic lesions are clinically relevant. Next-generation sequencing (NGS) is a valuable tool in clinical laboratories for capturing relevant alterations. However, comprehensive ALL panels are rare. Here, we design and validate an NGS panel (ALLseq) that can provide clinically relevant information to over 83% of pediatric patients, making it an attractive tool for molecular characterization in clinical settings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Rebecca C. Thomas, Jenny C. Dunn, Deborah A. Dawson, Helen Hipperson, Gavin J. Horsburgh, Antony J. Morris, Chris Orsman, John Mallord, Philip Grice, Keith C. Hamer, Cyril Eraud, Lormee Herve, Simon J. Goodman
Summary: Investigating parasite coinfections in European turtle doves revealed high diversity in T. gallinae strains, with significant spatiotemporal turnover and common coinfections with haemosporidians. The study suggests potential interactions between different parasite strains and highlights the need for longitudinal studies to fully understand coinfection epidemiology in natural populations.
Article
Physiology
Agnes Bloch-Zupan, Tristan Rey, Alexandra Jimenez-Armijo, Marzena Kawczynski, Naji Kharouf, Muriel de La Dure-Molla, Emmanuelle Noirrit, Magali Hernandez, Clara Joseph-Beaudin, Serena Lopez, Corinne Tardieu, Beatrice Thivichon-Prince, Tatjana Dostalova, Milan Macek Jr, Mustapha El Alloussi, Leila Qebibo, Supawich Morkmued, Patimaporn Pungchanchaikul, Blanca Urzua Orellana, Marie-Cecile Maniere, Benedicte Gerard, Isaac Maximiliano Bugueno, Virginie Laugel-Haushalter
Summary: In this study, next-generation sequencing was used to analyze a cohort of Amelogenesis imperfecta (AI) patients, revealing more than 70 genes associated with AI. The findings showed that 73% of the cases were non-syndromic AI and 27% were syndromic AI. The genetic diagnosis provided important insights for the diagnosis and treatment of AI. This study demonstrated the potential of next-generation sequencing in AI research and provided new insights into the classification and treatment of AI.
FRONTIERS IN PHYSIOLOGY
(2023)