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
Biochemical Research Methods
Diane Gleeson, Debarati Sethi, Radka Platte, Jonathan Burvill, Daniel Barrett, Shaheen Akhtar, Michaela Bruntraeger, Joanna Bottomley, James Bussell, Edward Ryder
Summary: Genotyping of knockout alleles in mice can be performed using endpoint PCR, qPCR, or NGS, with NGS being highly scalable and applicable to various allele types. One challenge is locating unique areas of the genome, especially when dealing with gene families or regions of high homology.
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
Cell Biology
In-Cheol Baek, Eun-Jeong Choi, Hyoung-Jae Kim, Haeyoun Choi, Tai-Gyu Kim
Summary: The range of HLA typing for successful HSCT is expanding with NGS-based improvement, but is influenced by finances and laboratory conditions.
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
Pharmacology & Pharmacy
Samuel D. Chorlton, Gordon Ritchie, Tanya Lawson, Elizabeth McLachlan, Marc G. Romney, Nancy Matic, Christopher F. Lowe
Summary: A next-generation sequencing (NGS) assay was developed for CMV antiviral drug resistance (AVDR) testing, which using MinION technology detected additional mutations compared to traditional Sanger sequencing. Through the application of an online bioinformatics pipeline, barriers associated with MinION and NGS in clinical laboratories were eliminated.
ANTIVIRAL RESEARCH
(2021)
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
Oncology
Shijun Li, Bo Wang, Miaomiao Chang, Rui Hou, Geng Tian, Ling Tong
Summary: A novel method for detecting MSI based on NGS data was developed, achieving comparable accuracy with PCR-based methods through histogram analysis and algorithm design.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemical Research Methods
Zheng Jiang, Hui Liu, Siwen Zhang, Jia Liu, Weitao Wang, Guoliang Zang, Bo Meng, Huixin Lin, Jichuan Quan, Shuangmei Zou, Dawei Yuan, Xishan Wang, Geng Tian, Jidong Lang
Summary: A novel analytical method using paired plasma/leukocyte samples and next-generation sequencing for MSI detection was proposed. Compared to traditional PCR, the new method showed advantages in sensitivity and specificity, providing a potential direction for increasing the specificity of liquid biopsy MSI detection in future studies.
CURRENT BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Pasquale Tripodi
Summary: This review examines the application of genomic technologies in studying the diversity of tomatoes, with a focus on next-generation sequencing strategies and methods. It also discusses how genomics has provided insights into the domestication process of tomatoes and presents perspectives on utilizing natural variation for breeding purposes through pan-genome construction and graphical pan-genome development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Oncology
Attila Mokanszki, Reka Bicsko, Lajos Gergely, Gabor Mehes
Summary: This study demonstrated a non-invasive approach to identify frequent gene fusions and variants in aggressive lymphomas by comparing tissue biopsy and peripheral blood liquid biopsy samples. Results showed that PB liquid biopsy samples effectively support the genetic diagnosis of lymphomas, detecting common gene mutations in 16 out of 24 cases.
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
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)
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)