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
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
Biochemical Research Methods
Paula J. Gomez-Gonzalez, Susana Campino, Jody E. Phelan, Taane G. Clark
Summary: This study compared the genome sequencing of clinical isolates of Mycobacterium tuberculosis using Oxford Nanopore Technologies (ONT) sequencing and Illumina HiSeq sequencing. The analysis showed that ONT sequencing is robust for detecting single nucleotide polymorphisms and provides improved coverage in repetitive regions. It also demonstrated high concordance in variants associated with drug resistance. ONT sequencing is a promising tool for tuberculosis genomic investigations and can inform clinical and surveillance decision-making to reduce the disease burden.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Oncology
Victor Tomacinschii, Adrian Mosquera Orgueira, Carlos Aliste Santos, Maria Robu, Sanda Buruiana, Maximo Francisco Fraga Rodriguez
Summary: This article provides a comprehensive overview of the importance of next-generation sequencing technologies in the field of oncology, including lymphoma classification and diagnosis, and selection of therapeutic targets, supporting the development of personalized medicine.
FRONTIERS IN ONCOLOGY
(2023)
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
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Cheng-Hong Yang, Sin-Hua Moi, Ming-Feng Hou, Li-Yeh Chuang, Yu-Da Lin
Summary: In this study, a method named FuzzyDeepCoxPH that combines machine learning and traditional survival analysis was proposed to identify high-risk missense mutation variants and candidate genes associated with cancer mortality. The results showed that FuzzyDeepCoxPH can effectively distinguish high-risk variants and candidate genes related to cancer mortality, providing comprehensive risk estimation for cancer medicine.
IEEE TRANSACTIONS ON FUZZY SYSTEMS
(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)
Review
Biochemistry & Molecular Biology
Mariem Ben Khedher, Kais Ghedira, Jean-Marc Rolain, Raymond Ruimy, Olivier Croce
Summary: The powerful combination of genome sequencing and bioinformatics analysis has been crucial in interpreting bacterial genomes. High-throughput sequencing technologies have revolutionized our understanding of biological questions. Long-read sequencing has expanded the applications in genomics. This review provides a brief history of bacterial genome sequencing, discusses its applications in public health and molecular epidemiology, and highlights the advantages of next-generation and long-read sequencing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Payal Ganguly, Bradley Toghill, Shelly Pathak
Summary: This article discusses the importance and research progress of bone marrow aging, explores inflammaging, and the application of next-generation sequencing technology in research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemical Research Methods
Matteo Chiara, Anna Maria D'Erchia, Carmela Gissi, Caterina Manzari, Antonio Parisi, Nicoletta Resta, Federico Zambelli, Ernesto Picardi, Giulio Pavesi, David S. Horner, Graziano Pesole
Summary: Various NGS-based strategies have been used to trace infectious agent origins and develop molecular diagnostic tests. The ongoing COVID-19 pandemic has caused severe societal and economic costs, emphasizing the importance of efficient sequencing methods. However, different technologies and approaches have their own advantages and limitations, highlighting the need for better integration and sharing of data.
BRIEFINGS IN BIOINFORMATICS
(2021)
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
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
Pharmacology & Pharmacy
Alireza Tafazoli, Henk-Jan Guchelaar, Wojciech Miltyk, Adam J. Kretowski, Jesse J. Swen
Summary: Pharmacogenomics (PGx) utilizes genetic data to optimize drug therapy, with next-generation sequencing (NGS) emerging as a more comprehensive and cost-effective approach. The advantages and challenges of implementing NGS-based tests in PGx are discussed, along with solutions for managing these technologies in clinical practice.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Medical Laboratory Technology
Deepali Yadav, Bhagyashri Patil-Takbhate, Anil Khandagale, Jitendra Bhawalkar, Srikanth Tripathy, Priyanka Khopkar-Kale
Summary: Next-generation sequencing (NGS) has revolutionized genomics and is dramatically changing clinical diagnosis and precision medicine. NGS enables rapid and cost-effective analysis of large-scale genomic data, facilitating comprehensive exploration of disease genetic landscape. It is a powerful tool for disease diagnosis, prognosis, and personalized treatment strategies, allowing accurate identification of disease-causing variants and discovery of novel disease-associated genes and variants. NGS enhances our understanding of disease mechanisms and enables tailored medical interventions based on individual characteristics, contributing to the development of noninvasive diagnostic approaches.
CLINICA CHIMICA ACTA
(2023)