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)
Review
Infectious Diseases
Rimjhim Kanaujia, Manisha Biswal, Archana Angrup, Pallab Ray
Summary: The study aimed to evaluate and compare the diagnostic efficacy of metagenomic NGS (mNGS) for bacterial meningoencephalitis (BM/E) diagnosis. The analysis showed that mNGS had moderate diagnostic accuracy in diagnosing BM/E from cerebrospinal fluid specimens, and it can be particularly helpful in cases with undiagnosed BM/E.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2022)
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)
Article
Veterinary Sciences
Rebecca P. Wilkes
Summary: Although still mainly used for research purposes, NGS has been adopted by some veterinary diagnostic laboratories. Metagenomics approaches offer the widest detection range for infectious disease diagnostics, but at a higher cost. tNGS maintains the ability to detect a broad range of pathogens at a lower cost compared to mNGS, making it a viable option for syndromic testing in veterinary diagnostic laboratories.
VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE
(2023)
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
Public, Environmental & Occupational Health
Quan Zhang, Wei Xu, Fei Peng, Si Lei, Yanjun Zhong, Jun Yi, Shangjie Wu
Summary: A case of aspiration pneumonia with radiological and clinical similarities to COVID-19 was reported. The study highlights the importance of careful examination of CT images, attention to clinical history, and judicious utilization of NGS for accurate diagnosis.
FRONTIERS IN PUBLIC HEALTH
(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
Biochemistry & Molecular Biology
Sushmaa Chandralekha Selvakumar, K. Auxzilia Preethi, Kehinde Ross, Deusdedit Tusubira, Mohd Wajid Ali Khan, Panagal Mani, Tentu Nageswara Rao, Durairaj Sekar
Summary: Personalized or precision medicine combines genetic information with phenotypic and environmental characteristics to tailor healthcare to individuals, enabled by cancer genome sequencing. The advantages of NGS, such as limited sample requirements and the development of biomarkers, have accelerated personalized medicine.
Article
Chemistry, Applied
Regina Klapper, Amaya Velasco, Maik Doring, Ute Schroeder, Carmen G. Sotelo, Erik Brinks, Marta Munoz-Colmenero
Summary: Tuna cans are regulated not to contain mixtures of different tuna species in Europe. To prevent food fraud and mislabelling, a next-generation sequencing method based on mitochondrial DNA markers was tested. The method allowed qualitative and some extent of quantitative identification of tuna species. The results showed the importance of using specific calibrators or normalization models in NGS for accurate quantification.
Review
Microbiology
Chi-Ching Tsang, Jade L. L. Teng, Susanna K. P. Lau, Patrick C. Y. Woo
Summary: NGS technology has matured into clinical applications, showing potential advantages in diagnosing difficult-to-grow fungi and cases with low fungal loads. Studies have revealed that fungal infections diagnosed by NGS present some different characteristics from general epidemiology, such as a low HIV-positive rate among patients with P.jirovecii infections.
Article
Microbiology
Olga Soutourina, Thomas Dubois, Marc Monot, Pavel Shelyakin, Laure Saujet, Pierre Boudry, Mikhail S. Gelfand, Bruno Dupuy, Isabelle Martin-Verstraete
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Pierre Boudry, Emma Piattelli, Emilie Drouineau, Johann Peltier, Anais Boutserin, Maxence Lejars, Eliane Hajnsdorf, Marc Monot, Bruno Dupuy, Isabelle Martin-Verstraete, Daniel Gautheret, Claire Toffano-Nioche, Olga Soutourina
Summary: High-throughput sequencing of RNA immunoprecipitation revealed a diverse set of mRNAs and ncRNAs interacting with the RNA chaperone protein Hfq in C. difficile, shedding light on the post-transcriptional regulatory network of this pathogen.
Article
Chemistry, Organic
Walaa Ibraheem, Quentin Wils, Emilie Camiade, Elhadi Ahmed, Jerome Thibonnet, Emilie Thiery, Julien Petrignet
Summary: A total synthesis of racemic paecilocin A, a natural marine phthalide, was achieved in four steps, allowing the synthesis of twelve analogs. The synthesized compounds were tested for antibacterial activity against MSSA and MRSA, with three analogs showing similar or better activity against MRSA compared to the natural compound.
TETRAHEDRON LETTERS
(2021)
Article
Genetics & Heredity
Adeline Pastuszka, Clemence Beauruelle, Emilie Camiade, Genevieve M. Rousseau, Sylvain Moineau, Laurent Mereghetti, Philippe Horvath, Philippe Lanotte
Summary: This study found that the CRISPR-Cas system in the hypervirulent ST17 strains of S. agalactiae has significantly fewer spacers, possibly due to a large deletion in the cas promoter region. Despite the absence of a regular cas promoter, the CRISPR-Cas system in ST17 strains can still function in interference and acquire new spacers. The promoter sequence upstream of srn036 was identified to be responsible for the CRISPR-Cas adaptation and interference activities in ST17 strains.
Article
Ecology
Yannick D. N. Tremblay, Benjamin A. R. Durand, Audrey Hamiot, Isabelle Martin-Verstraete, Marine Oberkampf, Marc Monot, Bruno Dupuy
Summary: Clostridioides difficile infection is a leading cause of hospital-acquired diarrhea, and successful infection relies on the absence of specific microbiota-produced metabolites. The study found that in the presence of deoxycholate, extracellular pyruvate induces biofilm formation, which may play a key role in driving C. difficile persistence in the gut.
Article
Multidisciplinary Sciences
Julian R. Garneau, Veronique Legrand, Martial Marbouty, Maximilian O. Press, Dean R. Vik, Louis-Charles Fortier, Matthew B. Sullivan, David Bikard, Marc Monot
Summary: PhageTermVirome (PTV) is a tool for the easy and rapid determination of phage termini and packaging mechanisms in large-scale metagenomic datasets. Successfully tested on mock and real virome datasets, PTV can quickly identify over 100 phage termini and packaging mechanisms with just a few hours of computing time. It complements other virus identification softwares and aids in predicting the true viral origin of contigs in viral metagenomics datasets.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Walaa Ibraheem, Capucine Chaar, Emilie Camiade, Virginie Herve, Delphine Fouquenet, Anne-Emmanuelle Roux, Mustapha Si-Tahar, Elhadi Ahmed, Jerome Thibonnet, Emilie Thiery, Julien Petrignet
Summary: The history of antibacterial discovery has shown that natural products, especially secondary metabolites, are important chemical substances for antibacterial discovery. Some natural phthalides exhibit interesting antibacterial activities and further research is needed on their potential.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Correction
Multidisciplinary Sciences
Julian R. Garneau, Veronique Legrand, Martial Marbouty, Maximilian O. Press, Dean R. Vik, Louis-Charles Fortier, Matthew B. Sullivan, David Bikard, Marc Monot
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Victoria Mesa, Marc Monot, Laurent Ferraris, Michel Popoff, Christelle Mazuet, Frederic Barbut, Johanne Delannoy, Bruno Dupuy, Marie-Jose Butel, Julio Aires
Summary: This study provides the closed genome assembly and functional annotation of Clostridium neonatale ATCC BAA-265(T) reference strain. Pan-genome, core-genome, and accessory genome analyses reveal the genetic diversity and plasticity of C. neonatale genomes. The findings contribute to the understanding of the biological capabilities of this species.
MICROBIAL GENOMICS
(2022)
Article
Infectious Diseases
Giulia Gallo, Petr Kotlik, Philippe Roingeard, Marc Monot, Guillaume Chevreux, Rainer G. Ulrich, Noel Tordo, Myriam Ermonval
Summary: This study investigated the interactions of different Orthohantaviruses with human and rodent host cells using cellular and molecular approaches. The results showed that cell susceptibility to virus infection is influenced by cell type and virus strain. Additionally, the study revealed differential interactions between Orthohantaviruses and host cells and tissues, which may be related to host specificity. Furthermore, the study found that interferon (IFN) dependent gene expression is regulated in a cell and virus species dependent manner.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Microbiology
Anne-Emmanuelle Roux, Sylvie Robert, Mathilde Bastat, Isabelle Rosinski-Chupin, Vanessa Rong, Sebastien Holbert, Laurent Mereghetti, Emilie Camiade
Summary: This study reveals the importance of the pleiotropic regulator CcpA in gene regulation in Streptococcus agalactiae. CcpA is not only involved in carbon catabolite repression, but also plays a critical role in acidic and oxidative stress resistance and survival in macrophages.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Nancy Jabbour, Eric Morello, Emilie Camiade, Marie-Frederique Lartigue
Summary: Regulatory small RNAs (sRNAs) play a role in bacterial adaptation, and CiaR-dependent sRNAs (csRNAs) controlled by the CiaRH two-component system are widely conserved in streptococci. In this study, the importance of a direct repeat TTTAAG-N5-TTTAAG in the regulation of csRNAs in Streptococcus agalactiae was demonstrated. The csRNA Srn024 was found to be involved in the posttranscriptional regulation of the sap gene, which encodes a pullulanase involved in biofilm formation and adhesion to human cervical epithelial cells. The disruption of the srn024-sap RNA pairing led to increased biofilm formation. The findings suggest that targeting regulatory RNAs like Srn024 could affect the abilities of pathogens to form biofilms and adapt to host niches.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Juliana Pipoli da Fonseca, Etienne Kornobis, Elodie Turc, Vincent Enouf, Laure Lemee, Thomas Cokelaer, Marc Monot
Summary: This paper assesses the ability of the hybridization technique, Capture-Seq, to detect the SARS-CoV-2 genome in patient samples. The study shows that SARS-CoV-2-only panels are highly effective, while multi-virus panels fail to capture low-abundance targets.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Emile Auria, Lise Hunault, Patrick England, Marc Monot, Juliana Pipoli Da Fonseca, Mariette Matondo, Magalie Duchateau, Yannick D. N. Tremblay, Bruno Dupuy
Summary: The ability of Clostridioides difficile to form biofilms during infection and its association with recurrence and persistence are discussed in this study. The researchers investigate the role of the lipoprotein CD1687 in biofilm formation induced by deoxycholate (DCA). They found that CD1687 is necessary for biofilm formation, and its overexpression alone can induce biofilm formation. Furthermore, CD1687 affects the expression of transporters and metabolic pathways and binds DNA in a non-specific manner, suggesting its involvement in mediating the interaction between cells and the biofilm matrix.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Immunology
Melanie Gaillet, Clara Pichard, Johana Restrepo, Anne Lavergne, Lucas Perez, Antoine Enfissi, Philippe Abboud, Yann Lambert, Laurence Ma, Marc Monot, Magalie Demar, Felix Djossou, Veronique Servas, Mathieu Nacher, Audrey Andrieu, Julie Prudhomme, Celine Michaud, Cyril Rousseau, Isabelle Jeanne, Jean-Bernard Duchemin, Loic Epelboin, Dominique Rousset
Summary: Oropouche fever, caused by Oropouche virus, has recently emerged in a remote rainforest village in French Guiana, affecting a significant number of patients with dengue-like symptoms. This highlights a potential new outbreak of the virus in the region.
EMERGING INFECTIOUS DISEASES
(2021)
