Article
Microbiology
Melanie A. Mallory, Weston C. Hymas, Keith E. Simmon, Michael T. Pyne, Jeffery B. Stevenson, Adam P. Barker, David R. Hillyard, Kimberly E. Hanson
Summary: This study developed and validated an amplicon-based Ion Torrent NGS method for simultaneous analysis of CMV resistance mutations in multiple genes. Compared to standard Sanger sequencing, the NGS assay had a low error rate and high accuracy, and generated high-quality sequence from low viral load specimens. The assay showed excellent agreement with Sanger and detected resistance mutations missed by Sanger in low-frequency variants.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yen-Yi Liu, Bo-Han Chen, Chih-Chieh Chen, Chien-Shun Chiou
Summary: This study evaluated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. The quality of assemblies was found to be mainly affected by read depth, regardless of the assembler used. Recommendations for cutoff values and cost-effective combinations for cgMLST were provided.
Review
Plant Sciences
Philomena Chu, Sarah Zanon Agapito-Tenfen
Summary: Classical genetic engineering and new genome editing techniques, especially CRISPR/Cas technology, have increased the possibilities for modifying genetic material in organisms, potentially offering novel agricultural traits. However, concerns arise from unintended genetic modifications reported as side-effects. This systematic review of scientific literature on unintended genomic alterations in plants modified through various techniques reveals a wide range of effects, from small nucleotide polymorphisms to large structural variations, with a potential underestimation due to limited use of comprehensive sequencing methods. Future research should focus on more thorough examination of analytical methods to provide regulators with valuable information for detection and identification of genomic interventions.
Review
Environmental Sciences
Sofia Ioannidou, Claudia Cascio, Mary B. Gilsenan
Summary: The European Food Safety Authority has developed open access tools for estimating dietary exposure to food-borne chemical hazards, tailored to various regulatory domains and based on FoodEx2 and the Comprehensive European food consumption database.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Immunology
Yanmin He, Xiaozhen Hong, Jingjing Zhang, Ji He, Faming Zhu, He Huang
Summary: In this study, we established an NGS method for analyzing the sequence of the start codon to the stop codon in the ABO gene. Through analysis of 110 individuals, we identified two novel ABO alleles and confirmed the presence of DNA recombination in ABO alleles.
FRONTIERS IN IMMUNOLOGY
(2022)
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
Virology
Federica Bichicchi, Niccolo Guglietta, Arthur Daniel Rocha Alves, Erika Fasano, Elisabetta Manaresi, Gloria Bua, Giorgio Gallinella
Summary: This study investigated the genomic sequence heterogeneity of Parvovirus B19 (B19V) using Next Generation Sequencing (NGS) techniques and a bioinformatics tool. The results showed that NGS analysis and the developed tool can effectively study sequence diversity, providing a better understanding of viral evolution dynamics within the quasispecies framework.
News Item
Multidisciplinary Sciences
Layal Liverpool
Summary: The group behind Plan S is proposing a more radical revolution for science publishing, after already accelerating the open-access movement.
Article
Biotechnology & Applied Microbiology
Stephan Weissbach, Stanislav Sys, Charlotte Hewel, Hristo Todorov, Susann Schweiger, Jennifer Winter, Markus Pfenninger, Ali Torkamani, Doug Evans, Joachim Burger, Karin Everschor-Sitte, Helen Louise May-Simera, Susanne Gerber
Summary: The study demonstrates systematic heterogeneity in variant calls between different experimental and data analysis setups, and highlights the benefit of reprocessing genomic data with harmonized pipelines for improving concordance.
Article
Computer Science, Hardware & Architecture
Aly S. S. Abdalla, Pratheek S. S. Upadhyaya, Vijay K. K. Shah, Vuk Marojevic
Summary: This article discusses the key features and limitations of the open radio access network (O-RAN) as a framework for 6G wireless research and development, and explores the technologies to overcome these limitations.
Review
Oncology
Renu Verma, Real Sumayya Abdul Sattar, Nimisha, Apurva, Arun Kumar, Abhay Kumar Sharma, Mamta Parveen Sumi, Ejaj Ahmad, Asgar Ali, Bhawna Mahajan, Sundeep Singh Saluja
Summary: The asymptomatic behavior of esophageal cancer cells in early stages leads to advanced clinical presentation, making therapeutic intervention difficult. Current diagnostic and prognostic markers are not consistently satisfactory, highlighting the need for biomarkers for early diagnosis and better prognosis. Next generation sequencing techniques have emerged as potential tools to study the mutations in tumor cells and potentially improve personalized therapy for esophageal cancer.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
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.
Article
Medicine, General & Internal
Namsoo Kim, Sinyoung Kim, Jong Rak Choi, Younhee Park
Summary: This study shared the experience of HLA typing using next-generation sequencing (NGS) in patients with hematologic malignancies and evaluated its association with hematologic diseases. The data from 211 Korean patients with a hematologic disease were reviewed, and NGS was performed for 11 HLA loci. The study found that NGS-based HLA typing enables detailed analysis of the HLA system and identified a specific HLA gene associated with myelodysplastic syndrome.
Article
Pathology
Ching-Yeuh Yanga, Yi-Che Yeh, Lei-Chi Wanga, Yen-Yu Lina, Shin-Ying Lina, Shu-Ying Wanga, Ping-Yuan Chua, Zih-Yu Liua, Yu-Chi Sua, Hsiang-Ling Ho, Teh-Ying Choua
Summary: This study aimed to investigate the value of large-scale next-generation sequencing (NGS) panels in distinguishing between separate primary lung cancers (SPLCs) and intrapulmonary metastases (IPMs). With NGS and a molecular classification algorithm, 97.6% of tumor pairs can be accurately classified as SPLCs or IPMs. The molecular classification was predictive of postoperative clinical outcomes in terms of overall survival and recurrence-free interval, providing accurate risk stratification.
Article
Microbiology
Bashir Hussain, Jung-Sheng Chen, Bing-Mu Hsu, I-Tseng Chu, Suprokash Koner, Tsung-Hsien Chen, Jagat Rathod, Michael W. Y. Chan
Summary: This study utilized high-throughput sequencing to analyze the bacterial composition in fermented fruit products, identifying low abundance potential opportunistic pathogens and validating major pathogenic species. The results indicated that fermentation is a reliable and safe process, as pathogenic bacteria were not detected in the fermentation products.
Article
Biotechnology & Applied Microbiology
G. Douglas Inglis, Jenny F. Gusse, Kathaleen E. House, Tara G. Shelton, Eduardo N. Taboada
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Genetics & Heredity
Catarina Mendes, Erley Lizarazo, Miguel P. Machado, Diogo N. Silva, Adriana Tami, Mario Ramirez, Natacha Couto, John W. A. Rossen, Joao A. Carrico
MICROBIAL GENOMICS
(2020)
Correction
Microbiology
G. Douglas Inglis, Jenny F. Gusse, Kathaleen E. House, Tara G. Shelton, Eduardo N. Taboada
Article
Microbiology
G. Douglas Inglis, Jenny F. Gusse, Kathaleen E. House, Tara G. Shelton, Eduardo N. Taboada
Article
Infectious Diseases
Aida Gonzalez-Diaz, Miguel P. Machado, Jordi Camara, Jose Yuste, Emmanuelle Varon, Miriam Domenech, Maria Del Grosso, Jose Maria Marimon, Emilia Cercenado, Nieves Larrosa, Maria Dolores Quesada, Dionisia Fontanals, Assiya El-Mniai, Meritxell Cubero, Joao A. Carrico, Sara Marti, Mario Ramirez, Carmen Ardanuy
Article
Microbiology
Benjamin M. Hetman, Steven K. Mutschall, Catherine D. Carrillo, James E. Thomas, Victor P. J. Gannon, G. Douglas Inglis, Eduardo N. Taboada
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
G. Douglas Inglis, Eduardo N. Taboada, Valerie F. Boras
Summary: A study in southwestern Alberta, Canada evaluated 1291 isolates of Campylobacter jejuni from diarrheic patients over a 15-year period. Results showed consistently high resistance to tetracycline, significant increases in resistance to ciprofloxacin and nalidixic acid, with the majority of ciprofloxacin-resistant isolates linked to domestically acquired infections, primarily related to cattle and chicken reservoirs. These findings highlight the importance of prioritizing monitoring of fluoroquinolone resistance in C. jejuni infections in Canada.
CANADIAN JOURNAL OF MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rafael Mamede, Pedro Vila-Cerqueira, Mickael Silva, Joao A. Carrico, Mario Ramirez
Summary: Chewie Nomenclature Server (chewie-NS) allows users to share genome-based gene-by-gene typing schemas, maintain a common nomenclature, and easily compare results. It strikes a balance between local analysis and a public repository of allelic data, facilitating the deployment of private instances for compliance with strict data policies. The integration with chewBBACA suite enables seamless uploading, downloading, and synchronization of schemas, making it easier to integrate into high-throughput analysis pipelines.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Public, Environmental & Occupational Health
Nadine A. Vogt, David L. Pearl, Eduardo N. Taboada, Steven K. Mutschall, Kristin J. Bondo, Claire M. Jardine
Summary: Campylobacter is a common cause of foodborne illness in humans globally, with recent research suggesting that wildlife may play a role in transmission to humans. A study in southern Ontario investigated the occurrence of Campylobacter jejuni in raccoons, finding that climatic factors were associated with the presence of the bacteria in raccoons, but the effects varied by location and year. Further research is needed to understand the transmission and movement of Campylobacter within the ecosystem.
ZOONOSES AND PUBLIC HEALTH
(2021)
Article
Genetics & Heredity
Genevieve Labbe, Peter Kruczkiewicz, James Robertson, Philip Mabon, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo N. Taboada, Catherine Yoshida, Kim Ziebell, Anil Nichani, Roger P. Johnson, Gary Van Domselaar, John H. E. Nash
Summary: Hierarchical genotyping approaches, such as BioHansel, provide rapid and high-resolution classification of bacterial pathogens. The tool is organism-agnostic and uses SNP-based genotyping schemes to distinguish predefined lineages, showing full concordance with traditional methods while being significantly faster. Additionally, the quality assurance module of BioHansel is effective in detecting contamination even in populations with low genetic diversity, making it ideal for use by public health agencies.
MICROBIAL GENOMICS
(2021)
Article
Microbiology
Lisa M. Hodges, Eduardo N. Taboada, Adam Koziol, Steven Mutschall, Burton W. Blais, G. Douglas Inglis, Daniel Leclair, Catherine D. Carrillo
Summary: This study found that the concordance between genotype and phenotype was influenced by computational pipelines, genome coverage, and the type of ARG, but not by input data.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Catarina Ines Mendes, Pedro Vila-Cerqueira, Yair Motro, Jacob Moran-Gilad, Joao Andre Carrico, Mario Ramirez
Summary: The study developed a flexible platform, LMAS, for evaluating the performance of de novo assemblers in metagenomic analysis. The k-mer De Bruijn graph assemblers outperformed other approaches but had higher computational cost. Metagenomic specific assemblers did not consistently outperform other genomic assemblers in metagenomic samples. Therefore, caution should be exercised when using certain assemblers for complex samples.
Article
Biotechnology & Applied Microbiology
G. Douglas Inglis, Nahal Ramezani, Eduardo N. Taboada, Valerie F. Boras, Richard R. E. Uwiera
Summary: This study highlights the importance of longitudinal examination of Campylobacter jejuni subtypes in the poultry production continuum to understand transmission mechanisms and foodborne risks. It shows that a limited number of C. jejuni subtypes from a small number of farms contaminate the abattoir, leading to a high prevalence of contaminated carcasses with diverse subtypes, which are transferred to retail settings. However, only a subset of these strains pose a high risk to human health.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Proceedings Paper
Computer Science, Artificial Intelligence
Luis Rita, Alexandre Francisco, Joao Carrico, Vitor Borges
XV MEDITERRANEAN CONFERENCE ON MEDICAL AND BIOLOGICAL ENGINEERING AND COMPUTING - MEDICON 2019
(2020)
Article
Multidisciplinary Sciences
Basil B. Xavier, Mohamed Mysara, Mattia Bolzan, Bruno Ribeiro-Goncalves, Blaise T. F. Alako, Peter Harrison, Christine Lammens, Samir Kumar-Singh, Herman Goossens, Joao A. Carrico, Guy Cochrane, Surbhi Malhotra-Kumar