Article
Biochemical Research Methods
Magnus Palmblad
Summary: Future single-molecule sequencing technologies focus on sequencing individual peptides or protein molecules to uniquely identify human proteins based on the number and types of amino acids. Simulation results suggest that the optimal choice of reading N amino acids performs similarly to the average choice of N+1 amino acids, and the discrimination power of amino acids scales with their frequency in the proteome.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Immunology
Ying Liu, Huifen Wang, Yaoguang Li, Zujiang Yu
Summary: The study aimed to evaluate the clinical diagnostic value of metagenomic next-generation sequencing (mNGS) for tuberculosis (TB). Retrospective analysis of 52 patients with suspected TB infection was conducted, and multiple detection methods were performed. The results showed that mNGS had a higher detection rate of MTB compared to acid-fast staining and PCR, but no statistical difference with T-SPOT.TB assay. As an adjunctive diagnostic technology, mNGS can be combined with traditional methods to guide the diagnosis and treatment of TB.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
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
Immunology
Xingxing Li, Shunda Liang, Dan Zhang, Miao He, Hong Zhang
Summary: This study found that mNGS had a higher sensitivity in diagnosing sepsis compared to conventional culture methods, especially in blood, BALF, CSF, sputum, and ascitic fluid samples. The common pathogens in immunocompromised patients with sepsis identified by mNGS were Pneumocystis jirovecii and Mucoraceae, which should receive more attention from clinicians. mNGS has a significant benefit in improving sepsis diagnosis and advancing patient treatment.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Shoji Takenaka, Naoki Edanami, Yasutaka Komatsu, Ryoko Nagata, Traithawit Naksagoon, Maki Sotozono, Takako Ida, Yuichiro Noiri
Summary: This study analyzed the microbiome of root caries lesions in patients with severe periodontitis and found compositionally distinct microbiota depending on the location of the lesions. Periodontal pathogens were identified in root caries lesions that extended beyond the gingival margin, providing new insights into the microbial etiology of root caries.
Article
Oncology
Anthony J. Scott, Molly C. Tokaz, Maryann Shango, Sumana Devata, Shannon A. Carty, Mark S. Kaminski, Arul M. Chinnaiyan, Tycel J. Phillips, Ryan A. Wilcox
Summary: Successful utilization of targeted treatments based on tumor sequencing in lymphoma patients remains challenging due to issues related to timing and availability of clinical trials. Despite the potential for complete response based on precision treatment recommendations, there are inherent clinical challenges that need to be addressed for successful application of this technology.
LEUKEMIA & LYMPHOMA
(2021)
Article
Immunology
Wenjing Tang, Yu Zhang, Chong Luo, Lina Zhou, Zhiyong Zhang, Xuemei Tang, Xiaodong Zhao, Yunfei An
Summary: This study evaluated the utility of mNGS for detecting pathogens in patients with PID, demonstrating its superiority over conventional methods in pathogen identification, especially in detecting rare opportunistic pathogens. Compared to traditional methods, mNGS can provide faster pathogen diagnosis, enabling clinicians to make more timely and targeted therapeutic decisions.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Mengjia Qian, Bijun Zhu, Yanxia Zhan, Lingyan Wang, Qi Shen, Miaomiao Zhang, Lei Yue, Duojiao Wu, Hao Chen, Xiangdong Wang, Yunfeng Cheng
Summary: The negative prediction accuracy rate of the original specimen is significant when the mNGS test is negative. However, other laboratory assays results and clinical presentations should always be carefully considered prior to drawing a diagnosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Ke Li, Yubao Ma, Rui Ban, Qiang Shi
Summary: This report describes a rare case of alveolar echinococcosis diagnosed using next-generation sequencing. NGS of cerebrospinal fluid accurately detected pathogenic microorganism nucleic acid sequences, providing a new and reliable method for the diagnosis of AE.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Bei Gao, Liang Chi, Yixin Zhu, Xiaochun Shi, Pengcheng Tu, Bing Li, Jun Yin, Nan Gao, Weishou Shen, Bernd Schnabl
Summary: This review summarizes commonly used computational tools for gut microbiome data analysis, which have expanded our understanding of the gut microbiome in health and diseases.
Article
Virology
Manasi Majumdar, Cristina Celma, Elaine Pegg, Krunal Polra, Jake Dunning, Javier Martin
Summary: The study focused on a detection method for enteroviruses using NGS analysis of clinical samples, showing high concordance with conventional Sanger sequencing and good sensitivity and specificity for different EV types. The NGS method identified previously untyped EVs and potential co-infections, demonstrating its potential for comprehensive EV detection and genetic analysis.
Article
Oncology
Wencke Walter, Nicole Pfarr, Manja Meggendorfer, Philipp Jost, Torsten Haferlach, Wilko Weichert
Summary: Molecular diagnostics has played a crucial role in precision oncology and has undergone revolutionary developments in recent years. In most cases, it is no longer possible to select treatments for cancer patients without molecular characterization. However, there has been limited scientific research on preanalytical and analytical requirements, and standardization and quality assessment have played a marginal role in the field.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Immunology
Guang Zhang, Hongqi Zhang, XiaoJiang Hu, Dongcheng Xu, Bo Tang, Mingxing Tang, Shaohua Liu, Yanbing Li, Wen Xu, Chaofeng Guo, Qile Gao
Summary: This study evaluated the impact of precise treatment based on metagenomic next-generation sequencing (mNGS) on the clinical outcomes of patients with spinal infections. The results showed that targeted antibiotics based on mNGS results can lead to faster clinical cure for spinal infection patients. The positive rate of mNGS for diagnosing spinal infections was significantly higher than that of traditional detection methods.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Infectious Diseases
Lisha Wang, Shixiao Li, Jiajia Qin, Tianbin Tang, Jiawen Hong, Tao-Hsin Tung, Chunyan Xu, Sufei Yu, Jiao Qian
Summary: The purpose of this study was to analyze the clinical concordance of mNGS test results from blood samples and improve the clinical efficiency of mNGS in the diagnosis of suspected sepsis pathogens.
INFECTION AND DRUG RESISTANCE
(2023)
Article
Immunology
Min Kong, Wei Li, Qingsheng Kong, Haixin Dong, Aizhong Han, Liqing Jiang
Summary: This study describes a case of a child infected with tuberculosis after being wounded. The use of metagenomic next-generation sequencing (mNGS) helped in identifying the specific pathogen and facilitating early treatment, leading to improved prognosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Mark McMillan, Luke Walters, Turra Mark, Andrew Lawrence, Lex E. X. Leong, Thomas Sullivan, Geraint B. Rogers, Ross M. Andrews, Helen S. Marshall
HUMAN VACCINES & IMMUNOTHERAPEUTICS
(2019)
Article
Critical Care Medicine
Steven L. Taylor, Lex E. X. Leong, Fredrick M. Mobegi, Jocelyn M. Choo, Steve Wesselingh, Ian A. Yang, John W. Upham, Paul N. Reynolds, Sandra Hodge, Alan L. James, Christine Jenkins, Matthew J. Peters, Melissa Baraket, Guy B. Marks, Peter G. Gibson, Geraint B. Rogers, Jodie L. Simpson
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2019)
Article
Infectious Diseases
Anushia Ashokan, Lito E. Papanicolas, Lex E. X. Leong, Maria Theodossi, Santhosh Daniel, Steve L. Wesselingh, Geraint B. Rogers, David L. Gordon
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2019)
Editorial Material
Medicine, General & Internal
Geraint B. Rogers, James Ward, Alex Brown, Steve L. Wesselingh
Review
Physiology
Alyce M. Martin, Emily W. Sun, Geraint B. Rogers, Damien J. Keating
FRONTIERS IN PHYSIOLOGY
(2019)
Article
Microbiology
Yanan Wang, Elissa K. Mortimer, Kondwani G. H. Katundu, Noel Kalanga, Lex E. X. Leong, Geetha L. Gopalsamy, Claus T. Christophersen, Alyson C. Richard, Aravind Shivasami, Guy C. J. Abell, Graeme P. Young, Geraint B. Rogers
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Medicine, General & Internal
Rebecca McLoughlin, Bronwyn S. Berthon, Geraint B. Rogers, Katherine J. Baines, Lex E. X. Leong, Peter G. Gibson, Evan J. Williams, Lisa G. Wood
Review
Respiratory System
Geraint B. Rogers, Steven L. Taylor, Lucas R. Hoffman, Lucy D. Burr
JOURNAL OF CYSTIC FIBROSIS
(2020)
Article
Multidisciplinary Sciences
Alyce M. Martin, Julian M. Yabut, Jocelyn M. Choo, Amanda J. Page, Emily W. Sun, Claire F. Jessup, Steve L. Wesselingh, Waliul I. Khan, Geraint B. Rogers, Gregory R. Steinberg, Damien J. Keating
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Microbiology
Kerry L. Ivey, Andrew T. Chan, Jacques Izard, Aedin Cassidy, Geraint B. Rogers, Eric B. Rimm
Article
Allergy
Bronwyn S. Berthon, Rebecca F. McLoughlin, Megan E. Jensen, Banafshe Hosseini, Evan J. Williams, Katherine J. Baines, Steven L. Taylor, Geraint B. Rogers, Kerry L. Ivey, Matthew Morten, Carla R. Da Silva Sena, Adam M. Collison, Malcolm R. Starkey, Joerg Mattes, Peter A. B. Wark, Lisa G. Wood
Summary: The study found that a high fruit and vegetable diet did not affect the time to first asthma exacerbation in children, but may have potential for improving lung function and protecting against systemic inflammation. In the intervention group, there was an increase in fruit and vegetable intake and plasma total carotenoids, but no significant difference in exacerbation rate and lung function indicators between the two groups.
CLINICAL AND EXPERIMENTAL ALLERGY
(2021)
Article
Nutrition & Dietetics
Kerry L. Ivey, Xuan-Mai T. Nguyen, Deirdre K. Tobias, Rebecca Song, Geraint B. Rogers, Yuk-Lam Ho, Ruifeng Li, Peter W. F. Wilson, Kelly Cho, J. Michael Gaziano, Walter C. Willett, Luc Djousse
Summary: This study found that yogurt consumption was positively associated with high-density lipoprotein cholesterol (HDLC) and negatively associated with triglyceride concentrations, which was distinct from non-yogurt dairy foods.
CLINICAL NUTRITION ESPEN
(2021)
Article
Respiratory System
Charlotte Rigauts, Juliana Aizawa, Steven L. Taylor, Geraint B. Rogers, Matthias Govaerts, Paul Cos, Lisa Ostyn, Sarah Sims, Eva Vandeplassche, Mozes Sze, Yves Dondelinger, Lars Vereecke, Heleen Van Acker, Jodie L. Simpson, Lucy Burr, Anne Willems, Michael M. Tunney, Cristina Cigana, Alessandra Bragonzi, Tom Coenye, Aurelie Crabbe
Summary: The presence of Rothia mucilaginosa in the lower airways has an inhibitory effect on pathogen-induced inflammation and is negatively correlated with pro-inflammatory markers in bronchiectasis patients. Mechanistically, R. mucilaginosa inhibits inflammation by reducing NF-kappa B pathway activation. These findings suggest that R. mucilaginosa in the lower airways could potentially mitigate inflammation and impact the severity and progression of chronic respiratory disorders.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Review
Biochemistry & Molecular Biology
Andrew P. Shoubridge, Jocelyn M. Choo, Alyce M. Martin, Damien J. Keating, Ma-Li Wong, Julio Licinio, Geraint B. Rogers
Summary: The gut microbiome has a significant influence on human neurophysiology and mental health, playing a role in the development of psychiatric conditions and the effectiveness of common therapies. With an increasing acceptance of its role, research is now shifting towards using this knowledge to improve clinical outcomes and understanding the mechanisms of gut microbiome-brain interactions.
MOLECULAR PSYCHIATRY
(2022)
Article
Nutrition & Dietetics
Jane Bowen, Natalie D. Luscombe-Marsh, Welma Stonehouse, Cuong Tran, Geraint B. Rogers, Nathan Johnson, Campbell H. Thompson, Grant D. Brinkworth
CLINICAL NUTRITION ESPEN
(2019)