scholarly journals Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing

2019 ◽  
Vol 221 (Supplement_3) ◽  
pp. S289-S291 ◽  
Author(s):  
Mariana Leguia ◽  
Anton Vila-Sanjurjo ◽  
Patrick S G Chain ◽  
Irina Maljkovic Berry ◽  
Richard G Jarman ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Infectious Diseases ◽  
Next Generation ◽  
The Past ◽  
Infectious Disease Research ◽  
History Of ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Health Applications

Abstract This brief report serves as an introduction to a supplement of the Journal of Infectious Diseases entitled “Next-Generation Sequencing (NGS) Technologies to Advance Global Infectious Disease Research.” We briefly discuss the history of NGS technologies and describe how the techniques developed during the past 40 years have impacted our understanding of infectious diseases. Our focus is on the application of NGS in the context of pathogen genomics. Beyond obvious clinical and public health applications, we also discuss the challenges that still remain within this rapidly evolving field.

scholarly journals Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity

2019 ◽  
Author(s):  
Irina Maljkovic Berry ◽  
Melanie C Melendrez ◽  
Kimberly A Bishop-Lilly ◽  
Wiriya Rutvisuttinunt ◽  
Simon Pollett ◽  
...  
Keyword(s):  
Public Health ◽  
Infectious Disease ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Human Pathogens ◽  
Sequencing Platform ◽  
Disease Research ◽  
Infectious Disease Research ◽  
Pathogen Discovery ◽  
Generation Sequencing

Abstract Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.

scholarly journals Guidelines for diagnostic next-generation sequencing

2015 ◽  
Vol 24 (1) ◽  
pp. 2-5 ◽  
Author(s):  
Gert Matthijs ◽  
Erika Souche ◽  
Mariëlle Alders ◽  
Anniek Corveleyn ◽  
Sebastian Eck ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diagnostic Tests ◽  
Human Genetics ◽  
Genetic Disorders ◽  
Next Generation ◽  
The Past ◽  
Supplementary Material ◽  
New Feature ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract We present, on behalf of EuroGentest and the European Society of Human Genetics, guidelines for the evaluation and validation of next-generation sequencing (NGS) applications for the diagnosis of genetic disorders. The work was performed by a group of laboratory geneticists and bioinformaticians, and discussed with clinical geneticists, industry and patients’ representatives, and other stakeholders in the field of human genetics. The statements that were written during the elaboration of the guidelines are presented here. The background document and full guidelines are available as supplementary material. They include many examples to assist the laboratories in the implementation of NGS and accreditation of this service. The work and ideas presented by others in guidelines that have emerged elsewhere in the course of the past few years were also considered and are acknowledged in the full text. Interestingly, a few new insights that have not been cited before have emerged during the preparation of the guidelines. The most important new feature is the presentation of a ‘rating system’ for NGS-based diagnostic tests. The guidelines and statements have been applauded by the genetic diagnostic community, and thus seem to be valuable for the harmonization and quality assurance of NGS diagnostics in Europe.

scholarly journals Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories

2016 ◽  
Vol 54 (12) ◽  
pp. 2857-2865 ◽  
Author(s):  
Amy S. Gargis ◽  
Lisa Kalman ◽  
Ira M. Lubin
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Next Generation ◽  
Standards And Guidelines ◽  
Control Procedures ◽  
Next Generation Sequencing Ngs ◽  
Professional Guidelines ◽  
Generation Sequencing

Clinical microbiology and public health laboratories are beginning to utilize next-generation sequencing (NGS) for a range of applications. This technology has the potential to transform the field by providing approaches that will complement, or even replace, many conventional laboratory tests. While the benefits of NGS are significant, the complexities of these assays require an evolving set of standards to ensure testing quality. Regulatory and accreditation requirements, professional guidelines, and best practices that help ensure the quality of NGS-based tests are emerging. This review highlights currently available standards and guidelines for the implementation of NGS in the clinical and public health laboratory setting, and it includes considerations for NGS test validation, quality control procedures, proficiency testing, and reference materials.

scholarly journals Next-generation sequencing (NGS) methods and their application in clinical microbiology, infectology and epidemiology

2021 ◽  
Vol 18 (4) ◽  
pp. 26-32
Author(s):  
V. M. Mitsura
Keyword(s):  
Next Generation Sequencing ◽  
Personalized Medicine ◽  
Infectious Diseases ◽  
Medical Research ◽  
Clinical Microbiology ◽  
Next Generation ◽  
Basic Principles ◽  
Treatment And Prevention ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

This review presents basic principles and methods of next-generation sequencing (NGS) and discusses a number of the latest papers on the possibilities, principles and stages of NGS, as well as the application of NGS in medical research, particularly, clinical microbiology and infectious diseases, epidemiology. The development of NGS technologies will allow improving the results of diagnostics, treatment and prevention of infectious diseases and opens up new prospects for personalized medicine.

scholarly journals A case of tick-transmitted Q fever in Lishui, China diagnosed by next-generation sequencing

2021 ◽  
Vol 49 (9) ◽  
pp. 030006052110253
Author(s):  
Jinwei Huang ◽  
Rui Wang ◽  
Can Gao ◽  
Yuankai Lü ◽  
Zhuo Cao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Coxiella Burnetii ◽  
Q Fever ◽  
Recurrent Fever ◽  
Next Generation ◽  
Imaging Data ◽  
History Of ◽  
Patient Responses ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Q fever is a zoonotic disease caused by Coxiella burnetii. Most patients have non-specific symptoms at onset. In addition, routine diagnostic tests for C. burnetii are not sensitive, and the bacterium cannot grow in general culture medium. The diagnosis of Q fever therefore poses a challenge. This case study describes a man with a clear history of tick bite who had recurrent fever, pneumonia, and liver damage. Routine tests and bacterial cultures failed to clarify the pathogeny, but laboratory and imaging data suggested infection. After routine tests were exhausted, we detected the presence of C. burnetii in a whole blood sample using next-generation sequencing (NGS). To our knowledge, this is the first report of Q fever associated with Coxiella burnetii detected directly from blood samples in Lishui, China. NGS has revolutionized the diagnosis of infectious diseases, especially those caused by rare or newly discovered pathogens, and patient responses have finally proved its substantial benefits. NGS has important clinical significance for the early diagnosis of chronic Q fever. This proof-of-concept study is worthy of promotion in clinical practice.

scholarly journals A Review of Bioinformatics Model and Computational Software of Next Generation Sequencing

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jalilah Arijah Mohd Kamarudin ◽  
Afnizanfaizal Abdullah ◽  
Roselina Sallehuddin
Keyword(s):  
Next Generation Sequencing ◽  
Review Paper ◽  
Bioinformatics Analysis ◽  
Variant Calling ◽  
Next Generation ◽  
The Past ◽  
Source Type ◽  
Next Generation Sequencing Ngs ◽  
Future Work ◽  
Generation Sequencing

In the past decade it has become increasingly the effort for researcher to surpass the bioinformatics challenges foremost in next generation sequencing (NGS). This review paper gives an overview of the computational software and bioinformatics model that has been used for next generation sequencing. In this paper, the description on functionalities, source type and website of the program or software are provided. These computational software and bioinformatics model are differentiating into three types of bioinformatics analysis stages including alignment, variant calling and filtering and annotation. Besides, we discuss the future work and the development for new bioinformatics tool to be advanced.

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