scholarly journals Next-Generation Sequencing and Its Application: Empowering in Public Health Beyond Reality

2019 ◽  
pp. 313-341
Author(s):  
Nidhi Gupta ◽  
Vijay K. Verma
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next-Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1)

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Rebecca J. Hutchins ◽  
Kristy L. Phan ◽  
Adeeba Saboor ◽  
Joseph D. Miller ◽  
Atis Muehlenbachs
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Quality Management ◽  
Process Management ◽  
Quality Management System ◽  
Phase 1 ◽  
Quality System ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Generation Sequencing

ABSTRACT Quality standards as part of an effective quality management system (QMS) are the cornerstone for generating high-quality test results. Next-generation sequencing (NGS) has the potential to improve both clinical diagnostics and public health surveillance efforts in multiple areas, including infectious diseases. However, the laboratories adopting NGS methods face significant challenges due to the complex and modular process design. This document summarizes the first phase of quality system guidance developed by the Centers for Disease Control and Prevention (CDC) NGS Quality Workgroup. The quality system essentials of personnel, equipment, and process management (quality control and validation) were prioritized based on a risk assessment using information gathered from participating CDC laboratories. Here, we present a prioritized QMS framework, including procedures and documentation tools, to assist laboratory implementation and maintenance of quality practices for NGS workflows.

scholarly journals A platform for leveraging next generation sequencing for routine microbiology and public health use

2015 ◽  
Vol 3 (S1) ◽  
Author(s):  
Laura I Rusu ◽  
Kelly L Wyres ◽  
Matthias Reumann ◽  
Carlos Queiroz ◽  
Alexe Bojovschi ◽  
...  
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution

2013 ◽  
Vol 18 (4) ◽  
Author(s):  
J A Carriço ◽  
A J Sabat ◽  
A W Friedrich ◽  
M Ramirez ◽  
Collective on behalf of the ESCMID Study Group
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Molecular Epidemiology ◽  
Next Generation ◽  
Generation Sequencing ◽  
Epidemiology And Public Health

scholarly journals Towards Translational Epidemiology: Next-Generation Sequencing and Phylogeography as Epidemiological Mainstays

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Crystal M. Hepp
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Phylogenetic Analyses ◽  
Federal State ◽  
Next Generation ◽  
Public Health Agencies ◽  
Health Agencies ◽  
Collaborative Activities ◽  
User Friendly ◽  
Generation Sequencing

ABSTRACT Next-generation sequencing, coupled with the development of user-friendly software, has achieved a level of accessibility that is revolutionizing the way we approach epidemiological investigations. We can sequence pathogen genomes and conduct phylogenetic analyses to assess transmission, identify from which country or city a pathogen originated, or which contaminated potluck item resulted in widespread foodborne illness. However, until recently, these types of studies have been rarities, limited to specific investigations usually conducted over the short term. Given the feasibility and realized public health benefits of ascertaining pathogen relationships, federal, state, and county agencies are building their sequencing capacities, either through acquisition of equipment or collaborative activities. In this perspective, I detail research projects that our group collaborates on with county and state public health agencies, where the objective is to identify pathogen source locations with the longer-term goal of implementing proactive interventions.

BPHL SARS-CoV-2 Tiled Amplicon Illumina Sequencing v2

2021 ◽  
Author(s):  
Jason Blanton
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Illumina Sequencing ◽  
Library Preparation ◽  
Next Generation ◽  
Florida Department ◽  
Wet Lab ◽  
Generation Sequencing

This protocol details the Florida Department of Health's Bureau of Public Health Laboratories' (BPHL) wet lab portion of our SARS-CoV-2 next generation sequencing workflow. The method is a tiled amplicon approach using ARTIC V3 primers. The amplicon generation was adapted from the Matteson protocol1. The library preparation is Illumina NexteraXT. Library pooling and normalization were adapted from the Gohl protocol3. This protocol is for loading a MiSeq, but we have had equal success running on iSeqs and NextSeqs as well. Up to 96 libraries can be run on a MiSeq and up to 384 on a NextSeq.

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.

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