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 Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis

2020 ◽  
Vol 59 (1) ◽  
pp. e00583-20
Author(s):  
Carol Smith ◽  
Tanya A. Halse ◽  
Joseph Shea ◽  
Herns Modestil ◽  
Randal C. Fowler ◽  
...  
Keyword(s):  
Public Health ◽  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Illumina Miseq ◽  
Drug Susceptibility ◽  
Clinical Diagnostics ◽  
Nanopore Sequencing ◽  
Next Generation ◽  
Content Type ◽  
Generation Sequencing

ABSTRACTNext-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the need for specialized staff remain major hurdles for laboratories with limited resources for implementing these technologies. This project aimed to assess the feasibility of using Oxford Nanopore MinION whole-genome sequencing data of Mycobacterium tuberculosis isolates for species identification, in silico spoligotyping, detection of mutations associated with antimicrobial resistance (AMR) to accurately predict drug susceptibility profiles, and phylogenetic analysis to detect transmission between cases. The results were compared prospectively in real time to those obtained with our current clinically validated Illumina MiSeq sequencing assay for M. tuberculosis and phenotypic drug susceptibility testing results when available. Our assessment of 431 sequenced samples over a 32-week period demonstrates that, when using the proper quality controls and thresholds, the MinION can achieve levels of genotyping analysis and phenotypic resistance predictions comparable to those of the Illumina MiSeq at a very competitive cost per sample. Our results indicate that nanopore sequencing can be a suitable alternative to, or complement, currently used sequencing platforms in a clinical setting and has the potential to be widely adopted in public health laboratories in the near future.

scholarly journals Next-Generation Sequencing: From Basic Research to Diagnostics

2009 ◽  
Vol 55 (4) ◽  
pp. 641-658 ◽  
Author(s):  
Karl V Voelkerding ◽  
Shale A Dames ◽  
Jacob D Durtschi
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Basic Research ◽  
Clinical Diagnostics ◽  
Massively Parallel ◽  
Next Generation ◽  
New Paradigm ◽  
The Impact ◽  
Generation Sequencing

Abstract Background: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). Content: This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. Summary: In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.

scholarly journals Erratum to: Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

2017 ◽  
Vol 36 (7) ◽  
pp. 1339-1342
Author(s):  
K. G. Joensen ◽  
A. L. Ø. Engsbro ◽  
O. Lukjancenko ◽  
R. S. Kaas ◽  
O. Lund ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diarrhoeal Disease ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Clinical diagnostic application of metagenomic next-generation sequencing in children with severe pneumonia

2019 ◽  
Author(s):  
Heping Wang ◽  
Zhiwei Lu ◽  
Yaomin Bao ◽  
Yonghong Yang ◽  
Ronald de Groot ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mycoplasma Pneumoniae ◽  
Severe Pneumonia ◽  
Clinical Diagnostics ◽  
Nucleic Acid Amplification ◽  
Direct Immunofluorescence ◽  
Specific Information ◽  
Next Generation ◽  
Blood Tests ◽  
Generation Sequencing

Abstract Background: Pneumonia is one of the most important causes of morbidity and mortality in children. Identification and characterization of pathogens that cause infections are crucial for accurate treatment and accelerated recovery of the patients. However, in most cases the causative agent cannot be identified partly due to the limited spectrum covered by current diagnostics based on nucleic acid amplification. Therefore, in this study we explored the application of metagenomic next-generation sequencing (mNGS) for the diagnosis of children with severe pneumonia. Methods: From April to July 2017, 32 children were hospitalized with severe pneumonia in Shenzhen Children’s Hospital. Blood tests were conducted immediately after hospitalization to assess infection, oropharygeal swabs were collected to identify common pathogens. After bronchoscopy, bronchoalveolar lavage fluids (BALFs) were collected for further pathogen identification using standardized laboratory and mNGS. Results: Blood tests were normal in 3 of the 32 children. In oropharygeal swabs from 5 patients Mycoplasma pneumoniae by qPCR, 27 cases showed negative results for common pathogens. In BALFs we detected 6 cases with Mycoplasma pneumoniae with qPCR, 9 patients with adenovirus by using a Direct Immunofluorescence Assay (DFA) and 4 patients with bacterial infections, as determined by culture, In 3 of the cases a co-infection was detected. In 15 cases no common pathogens were found in BALF samples, using the current diagnostics, while in all the 32 BALFS pathogens were identified using mNGS, including adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, cytomegalovirus andbocavirus. Conclusions: mNGS can increase the sensitivity of detection of the causative pathogens in children with severe pneumonia. In addition, mNGS will give more strain specific information, will help to identify new pathogens and could potentially help to trace and control outbreaks. In this study we have shown that it is feasible to have the results within 24 hours, making the application of mNGS feasible for clinical diagnostics.

scholarly journals Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory

2019 ◽  
Vol 19 ◽  
pp. 100464 ◽  
Author(s):  
Paige Hartman ◽  
Kenneth Beckman ◽  
Kevin Silverstein ◽  
Sophia Yohe ◽  
Matthew Schomaker ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Academic Laboratory ◽  
Generation Sequencing

scholarly journals Diagnostic applications of next generation sequencing: working towards quality standards/Diagnostische Anwendung von Next Generation Sequencing: Auf dem Weg zu Qualitätsstandards

2012 ◽  
Vol 36 (4) ◽  
Author(s):  
Ina Vogl ◽  
Sebastian H. Eck ◽  
Anna Benet-Pagès ◽  
Philipp A. Greif ◽  
Kaimo Hirv ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Genetic ◽  
Quality Criteria ◽  
Quality Standards ◽  
Clinical Diagnostics ◽  
Genetic Diagnostics ◽  
Next Generation ◽  
High Expectations ◽  
Diagnostic Applications ◽  
Generation Sequencing

AbstractOver the past 6 years, next generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. All major NGS technology companies providing commercially available instruments (Roche 454, Illumina, Life Technologies) have recently marketed bench top sequencing instruments with lower throughput and shorter run times, thereby broadening the applications of NGS and opening the technology to the potential use for clinical diagnostics. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry and data analysis need to be overcome. To facilitate the implementation of NGS as a routine method in molecular diagnostics, consistent quality standards need to be developed. Here the authors give an overview of the current standards in protocols and workflows and discuss possible approaches to define quality criteria for NGS in molecular genetic diagnostics.

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