scholarly journals A Multiplexed, Next Generation Sequencing Platform for High-Throughput Detection of SARS-CoV-2

2020 ◽  
Author(s):  
Jeff Wrana ◽  
Marie-Ming Aynaud ◽  
J Hernandez ◽  
Seda Barutcu ◽  
Ulrich Braunschweig ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Disease Transmission ◽  
Large Scale ◽  
Disease Onset ◽  
Clinical Diagnostics ◽  
Disease Spread ◽  
Contact Tracing ◽  
Next Generation ◽  
Viral Loads ◽  
Generation Sequencing

Abstract Population scale sweeps of viral pathogens, such as SARS-CoV-2, that incorporate large numbers of asymptomatic or mild symptom patients present unique challenges for public health agencies trying to manage both travel and local spread. Physical distancing is the current major strategy to suppress spread of the disease, but with enormous socio-economic costs. However, modelling and studies in isolated jurisdictions suggest that active population surveillance through systematic molecular diagnostics, combined with contact tracing and focused quarantining can significantly suppress disease spread and has significantly impacted disease transmission rates, the number of infected people, and prevented saturation of the healthcare system. However, reliable systems allowing for parallel testing of 10-100,000’s of patients in larger urban environments have not yet been employed. Here we describe “COVID-19 screening using Systematic Parallel Analysis of RNA coupled to Sequencing” (C19-SPAR-Seq), a scalable, multiplexed, readily automated next generation sequencing (NGS) platform that is capable of analyzing tens of thousands of COVID-19 patient samples in a single instrument run. To address the strict requirements in clinical diagnostics for control of assay parameters and output, we employed a control-based Precision-Recall and predictive Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of over 600 patients performed with a specificity of 100% and sensitivity of 91% on samples with low viral loads and a sensitivity of > 95% on high viral loads associated with disease onset and peak transmissibility. Our study thus establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.

scholarly journals A Multiplexed, Next Generation Sequencing Platform for High-Throughput Detection of SARS-CoV-2

2020 ◽  
Author(s):  
Marie-Ming Aynaud ◽  
J. Javier Hernandez ◽  
Seda Barutcu ◽  
Ulrich Braunschweig ◽  
Kin Chan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Disease Transmission ◽  
Large Scale ◽  
Disease Onset ◽  
Clinical Diagnostics ◽  
Disease Spread ◽  
Contact Tracing ◽  
Next Generation ◽  
Viral Loads ◽  
Generation Sequencing

AbstractPopulation scale sweeps of viral pathogens, such as SARS-CoV-2, that incorporate large numbers of asymptomatic or mild symptom patients present unique challenges for public health agencies trying to manage both travel and local spread. Physical distancing is the current major strategy to suppress spread of the disease, but with enormous socio-economic costs. However, modelling and studies in isolated jurisdictions suggest that active population surveillance through systematic molecular diagnostics, combined with contact tracing and focused quarantining can significantly suppress disease spread1-3 and has significantly impacted disease transmission rates, the number of infected people, and prevented saturation of the healthcare system4-7. However, reliable systems allowing for parallel testing of 10-100,000’s of patients in larger urban environments have not yet been employed. Here we describe “COVID-19 screening using Systematic Parallel Analysis of RNA coupled to Sequencing” (C19-SPAR-Seq), a scalable, multiplexed, readily automated next generation sequencing (NGS) platform8 that is capable of analyzing tens of thousands of COVID-19 patient samples in a single instrument run. To address the strict requirements in clinical diagnostics for control of assay parameters and output, we employed a control-based Precision-Recall and predictive Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of over 600 patients performed with a specificity of 100% and sensitivity of 91% on samples with low viral loads and a sensitivity of > 95% on high viral loads associated with disease onset and peak transmissibility. Our study thus establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.

scholarly journals A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Marie-Ming Aynaud ◽  
J. Javier Hernandez ◽  
Seda Barutcu ◽  
Ulrich Braunschweig ◽  
Kin Chan ◽  
...  
Keyword(s):  
Large Scale ◽  
Disease Onset ◽  
Clinical Diagnostics ◽  
Viral Pathogens ◽  
Sequencing Platform ◽  
Viral Loads ◽  
Quality Control Metrics ◽  
High Throughput Detection ◽  
Automated Platform ◽  
Generation Sequencing

AbstractPopulation scale sweeps of viral pathogens, such as SARS-CoV-2, require high intensity testing for effective management. Here, we describe “Systematic Parallel Analysis of RNA coupled to Sequencing for Covid-19 screening” (C19-SPAR-Seq), a multiplexed, scalable, readily automated platform for SARS-CoV-2 detection that is capable of analyzing tens of thousands of patient samples in a single run. To address strict requirements for control of assay parameters and output demanded by clinical diagnostics, we employ a control-based Precision-Recall and Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of several hundred patients performs with a specificity of 100% and sensitivity of 91% on samples with low viral loads, and a sensitivity of >95% on high viral loads associated with disease onset and peak transmissibility. This study establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.

scholarly journals Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

2020 ◽  
Author(s):  
Jonathan Foox ◽  
Scott W. Tighe ◽  
Charles M. Nicolet ◽  
Justin M. Zook ◽  
Marta Byrska-Bishop ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Large Scale ◽  
Error Rates ◽  
Clinical Diagnostics ◽  
Small Scale ◽  
Next Generation ◽  
Oxford Nanopore ◽  
Sequencing Platforms ◽  
Generation Sequencing

AbstractMassively parallel DNA sequencing is a critical tool for genomics research and clinical diagnostics. Here, we describe the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Phase II Study to measure quality and reproducibility of DNA sequencing. Replicates of human and bacterial reference DNA samples were generated across multiple sequencing platforms, including well-established technologies such as Illumina, ThermoFisher Ion Torrent, and Pacific Biosciences, as well as emerging technologies such as BGI, Genapsys, and Oxford Nanopore. A total of 202 datasets were generated to investigate the performance of a total of 16 sequencing platforms, including mappability of reads, coverage and error rates in difficult genomic regions, and detection of small-scale polymorphisms and large-scale structural variants. This study provides a comprehensive baseline resource for continual benchmarking as chemistries, methods, and platforms evolve for DNA sequencing.

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

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 NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0139868 ◽  
Author(s):  
Mohan A. V. S. K. Katta ◽  
Aamir W. Khan ◽  
Dadakhalandar Doddamani ◽  
Mahendar Thudi ◽  
Rajeev K. Varshney
Keyword(s):  
Quality Control ◽  
Next Generation Sequencing ◽  
Large Scale ◽  
Control Analysis ◽  
Next Generation ◽  
Quality Control Analysis ◽  
Illumina Data ◽  
Generation Sequencing

scholarly journals Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis

2021 ◽  
Vol 9 (11) ◽  
pp. 2309
Author(s):  
Wang-Da Liu ◽  
Ting-Yu Yen ◽  
Po-Yo Liu ◽  
Un-In Wu ◽  
Prerana Bhan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hematologic Malignancies ◽  
Blood Cultures ◽  
Diagnostic Methods ◽  
Next Generation ◽  
Viral Loads ◽  
A Prospective Study ◽  
Positive Results ◽  
Serology Testing ◽  
Generation Sequencing

Background: Sepsis remains a common but fatal complication among patients with immune suppression. We aimed to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in patients with hematologic malignancies. Methods: We performed a prospective study from June 2019 to December 2019. Adult patients with hematologic malignancies and a clinical diagnosis of sepsis were enrolled. Conventional diagnostic methods included blood cultures, serum galactomannan for Aspergillus, cryptococcal antigen and cytomegalovirus (CMV) viral loads. Blood samples for mNGS were collected within 24 h after hypotension developed. Results: Of 24 patients enrolled, mNGS and conventional diagnostic methods (blood cultures, serology testing and virus RT-PCR) reached comparable positive results in 9 cases. Of ten patients, mNGS was able to identify additional pathogens compared with conventional methods; most of the pathogens were virus. Conclusion: Our results show that mNGS may serve as adjunctive diagnostic tool for the identification of pathogens of hematologic patients with clinically sepsis.

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.

Sign in / Sign up

Export Citation Format

Share Document