scholarly journals Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells

2017 ◽  
Vol 28 (3) ◽  
pp. 148-162 ◽  
Author(s):  
Magalie Penaud-Budloo ◽  
Emilie Lecomte ◽  
Aurélien Guy-Duché ◽  
Sylvie Saleun ◽  
Alain Roulet ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Viral Vectors ◽  
Insect Cells ◽  
Next Generation ◽  
Accurate Identification ◽  
Generation Sequencing ◽  
Identification And Quantification

scholarly journals Pulmonary Targeting of Adeno-associated Viral Vectors by Next-generation Sequencing-guided Screening of Random Capsid Displayed Peptide Libraries

2016 ◽  
Vol 24 (6) ◽  
pp. 1050-1061 ◽  
Author(s):  
Jakob Körbelin ◽  
Timo Sieber ◽  
Stefan Michelfelder ◽  
Lars Lunding ◽  
Elmar Spies ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Viral Vectors ◽  
Peptide Libraries ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1023
Author(s):  
Hendrick Gao-Min Lim ◽  
Shih-Hsin Hsiao ◽  
Yuan-Chii Gladys Lee
Keyword(s):  
Next Generation Sequencing ◽  
Influenza A ◽  
Swine Flu ◽  
Identification Algorithm ◽  
Next Generation ◽  
Cloud Platform ◽  
Sequencing Data ◽  
Accurate Identification ◽  
Robust Identification ◽  
Generation Sequencing

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently become a novel pandemic event following the swine flu that occurred in 2009, which was caused by the influenza A virus (H1N1 subtype). The accurate identification of the huge number of samples during a pandemic still remains a challenge. In this study, we integrate two technologies, next-generation sequencing and cloud computing, into an optimized workflow version that uses a specific identification algorithm on the designated cloud platform. We use 182 samples (92 for COVID-19 and 90 for swine flu) with short-read sequencing data from two open-access datasets to represent each pandemic and evaluate our workflow performance based on an index specifically created for SARS-CoV-2 or H1N1. Results show that our workflow could differentiate cases between the two pandemics with a higher accuracy depending on the index used, especially when the index that exclusively represented each dataset was used. Our workflow substantially outperforms the original complete identification workflow available on the same platform in terms of time and cost by preserving essential tools internally. Our workflow can serve as a powerful tool for the robust identification of cases and, thus, aid in controlling the current and future pandemics.

scholarly journals Next-Generation Sequencing for Pathogen Identification in Infected Foot Ulcers

2021 ◽  
Vol 6 (3) ◽  
pp. 247301142110269
Author(s):  
Yoonjung Choi ◽  
Eimi Oda ◽  
Olivia Waldman ◽  
Thomas Sajda ◽  
Christopher Beck ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnostic ◽  
Diagnostic Study ◽  
Foot And Ankle ◽  
Next Generation ◽  
Accurate Identification ◽  
Conventional Culture ◽  
Corynebacterium Striatum ◽  
Standard Culture ◽  
Generation Sequencing

Background: Accurate identification of primary pathogens in foot infections remains challenging due to the diverse microbiome. Conventional culture may show false-positive or false-negative growth, leading to ineffective postoperative antibiotic treatment. Next-generation sequencing (NGS) has been explored as an alternative to standard culture in orthopedic infections. NGS is highly sensitive and can detect an entire bacterial genome along with genes conferring antibiotic resistance in a given sample. We investigated the potential use of NGS for accurate identification and quantification of microbes in infected diabetic foot ulcer (DFU). We hypothesize that NGS will aid identification of dominant pathogen and provide a more complete profile of microorganisms in infected DFUs compared to the standard culture method. Methods: Data were prospectively collected from 30 infected DFU patients who underwent operative treatment by a fellowship-trained orthopedic foot and ankle surgeon from October 2018 to September 2019. The average age of the patient was 60.4 years. Operative procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-the-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Concordance between the standard culture and NGS was assessed. Results: In 29 of 30 patients, pathogens were identified by both NGS and culture, with a concordance rate of 70%. In standard culture, Staphylococcus aureus (58.6%) was the most common pathogen, followed by coagulase-negative Staphylococcus (24.1%), Corynebacterium striatum (17.2%), and Enterococcus faecalis (17.2%). In NGS, Finegoldia magna (44.8%) was the most common microorganism followed by S. aureus (41.4%), and Anaerococcus vaginalis (24.1%). On average, NGS revealed 5.1 (range, 1-11) pathogens in a given sample, whereas culture revealed 2.6 (range, 1-6) pathogens. Conclusion: NGS is an emerging molecular diagnostic method of microbial identification in orthopedic infection. It frequently provides different profiles of microorganisms along with antibiotic-resistant gene information compared to conventional culture in polymicrobial foot infection. Clinical use of NGS for management of foot and ankle infections warrants further investigation. Level of Evidence: Level II, diagnostic study.

Survey study of barriers to evidence-based decision-making in oncology care using next-generation sequencing.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e18757-e18757
Author(s):  
Elizabeth A. Szamreta ◽  
Allysen Kaminski ◽  
Ruchit Shah ◽  
Ning Ning ◽  
Jyoti Aggarwal ◽  
...  
Keyword(s):  
Decision Making ◽  
Next Generation Sequencing ◽  
Clinical Utility ◽  
Online Survey ◽  
Survey Study ◽  
Next Generation ◽  
Efficient Technology ◽  
Accurate Identification ◽  
Cross Sectional ◽  
Generation Sequencing

e18757 Background: Next-generation sequencing (NGS) has the potential to accelerate precision medicine in oncology by informing efficient and improved clinical treatment decision-making. However, discussions on the utility of NGS in clinical practice are ongoing. This survey study examined clinical utility barriers to adoption of NGS into oncologic care. Methods: A cross-sectional online survey was sent to a nationally representative sample of oncologists/hematologists, surgeons, and pathologists (N=201). The survey gathered information on physician demographics, practice characteristics, perceived barriers to NGS testing, and potential strategies for increasing adoption. Results: Almost all physicians in the sample (99.5%) reported using NGS. Physicians reported the following aspects of NGS as the most valuable: ability to guide decision-making (73.1%), more accurate identification of corresponding treatment (56.7%), comprehensive genomic coverage (54.2%), efficient technology with faster turnaround time (49.8%), and more accurate diagnosis or prognosis (41.3%). Physicians reported that NGS results guided treatment decisions for 63% of patients (Range: 2% - 100%). Over 85% of physicians reported that confidence in interpreting results and availability of clinical guidelines were important in undertaking NGS. Correspondingly, limited evidence of clinical utility was a top barrier to testing (80.1%), with pathologists and surgeons more likely than oncologists/hematologists to consider this. Overall, 76% of physicians shared that strategies to alleviate these clinical utility barriers included increased evidence, standardized guidelines, and interpretation support. Conclusions: Given the high uptake of NGS testing in this physician sample, but the lower rates of application of test results to guide treatment, the clinical impact of NGS may not be fully optimized. This discrepancy highlights the ongoing need for real-world evidence to better understand and further optimize the evolving role of NGS in the context of the overall management of the cancer patient. [Table: see text]

scholarly journals Detection of aerobe–anaerobe mixed infection by metagenomic next-generation sequencing in an adult suffering from descending necrotizing mediastinitis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Duan ◽  
Chuncheng Zhang ◽  
Xiaoshuang Che ◽  
Juanjuan Fu ◽  
Feng Pang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mixed Infection ◽  
Clinical Laboratory ◽  
High Sensitivity ◽  
Future Trend ◽  
Descending Necrotizing Mediastinitis ◽  
Next Generation ◽  
Accurate Identification ◽  
Drainage Fluid ◽  
Generation Sequencing

Abstract Background Descending necrotizing mediastinitis (DNM) is one of the most virulent forms of mediastinitis. The main causes of high mortality in DNM are believed to stem from difficulty and delay in the diagnosis. Fast and accurate identification of pathogens is important for the treatment of these patients. Metagenomics next-generation sequencing (mNGS) is a powerful tool to identify all kinds of pathogens, especially for rare and complex infections. Case presentation A 64-year-old male patient was admitted to the intensive care unit (ICU) with unconsciousness, dyspnea, and swelling in the mandible and neck. Computed tomography (CT) scan results combined with clinical laboratory examination indicated DNM. Vancomycin and imipenem were used, and vacuum sealing drainage was applied for debridement and drainage of the infected area. The positive mNGS results of drainage fluid confirmed the presence of mixed infection caused by Streptococcus anginosus, Prevotella oris, and several other anaerobes. The antibiotics were adjusted to piperacillin/tazobactam and tinidazole according to the mNGS results and antimicrobial susceptibility testing of cultured pathogens. After 11 days of antibiotic therapy, the infection symptoms of the neck and mediastinum improved, and the patient was transferred out of the ICU on the 26th day after negative result of drainage fluid culture. Conclusion This case suggested that mNGS is a promising technology for precise and fast pathogens identification with high sensitivity, which may guide the diagnosis of infectious diseases in the future trend.

scholarly journals Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

2018 ◽  
Author(s):  
Sergey Knyazev ◽  
Viachaslau Tsyvina ◽  
Anupama Shankar ◽  
Andrew Melnyk ◽  
Alexander Artyomenko ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Treatment Plan ◽  
Sequencing Error ◽  
Next Generation ◽  
Accurate Identification ◽  
Detection And Identification ◽  
Consistent Performance ◽  
Sequencing Platforms ◽  
Generation Sequencing

ABSTRACTRapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. Therefore, early detection and identification of minority viral haplotypes may help to promptly adjust the patient's treatment plan preventing potential disease complications. Minority haplotypes can be identified using next-generation sequencing (NGS), but sequencing noise hinders accurate identification. The elimination of sequencing noise is a non-trivial task that still remains open. Here we propose CliqueSNV based on extracting pairs of statistically linked mutations from noisy reads. This effectively reduces sequencing noise and enables identifying minority haplotypes with the frequency below the sequencing error rate. We comparatively assess the performance of CliqueSNV using an in vitro mixture of nine haplotypes that were derived from the mutation profile of an existing HIV patient. We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms.

Sign in / Sign up

Export Citation Format

Share Document