scholarly journals Evaluation of TypeSeq, a Novel High-Throughput, Low-Cost, Next-Generation Sequencing-Based Assay for Detection of 51 Human Papillomavirus Genotypes

2019 ◽  
Vol 220 (10) ◽  
pp. 1609-1619 ◽  
Author(s):  
Sarah Wagner ◽  
David Roberson ◽  
Joseph Boland ◽  
Aimée R Kreimer ◽  
Meredith Yeager ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Vaccine Efficacy ◽  
Linear Array ◽  
Human Papillomaviruses ◽  
Next Generation ◽  
Hpv Genotyping ◽  
Positive Agreement ◽  
Generation Sequencing

AbstractBackgroundHuman papillomaviruses (HPV) cause over 500 000 cervical cancers each year, most of which occur in low-resource settings. Human papillomavirus genotyping is important to study natural history and vaccine efficacy. We evaluated TypeSeq, a novel, next-generation, sequencing-based assay that detects 51 HPV genotypes, in 2 large international epidemiologic studies.MethodsTypeSeq was evaluated in 2804 cervical specimens from the Study to Understand Cervical Cancer Endpoints and Early Determinants (SUCCEED) and in 2357 specimens from the Costa Rica Vaccine Trial (CVT). Positive agreement and risks of precancer for individual genotypes were calculated for TypeSeq in comparison to Linear Array (SUCCEED). In CVT, positive agreement and vaccine efficacy were calculated for TypeSeq and SPF10-LiPA.ResultsWe observed high overall and positive agreement for most genotypes between TypeSeq and Linear Array in SUCCEED and SPF10-LiPA in CVT. There was no significant difference in risk of precancer between TypeSeq and Linear Array in SUCCEED or in estimates of vaccine efficacy between TypeSeq and SPF10-LiPA in CVT.ConclusionsThe agreement of TypeSeq with Linear Array and SPF10-LiPA, 2 well established standards for HPV genotyping, demonstrates its high accuracy. TypeSeq provides high-throughput, affordable HPV genotyping for world-wide studies of cervical precancer risk and of HPV vaccine efficacy.

scholarly journals Development of the TypeSeq Assay for Detection of 51 Human Papillomavirus Genotypes by Next-Generation Sequencing

2019 ◽  
Vol 57 (5) ◽  
Author(s):  
Sarah Wagner ◽  
David Roberson ◽  
Joseph Boland ◽  
Meredith Yeager ◽  
Michael Cullen ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Analytical Sensitivity ◽  
Next Generation ◽  
Perfect Agreement ◽  
Hpv Genotyping ◽  
Wide Range ◽  
Positive Agreement ◽  
Generation Sequencing ◽  
Multiple Type

ABSTRACTWe have developed a new human papillomavirus (HPV) genotyping assay for detection of 51 HPV genotypes by next-generation sequencing (NGS). The TypeSeq assay consists of 3 PCR steps that equalize viral load and each type’s amplicon copies prior to genotyping by NGS, thereby maximizing multiple-type sensitivity with minimal sequencing reads. The analytical sensitivity of the TypeSeq assay is 10 copies per reaction for 49 of the 51 types, including 13 high-risk (HR) types. We tested 863 clinical cervical specimens previously evaluated with the Roche Linear Array HPV genotyping test (LA). TypeSeq achieved 94.4% positive agreement with LA for detection of any HR type. Positive agreement was 91.4% and 85.5% for HPV16 and HPV18, respectively. Low-risk (LR) types ranged from 40.0% positive agreement (HPV83) to 90.9% (HPV69). Our unique approach to HPV amplification achieved a multiple-type sensitivity comparable to that of LA, with 83.9% and 84.2% of specimens positive for multiple HPV types by TypeSeq or LA, respectively. A total of 48.2% of specimens showed perfect agreement for all 37 types common to both assays. The simplicity of our open-source TypeSeq assay allows for high-throughput yet scalable processing, with a single technician able to process up to 768 specimens within 3 days. By leveraging NGS sample multiplexing capabilities, the per-sample labor requirements are greatly reduced compared to those of traditional genotyping methods. These features and the broad spectrum of detectable types make TypeSeq highly suitable for a wide range of applications.

scholarly journals Human papillomavirus genotyping by Linear Array and Next-Generation Sequencing in cervical samples from Western Mexico

2015 ◽  
Vol 12 (1) ◽  
Author(s):  
María Guadalupe Flores-Miramontes ◽  
Luis Alberto Torres-Reyes ◽  
Liliana Alvarado-Ruíz ◽  
Salvador Angel Romero-Martínez ◽  
Verenice Ramírez-Rodríguez ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Linear Array ◽  
Next Generation ◽  
Western Mexico ◽  
Generation Sequencing

scholarly journals Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array

2017 ◽  
Vol 14 (1) ◽  
Author(s):  
Rebecca G. Nowak ◽  
Nicholas P. Ambulos ◽  
Lisa M. Schumaker ◽  
Trevor J. Mathias ◽  
Ruth A. White ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
High Risk ◽  
Linear Array ◽  
Ion Torrent ◽  
Next Generation ◽  
Generation 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 Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay

2021 ◽  
Vol 2 (1) ◽  
pp. 29-41
Author(s):  
Giorgia Acquaviva ◽  
Michela Visani ◽  
Viviana Sanza ◽  
Antonio De Leo ◽  
Thais Maloberti ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Turnaround Time ◽  
Hpv Infection ◽  
Human Papillomaviruses ◽  
Next Generation ◽  
Hybrid Capture ◽  
Capture Assay ◽  
Anogenital Area ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

(1) Background: Human papillomaviruses (HPVs) are known to be related to the development of about 5% of all human cancers. The clinical relevance of HPV infection has been deeply investigated in carcinomas of the oropharyngeal area, uterine cervix, and anogenital area. To date, several different methods have been used for detecting HPV infection. The aim of the present study was to compare three different methods for the diagnosis of the presence of the HPV genome. (2) Methods: A total of 50 samples were analyzed. Twenty-five of them were tested using both next generation sequencing (NGS) and VisionArray® technology, the other 25 were tested using Hybrid Capture (HC) II assay and VisionArray® technology. (3) Results: A substantial agreement was obtained using NGS and VisionArray® (κ = 0.802), as well as between HC II and VisionArray® (κ = 0.606). In both analyses, the concordance increased if only high risk HPVs I(HR-HPVs) were considered as “positive”. (4) Conclusions: Our data highlighted the importance of technical choice in HPV characterization, which should be guided by the clinical aims, costs, starting material, and turnaround time for results.

Comparison of three human papillomavirus DNA detection methods: Next generation sequencing, multiplex-PCR and nested-PCR followed by Sanger based sequencing

2015 ◽  
Vol 88 (5) ◽  
pp. 888-894 ◽  
Author(s):  
Allex Jardim da Fonseca ◽  
Renata Silva Galvão ◽  
Angelica Espinosa Miranda ◽  
Luiz Carlos de Lima Ferreira ◽  
Zigui Chen
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Multiplex Pcr ◽  
Nested Pcr ◽  
Dna Detection ◽  
Detection Methods ◽  
Next Generation ◽  
Papillomavirus Dna ◽  
Generation Sequencing

scholarly journals Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies

2012 ◽  
Vol 37 (5) ◽  
pp. 811-820 ◽  
Author(s):  
Rajeev K Varshney ◽  
Himabindu Kudapa ◽  
Manish Roorkiwal ◽  
Mahendar Thudi ◽  
Manish K Pandey ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Molecular Breeding ◽  
Next Generation ◽  
Legume Crops ◽  
Generation Sequencing ◽  
Semi Arid

HPV genotypes detected by linear array and next-generation sequencing in anal samples from HIV positive men who have sex with men in Mexico

2018 ◽  
Vol 163 (4) ◽  
pp. 925-935 ◽  
Author(s):  
Luz A. González-Hernández ◽  
María G. Flores-Miramontes ◽  
Adriana Aguilar-Lemarroy ◽  
Krissya S. Quintanilla-Peña ◽  
Fabiola L. Martin-Amaya-Barajas ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Linear Array ◽  
Hiv Positive ◽  
Next Generation ◽  
Hpv Genotypes ◽  
Sex With Men ◽  
Generation Sequencing ◽  
Hiv Positive Men

scholarly journals Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Wells W. Wu ◽  
Je-Nie Phue ◽  
Chun-Ting Lee ◽  
Changyi Lin ◽  
Lai Xu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Library Preparation ◽  
Next Generation ◽  
Generation Sequencing
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