Is next-generation sequencing an important tool in HPV subtype diagnosis?

Wood, Henry M.; Bolt, Robert J.; Hunter, Keith D.

doi:10.1586/erm.12.67

Cited by 4 publications

(5 citation statements)

References 19 publications

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“…In addition, reported methods based on PCR-Sanger sequencing generally require prior knowledge of the infecting HPV type since they use HPV type-specific primers for PCR [ 9 , 10 ]. These technical hurdles can be overcome by using massively parallel high-throughput sequencing (or NGS, next-generation sequencing) technologies, which allow sequencing of multiple HPV types and variants in clinical specimens and the identification of minority genetic variants in individual samples [ 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Reported NGS-based methods for HPV detection and typing consisted either in deep sequencing of amplicons obtained from the amplification of highly conserved regions in HPV genome or in the unbiased metagenomics sequencing of whole DNA or RNA from biological samples.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

Lavezzo

Masi

Toppo

et al. 2016

Viruses

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Different human papillomavirus (HPV) types are characterized by differences in tissue tropism and ability to promote cell proliferation and transformation. In addition, clinical and experimental studies have shown that some genetic variants/lineages of high-risk HPV (HR-HPV) types are characterized by increased oncogenic activity and probability to induce cancer. In this study, we designed and validated a new method based on multiplex PCR-deep sequencing of the E6/E7 region of HR-HPV types to characterize HPV intra-type variants in clinical specimens. Validation experiments demonstrated that this method allowed reliable identification of the different lineages of oncogenic HPV types. Advantages of this method over other published methods were represented by its ability to detect variants of all HR-HPV types in a single reaction, to detect variants of HR-HPV types in clinical specimens with multiple infections, and, being based on sequencing of the full E6/E7 region, to detect amino acid changes in these oncogenes potentially associated with increased transforming activity.

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Section: Introductionmentioning

confidence: 99%

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

Lavezzo

Masi

Toppo

et al. 2016

Viruses

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“…The increasing clinical requirements for accurate virus typing are therefore likely to play a fundamental role in how future HPV detection techniques become adopted [17]. NGS can be used to measure viral load and subtype, as well as providing a map of large-scale chromosomal damage [16].…”

Section: Next Generation Sequencing In the Hpv Fieldmentioning

confidence: 99%

“…Although currently more of a research method than a diagnostic assay, as the cost of sequencing decreases, NGS may become a useful technique giving information about genomic integration. The low-coverage genomic sequencing approach will give information about viral load and subtype, as well as genomic copy number patterns, which in turn could suggest whether the disease has a HPV-typical genome or one associated with other etiological factors, and aid clinical decision-making in the future [17]. Future developments are also bound to impact clinical decision-making.…”

Section: Next Generation Sequencing In the Hpv Fieldmentioning

confidence: 99%

“…Future developments are also bound to impact clinical decision-making. The assessment of the transcriptome could not only indicate whether any viral infection is active but also show if the viral integration site disrupted the normal function of neighboring genes [17]. …”

Section: Next Generation Sequencing In the Hpv Fieldmentioning

confidence: 99%

“…In the era of personalized medicine, we can expect that treatments will be increasingly tailored to individual disease, so subtype, integration site, transcriptional activity and subsequent genomic damage may all be taken into account. Applications that might seem unfeasible now will probably soon be commonplace [17]. …”

Section: Next Generation Sequencing In the Hpv Fieldmentioning

confidence: 99%

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Role of Next-Generation Sequencing in Understanding the Interactions between Human Papillomavirus and the Cervicovaginal Microbiome

Cervantes

Hong

2013

Gynecol Obstet Invest

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The applications of next-generation sequencing in the field of human papillomavirus and associated neoplasias have extended beyond the accurate genotyping of human papillomavirus types. Next-generation sequencing is able to provide important information on the interactions of the cervicovaginal microbiome and environment with the virus, and the role that these factors play on its transmission and persistence. The advances in sequencing technologies have greatly contributed to the current knowledge of human cervicovaginal microbiome in recent years, allowing the assessment of microbiome variability between species, individuals and populations.

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Utility of high-throughput DNA sequencing in the study of the human papillomaviruses

et al. 2017

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The Papillomaviridae family is probably the most diverse group of viruses that affect vertebrates. The study of the relationship between infection by certain types of human papillomavirus (HPV) and the development of neoplastic epithelial lesions is of particular interest because of the high prevalence of HPV-related carcinomas in populations of developing countries. To understand the mechanisms of infection and their association with different clinical manifestations, molecular tools play an important role in the description of new types of HPV, the characterization of effector properties of the viral factors, the specific diagnosis and monitoring of HPV types, and the alteration patterns at genetic level in the host. Technological advances in the field of DNA sequencing have led to the development of different next-generation sequencing systems, allowing obtaining a large amount of data and broadening the applications to study viral diseases. In this review, we summarize the main approaches and their perspectives where the use of massively parallel sequencing has been proved as a useful tool in the research of the HPV infection.

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Is next-generation sequencing an important tool in HPV subtype diagnosis?

Cited by 4 publications

References 19 publications

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

Role of Next-Generation Sequencing in Understanding the Interactions between Human Papillomavirus and the Cervicovaginal Microbiome

Utility of high-throughput DNA sequencing in the study of the human papillomaviruses

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