Next generation sequencing for human papillomavirus genotyping

Arroyo, L. Sara; Smelov, Vitaly; Bzhalava, Davit; Eklund, Carina; Hultin, Emilie; Dillner, Joakim

doi:10.1016/j.jcv.2013.07.013

Cited by 53 publications

(61 citation statements)

References 22 publications

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“…Next-generation techniques, as described herein, can also detect HPV with high sensitivity (20–23, 76), and has further been suggested to be useful for studying HPV-variant epidemiology (76). As these next-generation sequencing methods become increasingly applied in the clinic it will be important to further define the sensitivity and specificity of these methods for HPV detection, and to define which are optimal for clinical use.…”

Section: Clinical Perspectivesmentioning

confidence: 99%

Genomic Landscape of Human Papillomavirus–Associated Cancers

Rusan

Hammerman

2015

Clinical Cancer Research

109

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Recent next-generation sequencing studies have generated a comprehensive overview of the genomic landscape of Human Papillomavirus (HPV)-associated cancers. This review summarizes these findings to provide insight into the tumor biology of these cancers and potential therapeutic opportunities for HPV-driven malignancies. In addition to the tumorigenic properties of the HPV oncoproteins, integration of HPV DNA into the host genome is suggested to be a driver of the neoplastic process. Integration may confer a growth and survival advantage via enhanced expression of viral oncoproteins, alteration of critical cellular genes, and changes in global promoter methylation and transcription. Alteration of cellular genes may lead to loss of function of tumor suppressor genes, enhanced oncogene expression, loss of function of DNA repair genes, or other vital cellular functions. Recurrent integrations in RAD51B, NR4A2, and TP63, leading to aberrant forms of these proteins, are observed in both HPV-positive head and neck squamous cell carcinoma (HNSCC) and cervical carcinoma. Additional genomic alterations, independent of integration events, include recurrent PIK3CA mutations (and aberrations in other members of the PI3K pathway), alterations in receptor tyrosine kinases (primarily FGFR2 and FGFR3 in HPV-positive HNSCC, and ERBB2 in cervical squamous cell carcinoma), and genes in pathways related to squamous cell differentiation and immune responses. A number of the alterations identified are potentially targetable, which may lead to advances in the treatment of HPV-associated cancers.

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Section: Clinical Perspectivesmentioning

confidence: 99%

Genomic Landscape of Human Papillomavirus–Associated Cancers

Rusan

Hammerman

2015

Clinical Cancer Research

109

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“…Nearly two hundred human PVs (HPVs) have been recognized and PV co-infections have been reported using numerous molecular techniques that detect many distinct HPVs genotypes13141516. Several generic PV primer systems have been developed for the detection of HPV types rather than BPV types17.…”

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confidence: 99%

How many papillomavirus species can go undetected in papilloma lesions?

Daudt

Silva

Streck

et al. 2016

Sci Rep

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A co-infection comprising to at least seven papillomavirus (PV) types was detected by next generation sequencing (NGS) of randomly primed rolling circle amplification (RCA) products of a bovine (Bos taurus) papilloma lesion from the Brazilian Amazon region. Six putative new PV types that could not be detected by commonly used PCR protocols were identified. Their overall L1 nucleotide identities were less than 90% compared to described PV species and types. L1 nucleotide BLAST sequence hits showed that each new type was related to Beta, Gamma, Dyokappa, Dyoeta, and Xipapillomavirus, as well as two likely new unclassified genera. Our results show that the employment of NGS is relevant to the detection and characterization of distantly related PV and is of major importance in co-infection studies. This knowledge will help us understand the biology and pathogenesis of PV, as well as contribute to disease control. Moreover, we can also conclude that there are many unknown circulating PVs.

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“…Confirmation of analysis results; sensitivity and specificity calculations. All single identifications made with just one of the two methods were confirmed with a third method using either real time PCR with HPV type-specific primers (HPV6, 16, 18, 31, 33, 35, 39, 42, 43, 45, 51, 52, 56, 58, 66, 68, 90) and SYBR ® Select Master Mix (Thermo Fischer Scientific) or by sequencing of a 450 bp PGMY amplicon [18,19] on a MiSeq (Illumina) platform (HPV30, 32, 40, 53, 54, 62, 67, 73, 74, 82, 87, 89, 91 and 114). Type-specific HPV primers were designed using Primer3 [33] for HPV types: 68 (forward: , reverse: , T A = 54.2°C) and 90 (forward: , reverse: , T A = 51.9°C).…”

Section: Methodsmentioning

confidence: 99%

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

et al. 2017

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Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

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Next generation sequencing for human papillomavirus genotyping

Cited by 53 publications

References 22 publications

Genomic Landscape of Human Papillomavirus–Associated Cancers

Genomic Landscape of Human Papillomavirus–Associated Cancers

How many papillomavirus species can go undetected in papilloma lesions?

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

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