scholarly journals Human Papillomavirus and the Development of Different Cancers

2016 ◽  
Vol 150 (3-4) ◽  
pp. 185-193 ◽  
Author(s):  
Ge Gao ◽  
David I. Smith
Keyword(s):  
Cervical Cancer ◽  
Squamous Cell Carcinomas ◽  
Human Papillomaviruses ◽  
Whole Genome ◽  
Physical Status ◽  
Cervical Cancers ◽  
Mate Pair ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Human papillomaviruses (HPV) are responsible for the development of almost all cervical cancers. HPV is also found in 85% of anal cancer and in 50% of penile, vulvar, and vaginal cancers, and they are increasingly found in a subset of head and neck cancers, i.e., oropharyngeal squamous cell carcinomas (OPSCC). The model for how HPV causes cancer is derived from several decades of study on cervical cancer, and it is just presumed that this model is not only completely valid for cervical cancer but for all other HPV-driven cancers as well. Next-generation sequencing (NGS) has now provided the necessary tools to characterize genomic alterations in cancer cells and can precisely determine the physical status of HPV in those cells as well. We discuss recent discoveries from different applications of NGS in both cervical cancer and OPSCCs, including whole-genome sequencing and mate-pair NGS. We also discuss what NGS studies have revealed about the different ways that HPV can be involved in cancer formation, specifically comparing cervical cancer and OPSCC.

scholarly journals Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal–oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).

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.

scholarly journals Lack of Conserved miRNA Deregulation in HPV-Induced Squamous Cell Carcinomas

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 764
Author(s):  
Jaroslav Nunvar ◽  
Lucie Pagacova ◽  
Zuzana Vojtechova ◽  
Nayara Trevisan Doimo de Azevedo ◽  
Jana Smahelova ◽  
...  
Keyword(s):  
Squamous Cell ◽  
Mirna Expression ◽  
Hpv Infection ◽  
Squamous Cell Carcinomas ◽  
Human Papillomaviruses ◽  
Hpv Status ◽  
Mirna Expression Level ◽  
Cervical Tumors ◽  
Mirna Deregulation ◽  
Generation Sequencing

Squamous cell carcinomas (SCCs) in the anogenital and head and neck regions are associated with high-risk types of human papillomaviruses (HR-HPV). Deregulation of miRNA expression is an important contributor to carcinogenesis. This study aimed to pinpoint commonly and uniquely deregulated miRNAs in cervical, anal, vulvar, and tonsillar tumors of viral or non-viral etiology, searching for a common set of deregulated miRNAs linked to HPV-induced carcinogenesis. RNA was extracted from tumors and nonmalignant tissues from the same locations. The miRNA expression level was determined by next-generation sequencing. Differential expression of miRNAs was calculated, and the patterns of miRNA deregulation were compared between tumors. The total of deregulated miRNAs varied between tumors of different locations by two orders of magnitude, ranging from 1 to 282. The deregulated miRNA pool was largely tumor-specific. In tumors of the same location, a low proportion of miRNAs were exclusively deregulated and no deregulated miRNA was shared by all four types of HPV-positive tumors. The most significant overlap of deregulated miRNAs was found between tumors which differed in location and HPV status (HPV-positive cervical tumors vs. HPV-negative vulvar tumors). Our results imply that HPV infection does not elicit a conserved miRNA deregulation in SCCs.

scholarly journals Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

2019 ◽  
Vol 24 (2) ◽  
Author(s):  
Anja Berger ◽  
Alexandra Dangel ◽  
Tilmann Schober ◽  
Birgit Schmidbauer ◽  
Regina Konrad ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome ◽  
Next Generation ◽  
Insect Bites ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

scholarly journals Comment from the Editor on the Special Issue “Head and Neck Critical Illness: Basic and Clinical Research Implications”

2019 ◽  
Vol 8 (11) ◽  
pp. 1905
Author(s):  
Hiroyuki Tomita
Keyword(s):  
Head And Neck ◽  
Single Cell Analysis ◽  
Squamous Cell Carcinomas ◽  
Cell Analysis ◽  
Special Issue ◽  
Poor Survival ◽  
Know How ◽  
Oncogenic Mutations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

While oncogenic mutations of head and neck squamous cell carcinomas (HNSCC) in head and neck malignancies are uncommon, analysis using next-generation sequencing (NGS) technologies is growing. Further, single-cell analysis is being developed to overcome cancer cell heterogeneity and improve the poor survival of patients. However, it is important for researchers to know how to use this information to improve patients’ survival.

scholarly journals The Situation of Cervical Cancers in the Context of Female Genital Cancer Clustering and Burden of Disease in Arad County, Romania

2019 ◽  
Vol 8 (1) ◽  
pp. 96 ◽  
Author(s):  
Ana-Liana Tataru ◽  
Gheorghe Furau ◽  
Jompan Afilon ◽  
Cringu Ionescu ◽  
Mihai Dimitriu ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Squamous Cell ◽  
Histopathological Examination ◽  
Squamous Cell Carcinomas ◽  
Point Of View ◽  
Clinical Staging ◽  
Cervical Cancers ◽  
Genital Cancer ◽  
Disability Adjusted Life

Romania has the highest incidence of cervical cancer morbidity and mortality in Europe. This study identifies the major clusters for genital cancers, observes the features of genital and cervical cancer, and determines the extent to which cancer is a contributor to total Disability-Adjusted Life Year (DALY). Spatial analysis used Besag and Newell’s method for genital cancer distribution, prevalence considered Arad County patients records (2008–2017), and DALY was determined according to WHO methodology and GLOBOCAN 2013 data. Diagnosis was established by histopathological examination of diagnostic biopsies or tissues obtained by surgical procedures, followed by clinical staging. 1695 women were recorded with genital cancer. Of these, 14.9% of lesions were in situ (n = 252) and 74.20% of cases were recorded in stage III or IV (n = 1258) (p < 0.0001). Over 90% of cervical cancers were squamous cell carcinomas (n = 728), 33.76% of endometrial cancers were adenocarcinomas in situ (n = 131), 32.42% of ovarian cancers were serous adenocarcinomas (n = 131), and 70.58% of vulvar cancers were squamous cell carcinomas (n = 48) (p < 0.0001). DALY/1000 was 67.2 for genital cancers and 33 for cervical cancers. From the point of view of Romanian women, cervical cancer remains one of the major problems that need to be dealt with and access to optimal treatment proves to be extremely limited.

scholarly journals An Update on Zoonotic Cryptosporidium Species and Genotypes in Humans

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3307
Author(s):  
Una Ryan ◽  
Alireza Zahedi ◽  
Yaoyu Feng ◽  
Lihua Xiao
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Molecular Detection ◽  
Epidemiological Studies ◽  
Cryptosporidium Species ◽  
Transmission Dynamics ◽  
Whole Genome ◽  
Zoonotic Pathogen ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The enteric parasite, Cryptosporidium is a major cause of diarrhoeal illness in humans and animals worldwide. No effective therapeutics or vaccines are available and therefore control is dependent on understanding transmission dynamics. The development of molecular detection and typing tools has resulted in the identification of a large number of cryptic species and genotypes and facilitated our understanding of their potential for zoonotic transmission. Of the 44 recognised Cryptosporidium species and >120 genotypes, 19 species, and four genotypes have been reported in humans with C. hominis, C. parvum, C. meleagridis, C. canis and C. felis being the most prevalent. The development of typing tools that are still lacking some zoonotic species and genotypes and more extensive molecular epidemiological studies in countries where the potential for transmission is highest are required to further our understanding of this important zoonotic pathogen. Similarly, whole-genome sequencing (WGS) and amplicon next-generation sequencing (NGS) are important for more accurately tracking transmission and understanding the mechanisms behind host specificity.

scholarly journals Utility of Whole-Genome Next-Generation Sequencing of Plasma in Identifying Opportunistic Infections in HIV/AIDS

2019 ◽  
Vol 13 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Yang Zhou ◽  
Vagish Hemmige ◽  
Sudeb C. Dalai ◽  
David K. Hong ◽  
Kenneth Muldrew ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Opportunistic Infections ◽  
Case Series ◽  
Whole Genome ◽  
Next Generation ◽  
Invasive Procedures ◽  
First Case ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Hiv Aids

Background:AIDS-associated Opportunistic Infections (OIs) have significant morbidity and mortality and can be diagnostically challenging, requiring invasive procedures as well as a combination of culture and targeted molecular approaches.Objective:We aimed to demonstrate the clinical utility of Next-generation Sequencing (NGS) in pathogen identification; NGS is a maturing technology enabling the detection of miniscule amounts of cell-free microbial DNA from the bloodstream.Methods:We utilized a novel Next-generation Sequencing (NGS) test on plasma samples to diagnose a series of HIV-associated OIs that were diagnostically confirmed through conventional microbial testing.Results:In all cases, NGS test results were available sooner than conventional testing. This is the first case series demonstrating the utility of whole-genome NGS testing to identify OIs from plasma in HIV/AIDS patients.Conclusion:NGS approaches present a clinically-actionable, comprehensive means of diagnosing OIs and other systemic infections while avoiding the labor, expense, and delays of multiple tests and invasive procedures.

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