scholarly journals Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study

BMJ Open ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. e025129 ◽  
Author(s):  
Carmen Lía Murall ◽  
Massilva Rahmoun ◽  
Christian Selinger ◽  
Monique Baldellou ◽  
Claire Bernat ◽  
...  
Keyword(s):  
Natural History ◽  
Young Women ◽  
Statistical Power ◽  
Human Genetics ◽  
Human Papillomaviruses ◽  
Vaginal Microbiota ◽  
Chronic Infections ◽  
Reference Number ◽  
Hpv Status ◽  
Registration Number

IntroductionHuman papillomaviruses (HPVs) are responsible for one-third of all cancers caused by infections. Most HPV studies focus on chronic infections and cancers, and we know little about the early stages of the infection. Our main objective is to better understand the course and natural history of cervical HPV infections in healthy, unvaccinated and vaccinated, young women, by characterising the dynamics of various infection-related populations (virus, epithelial cells, vaginal microbiota and immune effectors). Another objective is to analyse HPV diversity within hosts, and in the study population, in relation to co-factors (lifestyle characteristics, vaccination status, vaginal microbiota, human genetics).Methods and analysisThe PAPCLEAR study is a single center longitudinal study following 150 women, aged 18–25 years, for up to 2 years. Visits occur every 2 or 4 months (depending on HPV status) during which several variables are measured, such as behaviours (via questionnaires), vaginal pH, HPV presence and viral load (via qPCR), local concentrations of cytokines (via MesoScale Discovery technology) and immune cells (via flow cytometry). Additional analyses are outsourced, such as titration of circulating anti-HPV antibodies, vaginal microbiota sequencing (16S and ITS1 loci) and human genotyping. To increase the statistical power of the epidemiological arm of the study, an additional 150 women are screened cross-sectionally. Finally, to maximise the resolution of the time series, participants are asked to perform weekly self-samples at home. Statistical analyses will involve classical tools in epidemiology, genomics and virus kinetics, and will be performed or coordinated by the Centre National de la Recherche Scientifique (CNRS) in Montpellier.Ethics and disseminationThis study has been approved by the Comité de Protection des Personnes Sud Méditerranée I (reference number 2016-A00712-49); by the Comité Consultatif sur le Traitement de l’Information en matière de Recherche dans le domaine de la Santé (reference number 16.504); by the Commission Nationale Informatique et Libertés (reference number MMS/ABD/AR1612278, decision number DR-2016–488) and by the Agence Nationale de Sécurité du Médicament et des Produits de Santé (reference 20160072000007). Results will be published in preprint servers, peer-reviewed journals and disseminated through conferences.Trial registration numberNCT02946346; Pre-results.

Vaginal microbiota composition and association with prevalent Chlamydia trachomatis infection: a cross-sectional study of young women attending a STI clinic in France

2018 ◽  
Vol 94 (8) ◽  
pp. 616-618 ◽  
Author(s):  
Jeanne Tamarelle ◽  
Bertille de Barbeyrac ◽  
Isabelle Le Hen ◽  
Anne Thiébaut ◽  
Cécile Bébéar ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Young Women ◽  
Statistical Power ◽  
Cross Sectional Study ◽  
Vaginal Microbiota ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Sectional Study ◽  
Cross Sectional

ObjectivesNew molecular techniques have allowed describing groups of bacterial communities in the vagina (community state types (CST)) that could play an important role in Chlamydia trachomatis (CT) infection. Our aim was to describe the distribution of CST in a population of young women in France.MethodsA cross-sectional study was carried out in June 2015 among anonymous young women attending a STI clinic in Bordeaux, France. Participants provided a vaginal sample for CT screening and sociodemographic data. CT was diagnosed using the Aptima-combo 2 transcription-mediated-amplification assay. Vaginal microbiota composition was characterised using 16S rRNA gene amplicon sequencing.ResultsMicrobiota composition and CT status were available for 132 women. CST dominated by Lactobacillus crispatus (CST-I), L. iners (CST-III) and a diversity of anaerobes (CST-IV) represented 37.1%, 38.6% and 22.0% of the sample, respectively. Twenty-one out of 132 women were CT positive. Proportions of CT-positive women were higher for samples belonging to CST-III (21.6%) and CST-IV (17.2%) than to CST-I (8.2%).ConclusionsFive CST were found in 132 young women from a STI clinic in France. These CSTs were not significantly associated with CT but higher proportions of CT-positive women were found in CST-III and CST-IV, consistent with a previous study in the Netherlands. Though our study lacked statistical power and was cross-sectional, it is a necessary first step to understand the structure of the vaginal microbiota in French women with or without infection before performing in-depth longitudinal studies.

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 Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

2018 ◽  
Author(s):  
Allison A. Regier ◽  
Yossi Farjoun ◽  
David Larson ◽  
Olga Krasheninina ◽  
Hyun Min Kang ◽  
...  
Keyword(s):  
Data Processing ◽  
Genome Sequencing ◽  
Statistical Power ◽  
Human Genetics ◽  
Variant Calling ◽  
Joint Analysis ◽  
Sequencing Analysis ◽  
Batch Effects ◽  
Many Sources ◽  
Genomic Regions

AbstractHundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years to interrogate a broad range of traits, across diverse populations. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size and statistical power for trait mapping, and will enable studies of genome biology, population genetics and genome function at unprecedented scale. A central challenge for joint analysis is that different WGS data processing and analysis pipelines cause substantial batch effects in combined datasets, necessitating computationally expensive reprocessing and harmonization prior to variant calling. This approach is no longer tenable given the scale of current studies and data volumes. Here, in a collaboration across multiple genome centers and NIH programs, we define WGS data processing standards that allow different groups to produce “functionally equivalent” (FE) results suitable for joint variant calling with minimal batch effects. Our approach promotes broad harmonization of upstream data processing steps, while allowing for diverse variant callers. Importantly, it allows each group to continue innovating on data processing pipelines, as long as results remain compatible. We present initial FE pipelines developed at five genome centers and show that they yield similar variant calling results – including single nucleotide (SNV), insertion/deletion (indel) and structural variation (SV) – and produce significantly less variability than sequencing replicates. Residual inter-pipeline variability is concentrated at low quality sites and repetitive genomic regions prone to stochastic effects. This work alleviates a key technical bottleneck for genome aggregation and helps lay the foundation for broad data sharing and community-wide “big-data” human genetics studies.

Folate Is Associated with the Natural History of High-Risk Human Papillomaviruses

2004 ◽  
Vol 64 (23) ◽  
pp. 8788-8793 ◽  
Author(s):  
Chandrika J. Piyathilake ◽  
Olga L. Henao ◽  
Maurizio Macaluso ◽  
Phillip E. Cornwell ◽  
Sreelatha Meleth ◽  
...  
Keyword(s):  
High Risk ◽  
Natural History ◽  
Human Papillomaviruses ◽  
History Of

The Natural History of Undiagnosed Wrist Pain in Young Women

1992 ◽  
Vol 17 (1) ◽  
pp. 51-54 ◽  
Author(s):  
J. P. RYLEY ◽  
R. J. LANGSTAFF ◽  
N. J. BARTON
Keyword(s):  
Natural History ◽  
Young Women ◽  
Wrist Pain ◽  
Psychiatric Disturbance ◽  
History Of

43 young women with undiagnosed wrist pain were followed up for a median of 13 years (range 3 to 19). 26% were now free of pain and 35% had improved; 30% were unchanged and 9% were worse. Overall, 40% were still significantly troubled. There was no evidence that those patients suffered or had suffered from emotional or psychiatric disturbance which might have been responsible for the pain. Only three patients had developed ganglia.

scholarly journals Evaluation of the Oncogenic Human Papillomavirus DNA Test with Liquid-Based Cytology in Primary Cervical Cancer Screening and the Importance of the ASC/SIL Ratio: A Belgian Study

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Xavier Catteau ◽  
Philippe Simon ◽  
Jean-Christophe Noël
Keyword(s):  
Human Papillomaviruses ◽  
Good Representation ◽  
Dna Test ◽  
Hpv Status ◽  
Cytological Abnormalities ◽  
French Speaking ◽  
Hybrid Capture 2 ◽  
Liquid Based Cytology ◽  
Meta Analyses ◽  
Quality Diagnosis

Objectives. In Belgium, very few studies have focused on cervical high-risk human papillomaviruses (hrHPV) prevalence and the relationship between HPV and cervical cytological abnormalities. The aim of this study was to investigate hrHPV prevalence and its relationship with cytological screening and histological results in the French-speaking community in Belgium (Brussels and Wallonia). Methods. A total of 58,265 liquid-based cytology tests were performed during this period. All cases of ASC-US, ASC-H, LSIL, and HSIL were tested by Hybrid Capture 2 for hrHPV screening. Results. The prevalence of cytological abnormalities was 3.1% for ASC-US, 0.3% for ASC-H, 1.5% for LSIL, and 0.3% for HSIL. The frequency of hrHPV infection was 47% in ASC-US, 90% in ASC-H, 86% in LSIL, and 98.4% in HSIL. CIN 2+ lesions were found in 12.2% of smears with an ASC-US result, in 54% of smears with an ASC-H result, in 12.5% of smears with a LSIL result, and in 89.3% of smears with a HSIL result. The ASC/SIL ratio was 1.9%. Conclusions. This study provides a good representation of cytological abnormalities and HPV status in patients living in Belgium’s French-speaking community. The prevalence in our study was similar to that derived from meta-analyses of European studies. Our ASC/SIL ratio was 1.9%, being within the lower and upper limits proposed in the literature, which tends to prove the good quality diagnosis of cervical smears in our laboratory.

scholarly journals Natural history of histologically moderate cervical dysplasia in adolescent and young women

2014 ◽  
pp. 2101 ◽  
Author(s):  
Jesus Jimenez ◽  
Salvador Piris ◽  
Victoria Bravo ◽  
Estela Lorenzo-Hernando ◽  
Reyes Oliver ◽  
...  
Keyword(s):  
Natural History ◽  
Young Women ◽  
Cervical Dysplasia ◽  
History Of

scholarly journals Issues with data transformation in genome-wide association studies for phenotypic variability

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 200 ◽  
Author(s):  
Xia Shen ◽  
Lars Rönnegård
Keyword(s):  
Statistical Power ◽  
Human Genetics ◽  
Association Studies ◽  
Phenotypic Variability ◽  
Data Transformation ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
The Real ◽  
Genome Wide

The purpose of this correspondence is to discuss and clarify a few points about data transformation used in genome-wide association studies, especially for phenotypic variability. By commenting on the recent publication by Sun et al. in the American Journal of Human Genetics, we emphasize the importance of statistical power in detecting functional loci and the real meaning of the scale of the phenotype in practice.

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