BIGenomics HPV zipcode array plasmid hybridizations
Ontology highlight
ABSTRACT:
ORGANISM(S): Human papillomavirus
SUBMITTER: Jarmo Ritari
PROVIDER: E-MEXP-3152 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:A dilution series experiment to determine the sensitivity of a microarray method for human papillomavirus genotyping. HPV genotyping is based on multiplex PCR (PGMY-t primers) followed by ligation step where two probes are ligated together if a matching template is present in the mixture. The ligated probes are then detected on microarray. Plasmids containing the full genome of HPV 16 or 18 were used in the experiment. The concentrations were 1000, 100, 10 ,1, 0.1 and 0 femtograms of plasmid as a template in HPV PCR reaction.<br><br>
2011-12-17 | E-MEXP-3477 | biostudies-arrayexpress
Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 1 ng or 1 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.
2011-05-01 | E-MEXP-3154 | biostudies-arrayexpress
Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 10 pg or 100 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.
2011-08-20 | E-MEXP-3268 | biostudies-arrayexpress
Project description:Replicates of detection of multiple plasmid PCR products by LDR probes on microarray.
2011-05-01 | E-MEXP-3153 | biostudies-arrayexpress
Project description:HPV genotyping of patient samples by multiplex PCR (PGMY-t primers) and ligation detection probes on microarray.
2011-05-01 | E-MEXP-3155 | biostudies-arrayexpress
Project description:Human papillomavirus infection is the cause of essentially all cases of cervical premalignant lesions and cervical cancer. Primary screening using HPV DNA testing with cytology triage has been shown to be more sensitive and, importantly, more specific than conventional testing based on cytology among women more than 35 years of age. <br><br><br><br>The aim of the experiment was to evaluate a HPV genotyping microarray method using patient sample DNA. HPV genotyping is based on multiplex PCR (PGMY-t primers) followed by ligation step where two probes are ligated together if a matching template is present in the mixture. The ligated probes are then detected on microarray.
2011-12-10 | E-MEXP-3466 | biostudies-arrayexpress
Project description:Hybridization of ligation probes to a zipcode (tag) microarray. The purpose of the experiment was to establish functionality and target specificity of the ligation probes by using pools of synthetic templates with all of the probes. The templates are 80-mer synthetic dsDNA molecules, each specific for a single probe. Each probe is a ssDNA molecule containing target recognition sequences, PCR primer binding sequences and a unique tag sequence. If a matching target sequence is present in the mixture, the probes is ligated into a circular molecule, which can be PCR amplified and hybrized on a microarray harbouring complementary tag sequences.
2012-02-24 | E-MEXP-3538 | biostudies-arrayexpress
Project description:Ligation probe pool was tested with different concentrations of synthetic dsDNA template molecules to determine analytical sensitivity of the method. Probes are ligated into circular molecules if their target sequence is present in the reaction. Ligated probes are then PCR amplified and the PCR products are hybridized to a microarray by tag sequences.
2012-02-06 | E-MEXP-3539 | biostudies-arrayexpress
Project description:The interaction between the transmembrane glycoprotein surface receptor CD40 expressed by skin keratinocytes (KCs) and its T cell-expressed ligand CD154 was suggested to exacerbate inflammatory skin diseases. However, the full spectrum of CD40-mediated effects by KCs underlying this observation is unknown. Therefore, changes in gene expression after CD40 ligation of KCs were studied by microarrays. CD40-mediated activation for 2 hours stimulated the expression of a coordinated network of immune-involved genes strongly interconnected by IL8 and TNF, while after 24 hours anti-proliferative and anti-apoptotic genes were upregulated. CD40 ligation stimulated the production of chemokines that attracted lymphocytes and myeloid cells from peripheral blood mononuclear cells (PBMCs). Thus, CD40-mediated activation of KCs resulted in a highly coordinated response of genes required for the local development and sustainment of adaptive immune responses. The importance of this process was confirmed by a study on the effects of human papilloma virus (HPV) infection to the KCâs response to CD40 ligation. HPV infection clearly attenuated the magnitude of the response to CD40 ligation and consequently the KCâs capacity to attract PBMCs. The fact that HPV attenuates CD40 signalling in KCs indicates the importance of the CD40-CD154 immune pathway in boosting cellular immunity within epithelia. Total RNA from eight 72 hours 50 IU/ml IFNgamma pre-stimulated primary undifferentiated keratinocyte cultures, four uninfected and four HPV-positive, that were either left unstimulated, or stimulated for 2 hours with IFNgamma and Control- or CD40L-expressing L-cells (mouse fibroblasts), or stimulated for 24 hours with IFNgamma and Control- or CD40L-expressing L-cells. The stimulated samples were generated in duplo. 72 samples were generated in total.
2015-10-26 | E-GEOD-54181 | biostudies-arrayexpress
Project description:The global rise of HPV(+) oropharyngeal squamous cell carcinoma (OPSCC) has generated considerable interest underlying its etiology and management. Despite an overall decline in head and neck malignancies, the incidence in OPSCC has by contrast sharply risen, with HPV(+) subtypes now comprising 80% of all OPSCC.1,2 Relative to HPV(-) OPSCC, HPV(+) patients are more responsive to chemoradiation and harbor a 52% risk-of-death reduction.3 Despite this distinct outcome, treatment regimens remain the same for all OPSCC subtypes (smoking-driven and virus-driven), rather than an adaptive approach to what most consider distinct diseases. The short-term effects (e.g., mucositis, odynophagia) and long-term toxicities (e.g., xerostomia, dysphagia, ototoxicity) from treatment substantially affect quality of life, and rival the impact of the cancer itself. Recently published as well as ongoing trials are actively examining deintensification approaches2,4-9, with the goal of diminishing treatment sequelae for HPV(+) subtypes. While deintensification may decrease chemoradiation-related toxicities, it nonetheless may also undertreat a meaningful percentage of HPV(+) patients who may then recur. In examining national trials, 19% of HPV(+) patients had disease progression after therapy, with a two-year survival rate of 60%.10 Current methods to ascertain HPV status involve p16 staining. However, on comparison with gold standard E6/E7 expression by qPCR, p16 harbored a 15% false positivity rate11, suggesting limited utility as a sole biomarker for deintensification. Improved molecular stratification would greatly enhance the clinician’s ability to precisely tailor treatment while minimizing the risk of jeopardizing outcomes. One approach encompasses in-depth proteomic profiling of HPV(+) OPSCC to reveal distinct protein expression profiles and delineate clinically relevant upstream pathways. In turn, these proteomic differences may distinguish higher-risk disease (cases predisposed to recurrence that may benefit from treatment intensification) from lower-risk phenotypes (cases whose treatment response is sufficiently robust to warrant deintensification). Here, two HPV(+) OPSCC cohorts stratified by treatment response are compared via a hybrid data dependent acquisition/data independent acquisition (DDA/DIA) approach via mass spectrometry. We focused on detection of low-abundance proteins to highlight proteomic signatures that can be potentially exploited for treatment stratification.
2022-05-05 | PXD028618 | Pride