Methylation_cin_discovery_ctrl
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002068 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genome wide DNA methylation profiling of normal and preinvasive cervical smear samples infected with the human papilloma virus (HPV) The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in liquid based cytology (LBC) cervical smear samples. Samples included 19 normal smears without HPV, 11 normal smears with HPV infection, and 18 smears with HPV and exhibiting dysplasia. email: a.teschendorff@ucl.ac.uk Keywords: DNA methylation
2010-03-01 | GSE20080 | GEO
Project description:Background: Offering self-sampling of cervico-vaginal material for human papillomavirus (HPV) testing is an effective method to increase the coverage in cervical screening programmes. Molecular triage directly on HPV-positive self-samples for colposcopy referral opens the way to full molecular cervical screening. Here, we set out to identify a methylation classifier for detection of precancer (CIN3) or cancer, applicable to self-samples obtained by different devices. Findings: Genome-wide DNA methylation profiling of HPV-positive self-samples revealed 12 methylation targets for CIN3 detection. Multiplex quantitative methylation-specific PCR of these targets yielded a 3-gene methylation classifier (ASCL1, LHX8 and ST6GALNAC5), showing a very good clinical performance for CIN3 detection in both lavage (AUC=0.88; sensitivity=74%; specificity=79%) and brush (AUC=0.90; sensitivity=88%; specificity=81%) self-samples in the validation set. All self-samples from women with cervical cancer scored methylation-positive. Conclusion: By genome-wide DNA methylation profiling on self-samples, we identified a highly effective 3-gene methylation classifier for direct triage on self-samples from HPV-positive women.
2018-01-01 | GSE99511 | GEO
Project description:We pursued the hypothesis that epigenetic regulators of transcription are involved in both the development and the progression of HPV-associated CIN. Using HELP-tagging, we performed the most comprehensive study to date of DNA methylation in HPV-associated cervical neoplasia, testing ~2 million loci throughout the human genome in biopsies from 78 HPV+ women, identifying changes starting in early CIN and maintained through carcinogenesis. We identified loci at which DNA methylation is consistently altered, beginning early in the course of neoplastic disease and progressing with disease advancement. DNA methylation profiles for cervical biopsies of 19 normals, 20 CIN1, 16 CIN2/3, and 23 cervical cancers.
2016-08-22 | E-GEOD-76986 | biostudies-arrayexpress
Project description:The Illumina 850k Human DNA methylation EPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in the formalin-fixed and paraffin-embedded tissue sections(FFPE). Samples included 3 normal samples without HPV and 6 cervical cancer samples (three HPV 16 positive,three HPV 18 positive).
2021-03-26 | GSE169622 | GEO
Project description:Identifying the differentially expressed miRNAs in Cervical cancer patients infected with only one virus i.e. either HIV or HPV-16 and patients infected with both viruses HIV and HPV-16 with respect to their controls which is the healthy population not infected by either HIV or any HPV The miRNA array was performed using the affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, California, United States). The chip was processed using a commercial Affymetrix array service (GeneTech Biotechnology Limited Company, Shanghai, China). The affymetrix GeneChip® miRNA 3.0 Array contains 2,999 probe sets unique to human, mouse and rat pre-miRNA hairpin sequences, 2,216 human snoRNA and scaRNA probe sets and covers 153 organisms (19,724 probe sets). Raw data sets were extracted from all Cel files (raw intensity file) after scanning of slides. These raw data sets were separately analyzed using Expression Console and GeneSpring GX12.5 software followed by differential miRNA expression, fold change & cluster analysis.
2018-08-01 | GSE81137 | GEO
Project description:Cervical cancer is the fourth most common cancer among women worldwide and screening pro-grams increase detection rate and survivability. Molecular screening of presence of human papil-loma viruses (HPV) as alternatives to physical examinations offers cost-efficient solutions and can be performed on self-collected samples. A persistent infection with HPV is necessary but not sufficient to develop cancer and additional biomarkers are needed to increase the precision. We have analyzed protein biomarkers found in self-collected dried cervico-vaginal fluid (CVF) from both controls and women with cervical cancer pre-stages.
2022-02-17 | PXD026064 | Pride
Project description:The aim of this study was to identify new candidate genes that are differentially methylated in squamous cell carcinoma compared to the DNA samples from cervical intraepithelial neoplasia grade 3 (CIN3) and normal cervical scrapes. The Illumina Infinium Human Methylation 450 K BeadChip method identifies genome-wide DNA methylation changes in CpG islands, CpG shores and shelves. In this study 20 normal cervical samples (HPV negative), 18 samples with CIN3 lesions (HPV positive) and 6 cervical cancer tissues (HPV positive) were included.
2014-01-06 | E-GEOD-46306 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal and preinvasive cervical smear samples infected with the human papilloma virus (HPV) The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in liquid based cytology (LBC) cervical smear samples. Samples included 19 normal smears without HPV, 11 normal smears with HPV infection, and 18 smears with HPV and exhibiting dysplasia. email: a.teschendorff@ucl.ac.uk Keywords: DNA methylation Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
2010-05-06 | E-GEOD-20080 | biostudies-arrayexpress
Project description:Raw methylation data from cervical samples in controls.
| EGAD00010002080 | EGA
Project description:Raw methylation data from cervical samples in controls.
| EGAD00010002079 | EGA