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Epigenome analysis of smear cells from the uterine cervix consisting of 24 normals and 24 cervical intraepithelial neoplasias (all HPV+)

ABSTRACT: The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in smear cells from the uterine cervix (liquid based cytology samples), obtained from 48 women. All women tested positive for the human papilloma virus (HPV+). Of the 48 samples, 24 were cytologically normal while the other 24 exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+).

ORGANISM(S): Homo sapiens

PROVIDER: GSE37020 | GEO | 2013/03/30

SECONDARY ACCESSION(S): PRJNA157499

REPOSITORIES: GEO

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Epigenome analysis of smear cells from the uterine cervix consisting of 24 normals and 24 cervical intraepithelial neoplasias (all HPV+)

Project description:The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in smear cells from the uterine cervix (liquid based cytology samples), obtained from 48 women. All women tested positive for the human papilloma virus (HPV+). Of the 48 samples, 24 were cytologically normal while the other 24 exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+). Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2013-03-30 | E-GEOD-37020 | biostudies-arrayexpress

Epigenome analysis of normal cells from the uterine cervix in a nested prospective case control study within the ARTISTIC trial

Project description:The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in normal cells from the uterine cervix (liquid based cytology samples), obtained from 152 women in a nested prospective case-control study within the ARTISTIC trial. Out of the 152 women, 75 developed a cervical intraepitelial neoplasia of grade 2 or higher (CIN2+) after 3 years of sample collection. The rest of women (77) remained disease free (CIN2-).

2012-02-23 | GSE30758 | GEO

Epigenome analysis of normal cells from the uterine cervix in a nested prospective case control study within the ARTISTIC trial

2012-02-23 | E-GEOD-30758 | biostudies-arrayexpress

Epigenome analysis of normal and preinvasive cervical smear samples

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

Epigenome analysis of normal and preinvasive cervical smear samples

2010-03-01 | GSE20080 | GEO

Proteomic alterations in early stage cervical cancer

Project description:Cervical cancer is characterized by a well-defined pre-malignant phase, cervical intraepithelial neoplasia (CIN). Identification of high grade CIN lesions by population-based screening programs and their subsequent treatment has led to a significant reduction of the incidence and mortality of cervical cancer. Cytology-based testing of cervical smears is the most widely used cervical cancer screening method, but is not ideal, as the sensitivity for detection of CIN2 and higher (CIN2+) is only ~55%. Therefore, more sensitive and specific biomarkers for cervical cancer and its precancerous stages are needed.

2018-05-03 | PXD008723 | Pride

Epigenome analysis of normal and cancer tissue from the uterine cervix

Project description:The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in normal and cancer tissue from the uterine cervix. There are a total of 63 samples, 15 samples of normal histology and 48 cervical cancers. The normal cervical samples were from women who underwent a hysterectomy for uterine fibroids. The 48 cervical cancers were from women who were treated at the Innsbruck Medical University between 1990 and 2006.

2012-02-23 | GSE30759 | GEO

Preoperative Diagnosis of Benign Thyroid Nodules with Indeterminate Cytology

Project description:BACKGROUND: Following fine needle aspiration, 15-30% of thyroid nodules are not clearly benign or malignant. These cytologically indeterminate nodules are often referred for diagnostic surgery, though most prove benign. A novel diagnostic test measuring the expression of 167 genes has shown promise in improving pre-operative risk assessment. We evaluated this test in a prospective, multicenter study. METHODS: Over 19 months, we performed a prospective study at 49 clinical sites enrolling 3,789 patients and collecting 4,812 samples from thyroid nodules >1cm requiring evaluation. We obtained 577 cytologically indeterminate aspirates with corresponding histopathology of excised lesions on 413. Central blinded histopathologic review served as the reference (“gold”) standard. After applying inclusion criteria, gene expression classifier results were obtained for 265 indeterminate nodules used in this analysis, and performance was calculated. RESULTS: 85 of 265 indeterminate nodules were malignant. The gene expression classifier correctly identified 78 of 85 as ‘suspicious’ (92% sensitivity, [84%-97%] 95% CI). Specificity was 52%, [44%-59%]. The negative predictive value was 95%, 94%, and 85%, respectively, for aspirates with AUS/FLUS, FN/SFN, or ‘suspicious’ cytology. Analysis of 7 false negative cases revealed 6 with a paucity of thyroid follicular cells, suggesting that insufficient sampling of the nodule had occurred. CONCLUSIONS: Though individualized clinical care is recommended, these data support consideration of a conservative approach for most patients with indeterminate FNA cytology and benign gene expression classifier results. 265 cytologically indetermine samples, 47 cytologically benign and 55 cytologically malignant samples

2012-06-24 | E-GEOD-34289 | biostudies-arrayexpress

Epigenome analysis of normal and cancer tissue from the uterine cervix

Project description:The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in normal and cancer tissue from the uterine cervix. There are a total of 63 samples, 15 samples of normal histology and 48 cervical cancers. The normal cervical samples were from women who underwent a hysterectomy for uterine fibroids. The 48 cervical cancers were from women who were treated at the Innsbruck Medical University between 1990 and 2006. Bisulphite converted DNA from the 63 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2012-02-23 | E-GEOD-30759 | biostudies-arrayexpress

miRNAs signature as potential biomarkers for cervical precancerous lesions in Human Papillomavirus Positive women

Project description:Cervical cancer ranks as the first in cancer mortality among women of low-middle income countries, where 80% of the 570,000 cases and 311,000 worldwide deaths estimated for 2018 occurred (Ferlay et al. 2018 ). Persistent infections with high-risk HPV (hrHPV) genotypes can lead to high-grade cervical intraepithelial (CIN) grade 2 (CIN2) or higher, (CIN2+), if untreated, a high percentage of these lesions may progress to cancer. Despite its high sensitivity, the hrHPV test has low specificity to detect CIN2+ lesions given that a high percentage of women (80 %) infected with hrHPV genotypes will resolve the infection spontaneously. microRNAs (miRNAs) are small non-coding RNAs and their differential expression patterns seen to be associated with cervical intraepithelial lesions. Our work aimed to identify miRNAs differentially expressed in CIN2+ respect with <CIN1 and to evaluate their potential use as biomarkers to distinguish low- from high-grade lesions within hrHPV positive women. For our discovery set we used small RNA sequencing (miRNA-seq) to compare the miRNA expression patterns in 20 Formalin-Fixed Paraffin-Embedded (FFPE) tissues from hrHPV-positive women from Medellin, Colombia presenting low- (n=10) and high-grade lesions (n=10). Top five miRNAs presenting high fold change and low coefficient of variation were used validated by RT-PCR in our validation set composed 210 age-matched independent hrHPV-positive FFPE tissues, and an in-silico approach was used to understand the function of the differentially expressed miRNAs in the context of HPV infection.

2023-05-07 | GSE167858 | GEO

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