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

ABSTRACT: 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-). Bisulphite converted DNA from the 152 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

ORGANISM(S): Homo sapiens

SUBMITTER: Andrew Teschendorff

PROVIDER: E-GEOD-30758 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer.

Zhuang Joanna J Jones Allison A Lee Shih-Han SH Ng Esther E Fiegl Heidi H Zikan Michal M Cibula David D Sargent Alexandra A Salvesen Helga B HB Jacobs Ian J IJ Kitchener Henry C HC Teschendorff Andrew E AE Widschwendter Martin M

PLoS genetics 20120209 2

Aberrant DNA methylation is an important cancer hallmark, yet the dynamics of DNA methylation changes in human carcinogenesis remain largely unexplored. Moreover, the role of DNA methylation for prediction of clinical outcome is still uncertain and confined to specific cancers. Here we perform the most comprehensive study of DNA methylation changes throughout human carcinogenesis, analysing 27,578 CpGs in each of 1,475 samples, ranging from normal cells in advance of non-invasive neoplastic tran ...[more]

PMID: 22346766

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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 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 endometrium tissue from women with metastatic endometrial cancer.

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 endometrium tissues from women with metastatic endometrial cancer. Endometrium tissue samples were drawn from 18 metastatic endometrial cancers. The metastatic endometrial cancer tissue samples were from women (mean age 67.1) who were diagnosed with metastatic endometrial cancer. Bisulphite converted DNA from the 18 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2012-02-20 | E-GEOD-33422 | biostudies-arrayexpress

DNA methylation profiling of serum DNA samples of the UKCTOCS cohort

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 serum DNA samples from a total of 282 healthy postmenopausal women of which 134 developed breast cancer within a 5-year follow-up period Bisulphite converted DNA from the serum were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2014-06-03 | E-GEOD-58119 | biostudies-arrayexpress

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

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Genome wide DNA methylation profiling of United Kingdom Ovarian Cancer Population Study (UKOPS)

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 whole blood samples from 540 samples, of which 266 were samples taken from postmenopausal women with ovarian cancer and 274 were from age-matched healthy controls Keywords: DNA methylation Bisulphite converted DNA from the 540 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2010-05-07 | E-GEOD-19711 | biostudies-arrayexpress

DNA methylation profiling of whole blood DNA samples from BRCA1 wild-types without breast cancer and BRCA1 mutants with and without breast cancer (Prague Set 1)

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 whole blood DNA samples from 84 women (42 BRCA1 wild-type and healthy, 7 BRCA1 mutants and healthy, 35 BRCA1 mutants with breast cancer) whole blood DNA from women, with and without breast cancer, and with or without BRCA1 mutation Bisulphite converted DNA from the whole blood samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2 The BRCA1 mutation status represent 0=healthy-brca1wt, 1=healthy-brca1mt, 2=breastcancer-brca1mt.

2014-05-06 | E-GEOD-57285 | 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

Epigenome analysis of white blood cells from healthy women with and without BRCA1 mutation.

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 white blood cells from women with and without BRCA1 mutation. Whole blood samples were drawn from 30 BRCA1 mutation carriers (15 women with breast cancer and 15 healthy women with mean age 57.2) and 30 females without BRCA1 mutation (15 breast cancers and 15 healthy with mean age 57.1). All samples were collected between 2001 and 2008. The samples were drawn from women attending the General Faculty Hospital in Prague and the complete coding sequence, intron-exon junctions and large rearrangements for BRCA1 and BRCA2 genes were tested. Bisulphite converted DNA from the 60 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2012-02-20 | E-GEOD-32396 | biostudies-arrayexpress

Epigenome analysis of breast tissue from women with and without breast cancer.

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 breast tissues from women with and without breast cancer. Breast tissue samples were drawn from 114 breast cancers and 23 non-neoplastic breast tissues. The breast cancer tissue samples were from women (mean age 59.4) who were diagnosed with breast cancer. Among the cancers, 33 were at stage 1 and 81 at stage 2/3/4; 34, 59, and 19 were grade 1, 2, and 3 respectively;and 91 were invasive ductal carcinoma breast cancers. The 23 non-neoplastic samples are from healthy woman (mean age 47.6). Bisulphite converted DNA from the 137 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2012-02-20 | E-GEOD-32393 | biostudies-arrayexpress

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