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

ABSTRACT: 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).

ORGANISM(S): Homo sapiens

PROVIDER: GSE32393 | GEO | 2012/02/20

SECONDARY ACCESSION(S): PRJNA147943

REPOSITORIES: GEO

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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

Proteomics Analysis of Human Breast Milk to Assess Breast Cancer Risk

Project description:Detection of breast cancer (BC) in young women is challenging because mammography, the most common tool for detecting BC, is not effective on the dense breast tissue characteristic of young women. In addition to the limited means for detecting their BC, young women face a transient increased risk of pregnancy-associated BC. As a consequence, reproductively active women could benefit significantly from a tool that provides them with accurate risk assessment and early detection of BC. One potential method for detection of BC is biochemical monitoring of proteins and other molecules in bodily fluids such as serum, nipple aspirate, ductal lavage, tear, urine, saliva and breast milk. Of all these fluids, only breast milk provides access to a large volume of breast tissue, in the form of exfoliated epithelial cells, and to the local breast environment, in the form of molecules in the milk. Thus, analysis of breast milk is a non-invasive method with significant potential for assessing BC risk. Here we analyzed human breast milk by mass spectrometry (MS)-based proteomics to build a biomarker signature for early detection of BC. Ten milk samples from 8 women provided 5 paired-groups (cancer versus control) for analysis of differentially expressed proteins: 2 within woman comparisons (milk from a diseased breast versus a healthy breast of the same woman) and 3 across women comparisons (milk from a woman with cancer versus a woman without cancer). Despite a wide range in the time between milk donation and cancer diagnosis (cancer diagnosis occurred from 1 month before to 24 months after milk donation), the levels of some proteins differed significantly between cancer and control in several of the 5 comparison groups. These pilot data are supportive of the idea that molecular analysis of breast milk will identify proteins informative for early detection and accurate assessment of BC risk, and warrant further research.

2017-12-18 | PXD007066 | Pride

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.

2012-02-20 | GSE32396 | GEO

Genome wide DNA methylation profiling of normal breast, normal adjacent and breast cancer tissue

Project description:The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 407 samples, including 50 normal samples from healthy women, 42 matched normal-adjacent breast cancer pairs (84 samples), 263 unmatched breast cancers, 7 normal samples from BRCA1 carriers and 4 BRCA1 breast cancers. ***WARNING: incomplete metadata supplied for this study***

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

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

aCGH data from age-dichotomized ER+ breast tumors

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Expression data from age-dichotomized ER+ breast tumors

Project description:To investigate the biological basis between aging and sporadic breast cancer incidence and prognosis, RNA samples from matched ER+ invasive breast cancers diagnosed in either young (≤45) or old (≥70) women were analyzed by expression microarrays Keywords: biomarker identification

2007-09-12 | GSE8193 | GEO

Genome wide DNA methylation profiling of normal breast, normal adjacent and breast cancer tissue

Project description:The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 407 samples, including 50 normal samples from healthy women, 42 matched normal-adjacent breast cancer pairs (84 samples), 263 unmatched breast cancers, 7 normal samples from BRCA1 carriers and 4 BRCA1 breast cancers. Bisulphite converted DNA from the 407 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2015-06-18 | E-GEOD-69914 | biostudies-arrayexpress

Lipid metabolism genes in contralateral unaffected breast and estrogen receptor status of breast cancer

Project description:The contralateral unaffected breast of women with unilateral breast cancer (cases) is a good model for defining subtype-specific risk since women with ER-negative index primaries are at high risk for subsequent ER-negative primary cancers. We performed random fine needle aspiration (rFNA) of the unaffected breasts of cases; samples from 30 subjects (15 ER-positive and 15 ER-negative cases matched for age, race and menopausal status), were used for Illumina expression array analysis. In this study, we have examined gene expression profiles in random fine needle aspirate (rFNA) samples from the contralateral breasts of women with new unilateral breast cancer (cases) to seek candidate panels of ER-specific risk biomarkers. On a discovery set of 30 women, we have identified gene expression differences in the contralateral breast that associate with ER+ or ER- index primary tumors.

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