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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Epigenome analysis of primary breast cancer tumors and different types of recurrences.

ABSTRACT: Genome wide DNA methylation profiling of primary breast cancer tumors and their axillary metastasis and/or ipsilateral breast recurrence and/or contralateral breast recurrence. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 20 primary breast tumors and their matched axillary metastasis, 17 primary breast tumors and their matched ipsilateral breast recurrence, and 11 primary breast tumors and their matched contralateral breast recurrence. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2 contributed by Institut Curie - Fabien Reyal

ORGANISM(S): Homo sapiens

SUBMITTER: Matahi MOARII

PROVIDER: E-GEOD-44870 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Epigenome analysis of primary breast cancer tumors and different types of recurrences.

Project description:Genome wide DNA methylation profiling of primary breast cancer tumors and their axillary metastasis and/or ipsilateral breast recurrence and/or contralateral breast recurrence. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 20 primary breast tumors and their matched axillary metastasis, 17 primary breast tumors and their matched ipsilateral breast recurrence, and 11 primary breast tumors and their matched contralateral breast recurrence.

2013-12-24 | GSE44870 | GEO

Epigenetic field cancerization in breast cancer using subject-matched tumor, ipsilateral-normal, and contralateral-normal tissues

Project description:Emerging work has demonstrated that histologically normal (non-tumor) tissue adjacent to breast tumor tissue shows evidence of molecular alterations related to tumorigenesis, referred to as field cancerization effects. Although changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumor DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumor. Matched tumor, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select breast epithelial cells from normal tissues, and neoplastic cells from tumor specimens for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal breast and tumor tissue (63,271 CpG loci q < 0.01), than between ipsilateral-normal tissue and tumor (38,346 CpG loci q < 0.01). In addition, we identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p < 0.01). Hypomethylated loci in ipsilateral normal relative to contralateral were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3. Hypermethylated loci in ipsilateral-normal relative to contralateral-normal tissue were significantly enriched for CpG island shore regions.

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Genome-wide DNA methylation analysis in hepatocellular carcinoma

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DNA methylation profile in well-differentiated cancer uncoves another source of diagnostic and prognostic markers

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2014-06-03 | E-GEOD-58119 | 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.

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