Genome-wide Scan for Methylation Profiles in Breast Cancer
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Maria Worsham
PROVIDER: E-GEOD-66695 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Down syndrome is characterized by a wide spectrum of clinical signs, which include cognitive and endocrine disorders and haematological abnormalities. Although it is well established that the causative defect of Down syndrome is the trisomy of chromosome 21, the molecular bases of Down syndrome phenotype are still largely unknown. We used the Infinium HumanMethylation450 BeadChip to investigate DNA methylation patterns in whole blood from 29 subjects affected by Down syndrome (DS), using their healthy relatives as controls (mothers and unaffected siblings). This family-based model allowed us to monitor possible confounding effects on DNA methylation patterns deriving from genetic and environmental (lifestyle) factors. The identified epigenetic signature of Down syndrome includes differentially methylated regions that, although enriched on chromosome 21, interest most of the other chromosomes and can be functionally linked to the developmental and haematological defects characteristic of the disease. DNA was extracted from whole peripheral blood using the QIAamp 96 DNA Blood Kit (QIAGEN) and quantified by Quant-iT™ PicoGreen (Invitrogen). Sodium bisulphite conversion of 500 ng of each sample was performed using the EZDNA Methylation-Gold Kit according to the manufacturer's recommendation for Illumina Infinium Assay. 4 ul of bisulfite converted DNA were hybridized on Infinium HumanMethylation 450 BeadChip, following manufacturer’s instructions. Arrays were scanned by HiScan SQ scanner (Illumina) and the intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation levels of each CpG is reported as beta value.
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Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 51 central chondrosarcoma. Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.
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