Project description:Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylation450 BeadChip (“450K array”) in DNA samples isolated from blood for schizophrenia cases and controls. This samples were profiled as part of a wider study where they were meta-analysed with other cohorts.
Project description:Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylation450K BeadChip (“450K array”) in DNA samples isolated from blood for schizophrenia cases, first episode psychosis patients and controls. These samples were profiled as part of a wider study where they were meta-analysed with other cohorts.
Project description:Genome wide DNA methylation profiling of whole blood in schizophrenia patients and healthy subjects of different ages. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 62 schizophrenia patients and 33 healthy subjects from Dutch descent. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Publication: Steve Horvath, Yafeng Zhang, Peter Langfelder, René S. Kahn, Marco P.M. Boks, Kristel van Eijk, Leonard H. van den Berg, Roel A. Ophoff. Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biology. Special Edition. The raw data (non-normalized Unmethylated and Methylated signal intensities) are not available.
Project description:Genome wide DNA methylation profiling and semi-supervised classification of blood samples from a case-control study of head and neck squamous cell carcinoma (HNSCC). The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood. Samples included peripheral blood samples from 92 incident cases of HNSCC and 92 control subjects.
Project description:To define methylation markers of breast cancer for circulating tumor DNA, we compare the methylation characteristics of breast cancer and blood DNA of healthy individuals.
Project description:Bilaterality of breast cancer is an indicator of constitutional cancer susceptibility, however, the molecular causes underlying this predisposition in the majority of cases is not known. We hypothesize that epigenetic misregulation of cancer related genes could partially account for this predisposition. We have performed methylation microarray analysis of peripheral blood DNA from 14 women with bilateral breast cancer compared to 14 unaffected matched controls throughout 17 candidate breast cancer susceptibility genes including BRCA1, BRCA2, CHEK2, ATM, ESR1, SFN, CDKN2A, TP53, GSTP1, CDH1, CDH13, HIC1, PGR, SFRP1, MLH1, RARB and HSD17B4. We show that the majority of methylation variability is associated with intragenic repetitive elements. Detailed validation of the tiled region around ATM was performed by bisulfite modification and pyrosequencing of the same samples and in a second set of peripheral blood DNA from 190 bilateral breast cancer patients compared to 190 controls. We show significant hypermethylation of one intragenic repetitive element in breast cancer cases compared to controls (p=0.0017) with the highest quartile of methylation associated with a three-fold increased risk of breast cancer (OR = 3.20, 95% C.I.=1.78-5.86, p=0.000083). Increased methylation of this locus is associated with lower steady state ATM mRNA level and correlates with age of cancer patients but not controls, suggesting a combined age-phenotype related association. This research demonstrates the potential for gene-body epigenetic misregulation of ATM and other cancer related genes in peripheral blood DNA that may be useful as a novel marker to estimate breast cancer risk. Keywords: Differential Methylation Hybridisation