GEO DataSets

(Submitter supplied) To investigate whether paternal tobacco smoke (PTS) was associated with prenatal epigenetic programming of CG site methylation, 20 cord blood DNA samples from newborns with and without PTS were subjected to microarray assay of 1,505 CG loci in 807 genes by Illumina GoldenGate® technology bead system to obtain high-throughput DNA Methylation profiles. Samples included 14 newborns without PTS exposure, and 6 newborns with PTS exposure.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

20 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide DNA methylation profiling of invasive breast cancer samples isolated from an ethnically diverse group of 80 patients in the Breast Cancer Care in Chicago (BCCC) study. DNA was extracted from formalin fixed, paraffin-embedded samples on 80 patients (21 White, 31 African-American, 23 Hispanic and 5 not reported) (training dataset) enrolled in the BCCC. Hormone receptor status was defined as negative if tumors were negative for both estrogen and progesterone (ER/PR) receptors (N=22/75). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

80 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array; Methylation profiling by array

Platforms:

GPL9183 GPL4091 GPL3720

148 Samples

Download data: CEL, TXT

(Submitter supplied) The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

58 Samples

Download data: TXT

(Submitter supplied) We investigated whether methylation in primary melanomas is associated with tumor pathologic features or defines subgroups of primary melanomas

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

47 Samples

Download data: TXT

(Submitter supplied) A microarray targeting promoters of cancer-related genes was used to evaluate DNA methylation at 935 CpG sites in 517 invasive breast tumors from the Carolina Breast Cancer Study (CBCS), a population-based study of invasive breast cancer. Concensus clustering using methylation (β) values for the 167 most variant CpG loci defined 4 clusters differing most distinctly in hormone receptor (HR) status, intrinsic subtype (luminal versus basal-like) and p53 mutation status. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

526 Samples

Download data: TXT

(Submitter supplied) Detection of DNA hypermethylation has emerged as a novel molecular biomarker for the evaluation of prostate cancer diagnosis and prognosis, but the use of single gene hypermethylation could produce unspecific results. Defining the specific gene hypermethylation profile for prostate cancer could provide groups of genes that specifically discriminate the patients with indolent and aggressive tumors. To compare the methylation profile of normal and malignant prostate we performed Genome-wide methylation analysis on 83 tumor samples, that included all clinical stages of the disease, 10 normal prostate samples and LNCaP, DU145 and PC3 prostate cancer cell lines using the GoldenGate Methylation Cancer Panel I (Illumina, Inc.) that interrogate for 1505 CpGs. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

96 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of tumor and normal samples with esophageal squamous cell carcinoma patients. The Illumina GolodenGate methylation cancer panel I was used to obtain DNA methylation profiles across approximately 1,505 CpGs in esophageal squemous cell carcinoma samples. Samples included normal, tumors and plasma samples with esophageal squamous cell carcinoma, also inculding the plasma samples with cancer-free individual.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

288 Samples

Download data: TXT

(Submitter supplied) Inter-individual variability in DNA methylation has been hypothesized to contribute to complex phenotypes through epigenetic modulation of gene expression levels. Population epigenetic studies have been examining differences in DNA methylation in a variety of accessible tissues for association with specific diseases or exposures, but relatively little is known about how this inter-individual variation differs between tissues. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

50 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL9183 GPL8490

79 Samples

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(Submitter supplied) Purpose: Accumulating evidence indicates aberrant DNA methylation is closely related to oral carcinogenesis, and it has been shown that methylation changes might be used as prognostic biomarker in oral squamous cell carcinoma. Oral lichenoid disease (OLD) is the most common oral potentially malignant disorder in our region. In this study, we have performed a wide DNA methylation study of a series of oral lichenoid disease in order to assess the relevance of DNA methylation changes in this premalignant disorder. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

57 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal and Prostate cancer samples. The Illumina GoldenGate Methylation Cancer Panel I with 1,505 CpG sites selected from 807 genes was used to obtain DNA methylation profiles. Samples included 24 normals and 87 tumors.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

111 Samples

Download data: TXT

(Submitter supplied) HIV-positive patients have a higher risk of non-Hodgkin's lymphoma with poor prognostic features. To characterize features of HIV-associated lymphoma, we compared the DNA methylation profiles of 803 cancer-related genes in between 9 HIV-associated and 12 non-HIV lymphoma samples by Illumina GoldenGate Methylation Cancer Panel I microarray.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

42 Samples

Download data: TXT

(Submitter supplied) DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

194 Samples

Download data: TXT

(Submitter supplied) We have discovered a striking connection between mitochondrial dysfunction and epigenomic instability, manifested by global biallelic DNA cytosine 5-methylation and loss of 5-hydroxymethycytosine within succinate dehydrogenase (SDH)-null gastrointestinal stromal tumors (GIST) relative to those bearing KIT or PDGFRA tyrosine kinase driver mutations. The duality of Krebs versus kinase molecular and epigenomic profiles in GIST provides compelling evidence linking mitochondrial process to nuclear structure and function and underscores an essential role for succinate metabolism in the maintenance of epigenomic programming and tumor suppression.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL9183 GPL13534

220 Samples

Download data: TXT

(Submitter supplied) DNA methylation profiling of cancer and control samples. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across 1,505 CpG sites CpGs distributed across 807 genes in blood DNA specimens.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

158 Samples

Download data: IDAT, JPG, SDF, TXT, XML

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL6884 GPL9183

158 Samples

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(Submitter supplied) Methylation array analysis of Ewing sarcoma primary tumors and cell lines compared to mesechymal stem cells

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

146 Samples

Download data: TXT

(Submitter supplied) The Illumina GoldenGate® methylation array was used to evaluate DNA methylation at 1,505 CpG sites in 807 cancer-related genes in 91 consecutive CRC samples and 28 matched normal colonic mucosa.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

119 Samples

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(Submitter supplied) Using paired tumor and non-tumor lung tissues from 47 individuals we identified common changes in DNA methylation associated with the development of non-small cell lung cancer. Pathologically normal lung tissue taken at the time of cancer resection was matched to tumorous lung tissue and together were probed for methylation status using Illumina GoldenGate arrays. For each matched pair the change in methylation at each CpG was calculated (the odds ratio), and these ratios were averaged across individuals and ranked by magnitude to identify the CpG’s with the greatest change in methylation associated with tumor development.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

94 Samples

Download data: TXT