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CaArray_EXP-550: TCGA (READ): Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27)(jhu-usc)

ABSTRACT: TCGA Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform

ORGANISM(S): Homo sapiens

PROVIDER: GSE68751 | GEO | 2015/05/12

SECONDARY ACCESSION(S): PRJNA283809

REPOSITORIES: GEO

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caArray_EXP-550: TCGA (READ): Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27)(jhu-usc)

Project description:TCGA Analysis of DNA Methylation for rectal adenocarcinoma (READ) Using Illumina Infinium Human DNA Methylation 27 platform EXP-550 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_OV.HumanMethylation27.v2 Organism: home sapiens (ncbitax) Tissue Sites: rectal Material Types: Primary solid_tumor, Control Cell Line, organism_part, Solid normal_tissue Disease States: Rectal Adenocarcinoma, NOT SPECIFIED, [Not Available], Rectal Mucinous Adenocarcinoma

2015-05-12 | E-GEOD-68751 | biostudies-arrayexpress

caArray_EXP-620: TCGA (Coad): Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform (Jhu-usc)

Project description:TCGA Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform

2015-05-14 | GSE68838 | GEO

caArray_EXP-598: TCGA (LUSC): Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform (jhu-usc)

Project description:TCGA Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform

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caArray_laird-00224: TCGA Ovarian: Analysis of DNA Methylation for Ovarian Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27) (USC)

Project description:TCGA Analysis of DNA Methylation Using Illumina Infinium Human DNA Methylation 27 platform

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caArray_laird-00224: TCGA Ovarian: Analysis of DNA Methylation for Ovarian Using Illumina Infinium Human DNA Methylation 27 platform (HumanMethylation27) (USC)

Project description:TCGA Analysis of DNA Methylation Using Illumina Infinium Human DNA Methylation 27 platform laird-00224 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_OV.HumanMethylation27.1.adf, jhu-usc.edu_OV.HumanMethylation27.v2 Organism: Homo sapiens (ncbitax) Tissue Sites: Ovary, Ovary, NOT SPECIFIED, PERITONEUM (OVARY), OMENTUM Material Types: Control Cell Line, Solid normal_tissue, organism_part, Primary solid_tumor, whole_organism, Recurrent Solid Tumor Disease States: Serous Cystadenocarcinoma, Serous cystadenocarcinoma, NOT SPECIFIED

2015-11-21 | E-GEOD-75268 | biostudies-arrayexpress

caArray_EXP-620: TCGA (Coad): Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform (Jhu-usc)

Project description:TCGA Analysis of DNA Methylation for COAD using Illumina Infinium HumanMethylation450 platform EXP-620 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_TCGA_HumanMethylation450 Organism: Homo sapiens (ncbitax) Tissue Sites: Colon Material Types: Control Analyte, Solid normal_tissue, organism_part, Primary solid_tumor

2015-05-14 | E-GEOD-68838 | biostudies-arrayexpress

caArray_EXP-598: TCGA (LUSC): Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform (jhu-usc)

Project description:TCGA Analysis of DNA Methylation for LUSC using Illumina Infinium HumanMethylation450 platform EXP-598 Assay Type: Methylation Provider: Illumina Array Designs: jhu-usc.edu_TCGA_HumanMethylation450 Organism: Homo sapiens (ncbitax) Tissue Sites: Lung Material Types: Control Analyte, Solid normal_tissue, organism_part, Primary solid_tumor Disease States: Lung Squamous Cell Carcinoma, NOT SPECIFIED

2015-05-14 | E-GEOD-68825 | biostudies-arrayexpress

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Project description:Epigenetic modifications of DNA, such as cytosine methylation are differentially abundant in diseases such as cancer. A goal for clinical research is finding sites that are differentially methylated between groups of samples to act as potential biomarkers for disease outcome. However, clinical samples are often limited in availability, represent a heterogeneous collection of cells or are of uncertain clinical class. Array-based methods for identification of methylation provide a cost-effective method to survey a proportion of the methylome at single base resolution. The Illumina Infinium array has become a popular and reliable high throughput method in this field and are proving useful in the identification of biomarkers for disease. Here, we compare a commonly used statistical test with a new intuitive and flexible computational approach to quickly detect differentially methylated sites. The method rapidly identifies and ranks candidate lists with greatest inter-group variability whilst controlling for intra-group variability. Intuitive and biologically relevant filters can be imposed to quickly identify sites and genes of interest.

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mLiftOver: harmonizing data across Infinium DNA methylation platforms.

Project description:MotivationInfinium DNA methylation BeadChips are widely used for genome-wide DNA methylation profiling at the population scale. Recent updates to probe content and naming conventions in the EPIC version 2 (EPICv2) arrays have complicated integrating new data with previous Infinium array platforms, such as the MethylationEPIC (EPIC) and the HumanMethylation450 (HM450) BeadChip.ResultsWe present mLiftOver, a user-friendly tool that harmonizes probe ID, methylation level, and signal intensity data across different Infinium platforms. It manages probe replicates, missing data imputation, and platform-specific bias for accurate data conversion. We validated the tool by applying HM450-based cancer classifiers to EPICv2 cancer data, achieving high accuracy. Additionally, we successfully integrated EPICv2 healthy tissue data with legacy HM450 data for tissue identity analysis and produced consistent copy number profiles in cancer cells.Availability and implementationmLiftOver is implemented R and available in the Bioconductor package SeSAMe (version 1.21.13+): https://bioconductor.org/packages/release/bioc/html/sesame.html. Analysis of EPIC and EPICv2 platform-specific bias and high-confidence mapping is available at https://github.com/zhou-lab/InfiniumAnnotationV1/raw/main/Anno/EPICv2/EPICv2ToEPIC_conversion.tsv.gz. The source code is available at https://github.com/zwdzwd/sesame/blob/devel/R/mLiftOver.R under the MIT license.

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Comparative epigenome analysis using Infinium DNA methylation BeadChips.

Project description:The arrival of the Infinium DNA methylation BeadChips for mice and other nonhuman mammalian species has outpaced the development of the informatics that supports their use for epigenetics study in model organisms. Here, we present informatics infrastructure and methods to allow easy DNA methylation analysis on multiple species, including domesticated animals and inbred laboratory mice (in SeSAMe version 1.16.0+). First, we developed a data-driven analysis pipeline covering species inference, genome-specific data preprocessing and regression modeling. We targeted genomes of 310 species and 37 inbred mouse strains and showed that genome-specific preprocessing prevents artifacts and yields more accurate measurements than generic pipelines. Second, we uncovered the dynamics of the epigenome evolution in different genomic territories and tissue types through comparative analysis. We identified a catalog of inbred mouse strain-specific methylation differences, some of which are linked to the strains' immune, metabolic and neurological phenotypes. By streamlining DNA methylation array analysis for undesigned genomes, our methods extend epigenome research to broad species contexts.

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