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DNA methylation analysis in oropharyngeal cancer [450K array]

ABSTRACT: DNA methylation analysis in oropharyngeal cancer [450K array]

PROVIDER: PRJNA512095 | ENA |

REPOSITORIES: ENA

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DNA methylation analysis in oropharyngeal cancer [450K array]

Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.

2020-01-20 | GSE124464 | GEO

DNA methylation analysis in oropharyngeal cancer [EPIC array]

Project description:DNA methylation analysis in oropharyngeal cancer [EPIC array]

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DNA methylation analysis in oropharyngeal cancer [EPIC array]

Project description:DNA methylation analysis in oropharyngeal squamous carcinoma (OPSCC) samples and oropharyngeal non-cancerous mucosa samples. Infinium MethylationEPIC BeadChip Kit was used to obtain DNA methylation profiles across more than 850,000 CpG sites. Total samples included 89 OPSCC samples and 5 non-cancerous mucosa samples.

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Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India

Project description:Methylation of CpG Islands within promoter regions of genes has been associated with gene silencing, suggesting loss of tumor suppressor function and tumorigenesis. The northeastern states of India are leaders in the country for cancers of several sites. Almost no reports are available of any DNA methylation biomarker for oropharyngeal cancers of the northeastern states. The present study aimed to identify targets of CpG hypermethylation and hypomethylation in oropharyngeal cancer prevalent in northeast India. Using Illumina Infinium Human Methylation 450K microarray platform a genome wide screening has been done for differentially methylated genes, including genes not previously implicated in carcinogenesis. Differential gene expression correlated to their methylation status was elaborated using transcriptome profiling. The new genes identified may be used to develop promising panels of DNA Methylation biomarkers for oropharyngeal screening and detection at a very early stage.

2020-09-25 | GSE136704 | GEO

DNA methylation analysis in oropharyngeal cancer

Project description:DNA methylation analysis in oropharyngeal cancer

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ICGC CLL 450k DNA methylation

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Differential Methylation Of The TRPA1 Promoter In Pain Sensitivity: DNA methylation 450k array

Project description:Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 43 samples with Illumina HumanMethylation450 BeadChip data. Bisulphite converted DNA from 43 of these samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

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DNA methylation analysis of oropharyngeal squamous cell carcinoma

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DNA methylation profiling for 850k reannotation and normalization evaluation [450k]

Project description:Illumina Infinium DNA Methylation (5mC) profiling arrays are a popular technology to measure genome-scale distribution of 5mC at low cost and high throughput, especially in cancer and other complex diseases. Following the success of the HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers in addition to regulatory regions primarily covered by the 450k (i.e. promoters, gene bodies). Despite its widespread use, the analysis of 850k data remains suboptimal as it mostly still relies on Illumina’s default annotation, which underestimates enhancers and long noncoding RNAs (lncRNAs). We thus developed an approach, based on ENCODE and LNCipedia databases, that greatly improves Illumina’s default annotation of enhancers and long noncoding transcripts. Comparisons between the re-annotated 850k and its precursor, the 450k, or RRBS, another high-throughput 5mC profiling technology, revealed that the 850k covers at least three times more enhancers and lncRNAs than the other two technologies. We further investigated the reproducibility of the three technologies and applied various normalisation methods to 850k data, showing that most of them reduce variability to a level below that of RRBS. When analyzed with our new annotation and normalization pipeline, profiling for 5mC changes in breast cancer biopsies with the 850k highlighted aberrant enhancers methylation as the predominant feature, confirming previous reports. In conclusion, our study provides an updated analysis pipeline for 850k data based on a refined probe annotation and normalization that allows for the improved analysis of methylation at enhancers and long noncoding transcripts.

2022-11-11 | GSE198626 | GEO

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