Novel DNA methylation targets in oral rinse samples predict survival of patients with oral squamous cell carcinoma
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ABSTRACT: Epigenome-wide association study (EWAS) of oral rinse samples from a cohort of 82 oral squamous cell carcinoma (OSCC) patients. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples. Bisulphite lsconverted DNA from the 82 oral rinse samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchip
Project description:Epigenome-wide association study (EWAS) of oral rinse samples from a cohort of 82 oral squamous cell carcinoma (OSCC) patients. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples.
Project description:Epigenome-wide association study (EWAS) of oral rinse samples from a case-control study of 154 cases and 72 controls. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples.
Project description:Epigenome-wide association study (EWAS) of blood samples from a case-control study of bladder cancer. 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 223 incident cases of bladder cancer and 205 control subjects. Bisulphite converted DNA from the 428 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2
Project description:We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence. Bisulfite-converted DNA for 2,664 human samples and 36 technical replicates were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2.
Project description:The objective of the study was to utilize DNA methylation to quantify human leukocyte subsets in human blood. This file contains data from an Illumina Infinium HumanMethlation450 for human whole blood samples as well as complex mixtures of DNA from purified human leukocyte subtypes in quantities that mimick human blood under different clinical conditions. Bisulphite converted DNA from the samples were hybridized to an Illumina Infinium HumanMethylation450 beadchip
Project description:Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip in 34 samples of non-cancerous pancreatic tissue and 82 samples of cancerous tissue samples obtained from 82 patients with pancreatic ductal adenocarcinoma.
Project description:We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence.
Project description:Genome wide DNA methylation profiling of non-pathologic peripheral blood from subjects with no history of cancer. 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 205 normal control peripheral blood samples. Bisulphite converted DNA from the 205 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2
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. Bisulphite converted DNA from the 184 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2
Project description:Genome wide methylation profiling of BM-MSC derived from AML patients in comparison to healthy donor controls using Illumina Infinium HumanMethylation450 Beadchip bisulfit converted genomic DNA extracted from BM-MSC samples (AML n=32) and healthy donor controls (n=12) were hybridized onto an Illumina Infinium HumanMethylation450 Beadchip