Tag: MethylationEPIC

Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer

Lung cancer ICB cohort Advanced non-small cell lung carcinoma patients who were treated with anti-PD-1/PD-L1 monotherapy at Samsung Medical Center, Seoul, Republic of Korea were enrolled for this study. The present study has been reviewed and approved by the Institutional Review Board (IRB) of the Samsung Medical Center (IRB no….

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Longitudinal changes and variation in human DNA methylation analysed with the Illumina MethylationEPIC BeadChip assay and their implications on forensic age prediction

In this study, genome-wide methylation profiles of 128 blood samples were examined. Two blood DNA methylation profiles from 64 individuals were obtained using the Illumina EPIC850k array. Two blood DNA methylation profiles were generated from samples collected in 2007 and 2021, respectively. All samples passed the SeSAMe quality control. A…

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Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls

World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….

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The association between neighborhood deprivation, DNA methylation, and gene expression in breast tissue for Black and White women with breast cancer

In a recent study published in JAMA Network Open, researchers investigated the association between neighborhood deprivation and alterations in deoxyribonucleic acid (DNA) methylation and gene expression in breast cancer tissues of Black and White women. Study: Neighborhood Deprivation and DNA Methylation and Expression of Cancer Genes in Breast Tumors. Image…

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Understanding the Impact on DNA and Gene Expression

A recent study published in JAMA Network Open delved into the relationship between neighborhood deprivation and changes in DNA methylation and gene expression in breast cancer tissues among Black and White women. While advancements in breast cancer treatment have lowered mortality rates for all racial and ethnic groups, Black women…

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The DNA Methylation Sequencing Market Analysis Report focuses on its Market Growth development, average selling price, and global market size is rising at a CAGR of 9.5% from 2023 – 2030

The “DNA Methylation Sequencing Market” is focused on controlling cost, and improving efficiency. Moreover, the reports offer both the demand and supply aspects of the market. The DNA Methylation Sequencing market is expected to grow annually by 9.5% (CAGR 2023 – 2030). DNA Methylation Sequencing Market Overview and Report Coverage…

Continue Reading The DNA Methylation Sequencing Market Analysis Report focuses on its Market Growth development, average selling price, and global market size is rising at a CAGR of 9.5% from 2023 – 2030

Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples

Background: The pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K…

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iGEM as a human iPS cell-based global epigenetic modulation detection assay provides throughput characterization of chemicals affecting DNA methylation

Chemicals Dimethyl sulfoxide (DMSO) was purchased from Sigma-Aldrich (St. Louis, MO, USA), and 5-aza-2′-deoxycytidine (5-aza-dc), trichostatin A (TSA), bisphenol A, benzo[a]pyrene (BaP), benzo[c]fluorene (BcF), and beryllium sulfate (BeSO4) were obtained from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). The SCREEN-WELL Cardiotoxicity Library was purchased from Enzo LifeScience Inc. (Supplementary Table…

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DNA Methylation-Based ‘Biological’ Age Associated With Race, Poverty

NEW YORK – Household income below the poverty level and African American racial identity are associated with faster epigenetic aging, according to a new study. “Environmental factors, including psychological stress, alter gene expression and physiological response through changes in the epigenome,” the authors wrote. “DNA methylation may be the mediation mechanism for the…

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Error when changing the database for minfi dropLociWithSnps

Error when changing the database for minfi dropLociWithSnps 2 I am currently filtering Illumina MethylationEPIC data with minfi, which has run smoothly so far. To remove polymorphic CpGs and SBEs I use the following code: NormFlt <- dropLociWithSnps(NormFlt, snps=c(“SBE”,”CpG”), snpAnno=”SNPs.147CommonSingle”) And get the following error: Error in getSnpInfo(object, snpAnno =…

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minfi support of illumina Infinium methylationEPIC v2.0

minfi support of illumina Infinium methylationEPIC v2.0 1 @lucas-24386 Last seen 2 days ago Italy Hi all. I have tried to process Infinium methylationEPIC v2.0 with minfi v1.44.0 but it did not work, apparently not recognizing the arrays: function “read.metharray.exp” results in “unknown” for the annotation. Is there a way…

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conumee with Infinium MethylationEPIC v2.0

conumee with Infinium MethylationEPIC v2.0 0 @lucas-24386 Last seen 10 hours ago Italy Dear all, we are planning to perform methylation profiling of FFPE tumor samples with the Infinium MetlylationEPIC v2.0 chips, and we would like to use the data to do CNV analysis as well. Can conumee be run…

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Accurate Prenatal Diagnosis of Fetal CHD

The following is a summary of “Cell-free DNA in maternal blood and artificial intelligence: accurate prenatal detection of fetal congenital heart defects,” published in the January 2023 issue of Obstetrics and Gynecology by Singh, et al. One crucial process for regulating gene expression in the development of the heart is…

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Aging | Epigenetic age and lung cancer risk i

image: Epigenetic Age and Lung Cancer Risk in the CLUE II Prospective Cohort Study view more  Credit: 2023 Michaud et al. BUFFALO, NY- February 16, 2023 – A new research paper was published in Aging (listed as “Aging (Albany NY)” by MEDLINE/PubMed and “Aging-US” by Web of Science) Volume 15, Issue…

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DNA methylation GrimAge acceleration in US military veterans with PTSD

doi: 10.1038/s41386-023-01537-z. Online ahead of print. Affiliations Expand Affiliations 1 Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA. 2 Department of Psychiatry & Behavioral Health, and Institute for Behavioral Medicine Research, The Ohio State University, Columbus, OH, USA. Anthony.King@osumc.edu. 3 Department of Psychiatry, Michigan Medicine, University of Michigan,…

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I want to identify the version of MethylationEPIC from the idat file.

I want to identify the version of MethylationEPIC from the idat file. 1 I have idat files of Infinium MethylationEPIC. I would like to know if the array of this file is Infinium MethylationEPIC v1.0 or Infinium MethylationEPIC v2.0. Is it possible to investigate the version of the MethylationEPIC from…

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Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential

Weisman, D. & McKeith, I. Dementia with Lewy Bodies. Semin. Neurol. 27, 042–047 (2007). Article  Google Scholar  Foguem, C. & Manckoundia, P. Lewy Body Disease: Clinical and Pathological “Overlap Syndrome” Between Synucleinopathies (Parkinson Disease) and Tauopathies (Alzheimer Disease). Curr. Neurol. Neurosci. Rep. 2018 18:5 18, 1–9 (2018). CAS  Google Scholar …

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re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods

Illumina Infinium DNA Methylation (5mC) arrays are a popular technology for low-cost, high-throughput, genome-scale measurement of 5mC distribution, especially in cancer and other complex diseases. After the success of its HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers. Despite the widespread use of 850k,…

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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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From idat Illumina Infinium MethylationEPIC to CNV analysis for homo/hetero-zigous deletion

From idat Illumina Infinium MethylationEPIC to CNV analysis for homo/hetero-zigous deletion 0 Hi, My group works on cancer and we have difficulty on a little part of our last project about malignant pleuric mesothelioma. I’m looking for help in the analysis of .idat from genome-wide DNA methylation profiles obtained via…

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