scholarly journals On-Chip DNA Methylation Analysis Using Osmium Complexation

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Kaori Sugizaki ◽  
Tadashi Umemoto ◽  
Akimitsu Okamoto
Keyword(s):  
Dna Methylation ◽  
Research Subject ◽  
Methylation Analysis ◽  
Methylated Dna ◽  
Chemical Assay ◽  
Challenging Research ◽  
Detection Probe ◽  
On Chip ◽  
Dna Strand ◽  
Dna Methylation Analysis

The development of a reaction for detecting the presence/absence of one methyl group in a long DNA strand is a chemically and biologically challenging research subject. A newly designed chemical assay on a chip for the typing of DNA methylation has been developed. A methylation-detection probe fixed at the bottom of microwells was crosslinked with methylated DNA mediated by osmium complexation and contributes to selective amplification of methylated DNA.

scholarly journals Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis

Epigenomics ◽  
2016 ◽  
Vol 8 (8) ◽  
pp. 1061-1077 ◽  
Author(s):  
Hae Min Jeong ◽  
Sangseon Lee ◽  
Heejoon Chae ◽  
RyongNam Kim ◽  
Mi Jeong Kwon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Whole Genome ◽  
Methylation Analysis ◽  
Methylated Dna ◽  
Bisulphite Sequencing ◽  
Dna Methylation Analysis

LoMA-B: a simple and versatile lab-on-a-chip system based on single-channel bisulfite conversion for DNA methylation analysis

Lab on a Chip ◽  
2015 ◽  
Vol 15 (17) ◽  
pp. 3530-3539 ◽  
Author(s):  
Jaeyun Yoon ◽  
Mi Kyoung Park ◽  
Tae Yoon Lee ◽  
Yong-Jin Yoon ◽  
Yong Shin
Keyword(s):  
Dna Methylation ◽  
Single Channel ◽  
Methylation Status ◽  
Lab On A Chip ◽  
Label Free ◽  
Bisulfite Conversion ◽  
Methylation Analysis ◽  
Processing Module ◽  
On Chip ◽  
Dna Methylation Analysis

Here, we present a Lab-on-a-Chip system for DNA Methylation Analysis based on Bisulfite conversion (LoMA-B), which is coupled to a sample pre-processing module for on-chip bisulfite conversion and a label-free, real-time detection module for rapid analysis of DNA methylation status.

scholarly journals Detection of colorectal cancer in urine using DNA methylation analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
S. Bach ◽  
I. Paulis ◽  
N. R. Sluiter ◽  
M. Tibbesma ◽  
I. Martin ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Methylation ◽  
Regression Tree ◽  
Classification And Regression Tree ◽  
Multivariate Logistic Regression ◽  
Methylation Analysis ◽  
Methylated Dna ◽  
Non Invasive ◽  
Regression Tree Analysis ◽  
Dna Methylation Analysis

AbstractColorectal cancer (CRC) is the second leading cause for cancer-related death globally. Clinically, there is an urgent need for non-invasive CRC detection. This study assessed the feasibility of CRC detection by analysis of tumor-derived methylated DNA fragments in urine. Urine samples, including both unfractioned and supernatant urine fractions, of 92 CRC patients and 63 healthy volunteers were analyzed for DNA methylation levels of 6 CRC-associated markers (SEPT9, TMEFF2, SDC2, NDRG4, VIM and ALX4). Optimal marker panels were determined by two statistical approaches. Methylation levels of SEPT9 were significantly increased in urine supernatant of CRC patients compared to controls (p < 0.0001). Methylation analysis in unfractioned urine appeared inaccurate. Following multivariate logistic regression and classification and regression tree analysis, a marker panel consisting of SEPT9 and SDC2 was able to detect up to 70% of CRC cases in urine supernatant at 86% specificity. First evidence is provided for CRC detection in urine by SEPT9 methylation analysis, which combined with SDC2 allows for an optimal differentiation between CRC patients and controls. Urine therefore provides a promising liquid biopsy for non-invasive CRC detection.

scholarly journals P46.03 DNA Methylation Analysis in Smokers and Non-Smokers (Passive and ex-Smokers)

2021 ◽  
Vol 16 (3) ◽  
pp. S490
Author(s):  
D.M. Aguilar-Beltrán ◽  
A.G. Alcázar-Ramos ◽  
A.L. Vega-Rodríguez ◽  
D.G. García-Gutiérrez ◽  
A.D. Bertadillo-Jilote ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Analysis ◽  
Dna Methylation Analysis

scholarly journals DNA Methylation in Solid Tumors: Functions and Methods of Detection

2021 ◽  
Vol 22 (8) ◽  
pp. 4247
Author(s):  
Andrea Martisova ◽  
Jitka Holcakova ◽  
Nasim Izadi ◽  
Ravery Sebuyoya ◽  
Roman Hrstka ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Solid Tumors ◽  
Epigenetic Modification ◽  
Single Gene ◽  
Restriction Enzymes ◽  
Methylation Analysis ◽  
Cpg Dinucleotides ◽  
Sequencing Technologies ◽  
Genome Level ◽  
Dna Methylation Analysis

DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.

scholarly journals Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy

GigaScience ◽  
2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Katarzyna Murat ◽  
Björn Grüning ◽  
Paulina Wiktoria Poterlowicz ◽  
Gillian Westgate ◽  
Desmond J Tobin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Association Studies ◽  
Methylation Analysis ◽  
Web Based ◽  
Array Platform ◽  
Complex Evaluation ◽  
The Galaxy ◽  
Population Epigenetics ◽  
Analyse Data ◽  
Dna Methylation Analysis

Abstract Background Infinium Human Methylation BeadChip is an array platform for complex evaluation of DNA methylation at an individual CpG locus in the human genome based on Illumina’s bead technology and is one of the most common techniques used in epigenome-wide association studies. Finding associations between epigenetic variation and phenotype is a significant challenge in biomedical research. The newest version, HumanMethylationEPIC, quantifies the DNA methylation level of 850,000 CpG sites, while the previous versions, HumanMethylation450 and HumanMethylation27, measured &gt;450,000 and 27,000 loci, respectively. Although a number of bioinformatics tools have been developed to analyse this assay, they require some programming skills and experience in order to be usable. Results We have developed a pipeline for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Human Methylation BeadChip. Our tool is integrated into Galaxy (http://galaxyproject.org), a web-based platform. This allows users to analyse data from the Infinium Human Methylation BeadChip in the easiest possible way. Conclusions The pipeline provides a group of integrated analytical methods wrapped into an easy-to-use interface. Our tool is available from the Galaxy ToolShed, GitHub repository, and also as a Docker image. The aim of this project is to make Infinium Human Methylation BeadChip analysis more flexible and accessible to everyone.

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