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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

DMRforPairs: identifying differentially methylated regions between unique samples using array based methylation

Martin A Rijlaarsdam, Yvonne G van der Zwan, Lambert C J Dorssers

¹Department of Pathology, Laboratory for Experimental Patho-Oncology, Erasmus MC - University Medical Center Rotterdam, Be-432, P,O, Box 2040, Rotterdam 3000 CA, Netherlands. l.looijenga@erasmusmc.nl.

BMC Bioinformatics

|June 3, 2014

Summary

DMRforPairs analyzes DNA methylation patterns in individual samples, identifying differentially methylated regions (DMRs) crucial for understanding disease and development when group comparisons aren't feasible.

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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

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Published on: September 18, 2020

Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Array-based methylation profiling, such as the Illumina Infinium HumanMethylation450 BeadChip, is vital for studying genome methylation in disease and development.
Existing analysis tools primarily focus on comparing methylation levels across sample groups or identifying differential methylated regions (DMRs) within groups.
There is a need for tools capable of comparing methylation patterns between unique, individual samples, especially when large sample sizes are not available.

Purpose of the Study:

To introduce DMRforPairs, a novel computational tool designed for the analysis of regional methylation status between unique samples.
To enable the identification and quantification of differentially methylated regions (DMRs) in individual samples.

Main Methods:

DMRforPairs identifies probe-dense genomic regions and quantifies methylation differences between individual samples.
The tool was validated using public data from four human cell lines (two lymphoblastoid, two cancer cell lines) with technical replicates.

Main Results:

DMRforPairs successfully identified DMRs between unique samples.
The number of identified DMRs correlated with the decreasing biological similarity between samples.
The detected DMRs were associated with the biological origin and phenotype of the cell lines.

Conclusions:

DMRforPairs is the first tool developed to identify and visualize significant differentially methylated regions between unique samples.
This advancement facilitates methylation analysis in scenarios with limited sample sizes.