Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA Microarrays02:34

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The promise of adaptive health in the United Arab Emirates and beyond.

Nature genetics·2026
Same author

Estimation of direct and indirect polygenic effects and gene-environment interactions using polygenic scores in case-parent trio studies.

Nature genetics·2026
Same author

Perceived Stress During Pregnancy and Offspring Attention-Deficit/Hyperactivity Disorder: Findings From the ECHO Cohort Study.

JAACAP open·2026
Same author

Non-Mendelian inheritance of DNA methylation patterns in mice.

Nature genetics·2026
Same author

Associations between maternal occupational history and autism spectrum disorder diagnosis in offspring in Denmark.

Occupational and environmental medicine·2026
Same author

DNA Methylation Stochasticity Is Linked to Transcriptional Variability and Convergent Epigenetic Disruption across Genetic Subtypes of Acute Myeloid Leukemia.

Cancer research·2026

Related Experiment Video

Updated: Jun 14, 2026

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
14:56

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Published on: May 6, 2022

Comprehensive high-throughput arrays for relative methylation (CHARM).

Christine Ladd-Acosta1, Martin J Aryee, Jared M Ordway

  • 1Department of Medicine, Johns Hopkins University School of Medicine, Center for Epigenetics, Baltimore, Maryland, USA.

Current Protocols in Human Genetics
|April 8, 2010
PubMed
Summary

Comprehensive high-throughput arrays for relative methylation (CHARM) offers a sensitive, genome-wide DNA methylation measurement. This method analyzes all genomic regions, correcting for biases to study epigenomic changes in health and disease.

More Related Videos

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
07:50

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Related Experiment Videos

Last Updated: Jun 14, 2026

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
14:56

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Published on: May 6, 2022

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
07:50

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Area of Science:

  • Epigenetics
  • Genomics
  • Molecular Biology

Background:

  • DNA methylation (DNAm) is a heritable epigenetic modification crucial for gene regulation in mammals.
  • Existing methods for DNA methylation analysis often focus on specific loci, limiting genome-wide insights.
  • Technological advancements are enabling comprehensive, genome-wide DNA methylation profiling.

Purpose of the Study:

  • To introduce Comprehensive High-throughput Arrays for Relative Methylation (CHARM) as a novel method for genome-wide DNA methylation analysis.
  • To present CHARM as a sensitive and specific approach for measuring DNA methylation across the entire genome.
  • To highlight CHARM's applicability in studying epigenomic alterations in both normal and diseased states.

Main Methods:

  • CHARM utilizes high-throughput arrays to quantify DNA methylation status genome-wide.
  • The method does not presuppose functionally important DNA methylation regions, including CpG islands and promoter regions.
  • A novel genome-weighted smoothing algorithm corrects for CpG density and fragment biases inherent in DNA fractionation techniques.

Main Results:

  • CHARM provides a sensitive and specific measurement of DNA methylation across the genome.
  • The method effectively analyzes DNA methylation in both high and low CpG-density regions.
  • CHARM's algorithm corrects for biases, improving the accuracy of methylation data.

Conclusions:

  • CHARM is a powerful tool for comprehensive genome-wide DNA methylation analysis.
  • This method facilitates the study of epigenomic changes associated with various biological conditions, including diseases.
  • CHARM offers a robust approach for advancing epigenomic research.