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

You might also read

Related Articles

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

Sort by
Same author

DNA methylation profiling in Huntington's disease reveals disease associated changes in the striatum.

Clinical epigenetics·2026
Same author

Schizophrenia risk gene ZNF804A controls ribosome localization and synaptogenesis in developing human neurons.

Science advances·2026
Same author

The prenatal sex steroid theory of autism after 25 years.

Nature human behaviour·2026
Same author

Epigenetic biomarkers in neurodegenerative diseases: from molecular signatures to therapeutic targets.

Trends in neurosciences·2026
Same author

Methylomic signatures of tau and amyloid-beta in transgenic mouse models of Alzheimer's disease neuropathology.

NPJ dementia·2026
Same author

Gene-Environment Correlation Across Trauma Subtypes and Developmental Timing: Evidence From the EU-GEI and ALSPAC.

Biological psychiatry·2026
Same journal

pGWAS-Portal: a comprehensive online platform for integrative post-genome-wide association study analysis.

BMC genomics·2026
Same journal

Physiological and transcriptomic analyses of Rosa persica in response to drought stress and functional validation of the transcription factor RpERF113-like.

BMC genomics·2026
Same journal

Integrated analysis of chromatin accessibility and transcriptome profiles in granulosa cells of sheep with different FecB genotypes.

BMC genomics·2026
Same journal

Correction: TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations.

BMC genomics·2026
Same journal

Chromosomal scale genome assembly of medicinal plant Sophora tonkinensis.

BMC genomics·2026
Same journal

Variant-specific RNA testing resolves variants of uncertain significance in exome testing.

BMC genomics·2026
See all related articles

Related Experiment Video

Updated: May 11, 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

A data-driven approach to preprocessing Illumina 450K methylation array data.

Ruth Pidsley1, Chloe C Y Wong, Manuela Volta

  • 1Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, King's College London, De Crespigny Park, London, UK.

BMC Genomics
|May 2, 2013
PubMed
Summary
This summary is machine-generated.

Optimizing DNA methylation analysis on the 450K BeadChip is crucial for understanding disease. Quantile normalization of methylated and unmethylated signals, separately for Type I and Type II assays, significantly improves data quality and statistical power.

More Related Videos

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

Methodology for Accurate Detection of Mitochondrial DNA Methylation
12:11

Methodology for Accurate Detection of Mitochondrial DNA Methylation

Published on: May 20, 2018

Related Experiment Videos

Last Updated: May 11, 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

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

Methodology for Accurate Detection of Mitochondrial DNA Methylation
12:11

Methodology for Accurate Detection of Mitochondrial DNA Methylation

Published on: May 20, 2018

Area of Science:

  • Epigenetics and Genomics
  • Bioinformatics and Computational Biology

Background:

  • DNA methylation is a key epigenetic mark with implications in development and disease.
  • Genome-wide DNA methylation analysis requires efficient and cost-effective methods.
  • The Illumina Infinium HumanMethylation450 (450K) BeadChip offers a valuable tool but requires careful normalization due to its complex design.

Purpose of the Study:

  • To evaluate and improve normalization strategies for the 450K BeadChip data.
  • To develop metrics for assessing data quality in DNA methylation studies.
  • To enhance statistical power for detecting small DNA methylation changes relevant to complex diseases.

Main Methods:

  • Utilized known DNA methylation patterns (genomic imprinting, X-chromosome inactivation) and SNP assay performance to derive quality metrics.
  • Tested various normalization schemes, including quantile normalization, on 11 methylomic datasets.
  • Compared normalization of raw beta values versus separate normalization of methylated (M) and unmethylated (U) signal intensities for Type I and Type II assays.

Main Results:

  • Quantile normalization significantly improves data consistency across all tested metrics compared to default methods.
  • Separate normalization of M and U signal intensities is superior to normalizing beta values.
  • Separate normalization for Type I and Type II assays yields better results than combined normalization.

Conclusions:

  • Careful selection of preprocessing and normalization steps is vital for minimizing variance and increasing statistical power in DNA methylation studies.
  • The developed metrics can serve as quality scores for 450K datasets.
  • A user-friendly R software package, wateRmelon, was created to facilitate the application of these normalization methods and quality tests.