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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

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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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Related Experiment Video

Updated: Apr 30, 2026

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

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GoldenGate assay for DNA methylation profiling.

Marina Bibikova1, Jian-Bing Fan

  • 1Illumina Inc., San Diego, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 7, 2008
PubMed
Summary

The GoldenGate assay for methylation offers a reproducible, high-throughput method for DNA methylation analysis. This technique enables precise quantification of methylation levels across numerous samples and CpG sites.

Area of Science:

  • Epigenetics
  • Molecular Biology
  • Genomics

Background:

  • DNA methylation is a critical epigenetic mechanism influencing gene expression.
  • Accurate and high-throughput methods are needed for large-scale DNA methylation studies.
  • Existing methods can be labor-intensive or lack the capacity for broad screening.

Purpose of the Study:

  • To introduce and validate the GoldenGate assay for high-throughput, quantitative DNA methylation analysis.
  • To demonstrate the assay's reproducibility and sensitivity.
  • To provide a scalable solution for population-based epigenomic research.

Main Methods:

  • The GoldenGate assay utilizes bisulfite-converted DNA and Illumina bead arrays for targeted CpG site interrogation.
  • It allows simultaneous analysis of up to 1,536 CpG sites in 96 samples with minimal DNA input (250 ng).

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  • Probes can be designed to target specific strands or both strands at each CpG site.

    • Main Results:

    • The assay achieves high reproducibility and sensitivity, detecting as little as 2.5% methylation.
    • It can distinguish a 17% difference in absolute methylation levels between samples.
    • Performance compares favorably with methylation-specific PCR and bisulfite sequencing.

    Conclusions:

    • The GoldenGate assay for methylation is a robust and scalable tool for quantitative DNA methylation profiling.
    • It facilitates efficient analysis of large populations, aiding biomarker discovery and validation.
    • The technology offers flexibility without the need for custom array development.