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Related Experiment Video

Updated: Apr 8, 2026

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
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SNP-Based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing®.

Florence Busato1, Jörg Tost

  • 1Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.

Methods in Molecular Biology (Clifton, N.J.)
|June 25, 2015
PubMed
Summary

This study introduces a novel method for analyzing allele-specific DNA methylation using heterozygous Single Nucleotide Polymorphisms (SNPs) and Pyrosequencing. This approach enhances understanding of genotype-phenotype relationships in complex diseases.

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Last Updated: Apr 8, 2026

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Area of Science:

  • Epigenetics
  • Genetics
  • Molecular Biology

Background:

  • Allele-specific DNA methylation patterns are increasingly linked to complex disease risk loci.
  • Understanding these patterns is crucial for interpreting non-coding genetic variants and genotype-phenotype correlations.

Purpose of the Study:

  • To present a reliable protocol for analyzing DNA methylation patterns on both alleles separately.
  • To enable fine-mapping and interpretation of genetic variants associated with complex diseases.

Main Methods:

  • Utilizes heterozygous Single Nucleotide Polymorphisms (SNPs) as anchors for allele-specific PCR amplification.
  • Employs Pyrosequencing for quantitative, real-time analysis of DNA methylation patterns.
  • Incorporates Locked Nucleic Acids (LNA) in allele-specific primers for enhanced allele enrichment.

Main Results:

  • Successfully identified allele-specific DNA methylation patterns surrounding heterozygous SNPs.
  • Demonstrated proof-of-principle for imprinted genes (IGF2, IGF2R, PEG3).
  • The developed method showed higher reliability compared to existing protocols.

Conclusions:

  • The presented protocol offers a robust method for allele-specific DNA methylation analysis.
  • This technique can improve the understanding of genetic contributions to complex diseases.
  • The findings contribute to bridging the gap between genotype and phenotype through epigenetic analysis.