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Related Experiment Videos

A single nucleotide polymorphism based approach for the identification and characterization of gene expression

Christian Jurinke1, Mikhail F Denissenko, Paul Oeth

  • 1SEQUENOM Inc., 3595 John Hopkins Court, San Diego, CA, USA. cjurinke@sequenom.com

Mutation Research
|April 15, 2005
PubMed
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This study introduces an integrated platform for analyzing genetic variations, including single nucleotide polymorphisms (SNPs), allele-specific expression, and DNA methylation. This approach simplifies complex functional genomic studies by assaying genomic and transcript variations.

Area of Science:

  • Genomics
  • Molecular Biology
  • Genetic Variation Analysis

Background:

  • Single nucleotide polymorphisms (SNPs) are common genetic variations.
  • SNPs are increasingly used beyond genotyping for quantitative transcript level determination.
  • Allelic variation can influence gene expression and be associated with genomic/transcript modifications like DNA methylation.

Purpose of the Study:

  • To describe an integrated genetic analysis platform for discovering coding SNPs (cSNPs).
  • To utilize cSNPs for analyzing allele-specific expression and DNA methylation patterns.
  • To validate the platform using the human tumor protein 73 (TP73) gene model.

Main Methods:

  • Utilized matrix-assisted laser desorption/ionisation-time-of-flight (MALDI-TOF) MassARRAY platform.

Related Experiment Videos

  • Integrated discovery of cSNPs, analysis of allele-specific expression, and methylation pattern analysis.
  • Employed the TP73 gene for model system validation.

    • Main Results:

    • Successfully discovered coding SNPs (cSNPs).
    • Identified and analyzed allele-specific expression patterns.
    • Correlated allele-specific expression with DNA methylation patterns.
    • Validated the integrated platform's efficacy using the TP73 gene.

    Conclusions:

    • The integrated MassARRAY platform simplifies complex functional genomic studies.
    • Enables simultaneous assaying of stable (genomic) and dynamic (transcript, methylation) variation.
    • Facilitates a comprehensive understanding of genetic variation's impact on gene expression.