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SNP genotyping using Sequenom MassARRAY 7K platform.

Stacey Gabriel1, Liuda Ziaugra

  • 1Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

Current Protocols in Human Genetics
|April 23, 2008
PubMed
Summary
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This study details an accurate single-nucleotide polymorphism (SNP) genotyping assay using the Sequenom MassARRAY platform. The homogeneous Mass Extend (hME) assay combines PCR and primer extension with MALDI-TOF mass spectrometry for precise variant detection.

Area of Science:

  • Genetics
  • Molecular Biology
  • Biotechnology

Background:

  • High-throughput single-nucleotide polymorphism (SNP) genotyping is crucial for genetic research.
  • Existing technologies offer various approaches for SNP analysis.
  • The Sequenom MassARRAY platform provides a robust system for accurate genotyping.

Purpose of the Study:

  • To describe a specific SNP genotyping assay based on primer extension.
  • To highlight the utility of the Sequenom MassARRAY platform for SNP analysis.
  • To provide detailed methods for probe and genomic DNA preparation.

Main Methods:

  • The assay utilizes a locus-specific polymerase chain reaction (PCR) followed by a homogeneous Mass Extend (hME) reaction.
  • Oligonucleotide primers anneal upstream of the polymorphic site and are extended based on the variant sequence.

Related Experiment Videos

  • Mass identification of extended primers is performed using MALDI-TOF mass spectrometry.

    • Main Results:

    • The described method offers two levels of specificity for accurate SNP genotyping.
    • The hME assay provides precise detection of single-nucleotide variations.
    • MALDI-TOF mass spectrometry enables accurate mass determination of extended primers.

    Conclusions:

    • The Sequenom MassARRAY-based hME assay is an accurate and specific method for SNP genotyping.
    • This assay is suitable for researchers requiring reliable genetic variant detection.
    • Detailed protocols for sample preparation enhance the assay's applicability.