Mass Spec Genotyping

Sequenom SNP genotyping uses a bead-less and label-free primer-extension chemistry to generate allele-specific products with distinct masses. The backbone of its high-throughput detection capabilities is the speed and accuracy of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS). Allele discrimination is conferred by primer extension with a high-fidelity polymerase enzyme across the SNP site, leading to differences in mass of extended products. Differentiation of genotypes for each of the SNPs multiplexed in one assay is a result of unique mass ranges for the extension primers.

The Genomics Platform currently offers Sequenom's hME technology, allowing the rapid design and deployment of pooled assays with up to seven SNPs, and Sequenom's higher complexity iPLEX technology, where up to 36 SNPs are simultaneously assayed.

Assays available
hME: any number of custom SNPs in pooled assays of up to 7 SNPs
iPLEX: any number of custom SNPs in pooled assays of up to 36 SNPs

Details about Sequenom technology
Sequenom technology combines a homogeneous reaction format with standardized assay conditions. Each assay has a single extension primer to interrogate both alleles, minimizing the total number of reactions required.

The MassEXTEND reaction has three levels of biological stringency:

  • Polymerase chain reaction (PCR) target amplification
  • Extension primer binding
  • Primer extension across polymorphic base(s) with a high-fidelity DNA polymerase enzyme

For more information from Sequenom about this technology, please click here.

Minimum requirements

A minimum of 100,000 planned genotypes (samples x SNPs) is required for new projects