Genotyping with Sequenom

  • Martina Bradić
  • João Costa
  • Ivo M. Chelo
Part of the Methods in Molecular Biology book series (MIMB, volume 772)


Often in evolutionary genetics research, one needs to analyze polymorphisms in populations for which cost-efficient high-throughput arrays are nonexistent, either because the species is not a model organism or because the populations have been subjected to such specific conditions that their base variation is almost unique. In this situation, custom-made genotyping assays are required. Sequenom’s MassARRAY® genotyping platform is a powerful and flexible method for assaying up to a few thousand markers and up to thousands of individuals. It is based on distinguishing allele-specific primer extension products by mass spectrometry (MALDI-TOF). Most stages of the experimental protocol reflect adaptations of established PCR protocols to multiplexing, which allows the simultaneous amplification and detection of multiple markers per reaction.

Key words

Genotyping SNP MALDI-TOF Sequenom MassARRAY® 



We thank to Henrique Teotónio and Richard Borowsky for their support and useful comments and everyone at the Instituto Gulbenkian de Ciência Genomics Unit, especially Isabel Marques for the help with the overall procedure and data analysis.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of BiologyNew York UniversityNew YorkUSA
  2. 2.Instituto Gulbenkian de CiênciaOeirasPortugal

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