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Qualitative and Quantitative Genotyping Using Single Base Primer Extension Coupled with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MassARRAY®)

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Single Nucleotide Polymorphisms

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 578))

Abstract

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has developed over the past decade into a versatile tool for the analysis of nucleic acids and especially as a reliable genotyping platform. This chapter summarizes its use in the context of the most widely used MALDI-TOF MS genomics platform, the Sequenom® MassARRAY® system. MassARRAY® genotyping is based upon region-specific PCR followed by allele-specific single base primer extension reactions which are then desalted, dispensed onto a silica array preloaded with matrix, and the genotyping products are resolved on the basis of mass using MALDI-TOF MS. The platform is versatile in that it can resolve multiplexed reactions (40+ separate loci per reaction), acquires and interprets data quickly, gives a quantitative output which reflects the amount of product generated for each allele within an assay for multiplexed reactions, and is highly sensitive. These characteristics coupled with integrated software for sequence annotation, assay design, data interpretation, and data storage have lead to its wide adoption and use for multiple nucleic acid analysis applications in both the realm of genomics research and molecular diagnostics.

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Author information

Authors and Affiliations

  1. Research and Development, Sequenom, Inc, San Diego, CA, USA

    Paul Oeth, Guy del Mistro, George Marnellos, Tao Shi & Dirk van den Boom

Authors
  1. Paul Oeth
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  2. Guy del Mistro
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  3. George Marnellos
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  4. Tao Shi
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  5. Dirk van den Boom
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Editor information

Editors and Affiliations

  1. Center for Gene Regulation in, Cleveland State University, Euclid Ave. 2121, Cleveland, 44115, U.S.A.

    Anton A. Komar

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC 2003

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Oeth, P., Mistro, G.d., Marnellos, G., Shi, T., van den Boom, D. (2009). Qualitative and Quantitative Genotyping Using Single Base Primer Extension Coupled with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MassARRAY®). In: Komar, A. (eds) Single Nucleotide Polymorphisms. Methods in Molecular Biology™, vol 578. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-411-1_20

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  • DOI: https://doi.org/10.1007/978-1-60327-411-1_20

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-410-4

  • Online ISBN: 978-1-60327-411-1

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