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Analysis of DNA Single Nucleotide Polymorphisms by Mass Spectrometry



Peter Vallone, John Butler


Single nucleotide polymorphisms(SNP) are the most frequent form of DNA sequence variation in the human genome and are becoming increasingly useful as genetic markers for genome mapping studies, medical diagnostics, and human identity testing. The primer extension reaction is a commonly employed molecular biology assay for probing a known single nucleotide polymorphism site in genomic DNA. In the primer extension assay a short (<30 bases) DNA oligonucleotide or primer is extended by a single nucleotide unit. The identity of the extended base allows the sample to be accurately genotyped.One method for SNP detection currently employed relies on the mass resolution between a primer and its single base extention product(s) utilizing Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry or MALDI-TOF MS. The speed of data collection by this technique is on the order of 5 sec per sample and has the potential for high throughput when interfaced with a robotic system and automated data analysis. The primer extension assay and variations upon it are described here as well as MALDI-TOF MS data collection and interpretation of primer extension reactions.
Encyclopedia of Mass Spectrometry


DNA, genetic markers, genotyping, mass spectrometry, multiplex, single nucleotide polymorphism, time-of-flight


Vallone, P. and Butler, J. (2006), Analysis of DNA Single Nucleotide Polymorphisms by Mass Spectrometry, Encyclopedia of Mass Spectrometry (Accessed June 16, 2024)


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Created March 16, 2006, Updated October 15, 2021