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Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry

Item Type:Article
Title:Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry
Creators Name:Sauer, S. and Gelfand, D.H. and Boussicault, F. and Bauer, K. and Reichert, F. and Gut, I.G.
Abstract:In the future, analysis of single nucleotide polymorphisms (SNPs) should become a powerful tool for many genetic applications in areas such as association studies, pharmacogenetics and traceability in the agro-alimentary sector. A number of technologies have been developed for high-throughput genotyping of SNPs. Here we present the simplified GOOD assay for SNP genotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI). The simplified GOOD assay is a single-tube, purification-free, three-step procedure consisting of PCR, primer extension and phosphodiesterase II digestion followed by mass spectrometric analysis. Due to the application of charge-tag technology, no sample purification is required prior to the otherwise very impurity-sensitive MALDI analysis. The use of methylphosphonate containing primers and ddNTPs or alpha-S-ddNTPs together with a novel DNA polymerase derived from Thermotoga maritima for primer extension allow the fluent preparation of negatively charge-tagged, allele-specific products. A key feature of this polymerase is its preference for ddNTPs and alpha-S-ddNTPs over dNTPs. The simplified GOOD assay was run with automatic liquid handling at the lowest manageable volumes, automatic data acquisition and interpretation. We applied this novel procedure to genotyping SNPs of candidate genes for hypertension and cardiovascular disease.
Keywords:Automation, Cardiovascular Diseases, DNA Primers, DNA-Directed DNA Polymerase, Genotype, Hypertension, Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry, Organophosphorus Compounds, Polymerase Chain Reaction, Single Nucleotide Polymorphism, beta-2 Adrenergic Receptors
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:e22
Date:1 March 2002
Official Publication:https://doi.org/10.1093/nar/30.5.e22
PubMed:View item in PubMed

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