A standard protocol for single nucleotide primer extension in the human genome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

C.A. Wise; M. Paris; B. Morar; W. Wang; L. Kalaydjieva; A.H. Bittles

doi:10.1002/rcm.1038

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A standard protocol for single nucleotide primer extension in the human genome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Journal article

Peer reviewed

A standard protocol for single nucleotide primer extension in the human genome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

C.A. Wise, M. Paris, B. Morar, W. Wang, L. Kalaydjieva and A.H. Bittles

Rapid Communications in Mass Spectrometry, Vol.17(11), pp.1195-1202

2003

DOI: https://doi.org/10.1002/rcm.1038

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Abstract

Analysis of single nucleotide polymorphisms (SNPs) has become an increasingly important area of research, with numerous applications in medical genetics, population genetics, forensic science, and agricultural biotechnology. Large-scale SNP analyses require the development of methodologies that are economical, flexible, accurate and capable of automation. Primer extension in conjunction with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is currently emerging as a potential method for high-throughput SNP genotyping. We have evaluated a number of published primer extension methods and refined a simple and robust protocol to analyze human autosomal disease-causing mutations and population genetic markers on the Y-chromosome. Twelve different variant sites were examined, and homozygotes, heterozygotes and hemizygotes were accurately typed. A 100% concordance was observed between SNP genotypes obtained using the MALDI-TOFMS technique and alternative genotyping methods, such as restriction fragment length polymorphism (RFLP) assays and denaturing high-performance liquid chromatography (DHPLC). Since multiple polymorphisms can be detected in single reactions, the method provides a cost-effective approach for SNP analysis. The protocol is also extremely flexible (able to accommodate new markers) and can be adapted to a number of platforms without the use of commercial kits.

Details

Title: A standard protocol for single nucleotide primer extension in the human genome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Authors/Creators: C.A. Wise (Author/Creator) - Edith Cowan University
M. Paris (Author/Creator) - Murdoch University
B. Morar (Author/Creator) - Edith Cowan University
W. Wang (Author/Creator) - Edith Cowan University
L. Kalaydjieva (Author/Creator) - Edith Cowan University
A.H. Bittles (Author/Creator) - Edith Cowan University
Publication Details: Rapid Communications in Mass Spectrometry, Vol.17(11), pp.1195-1202
Publisher: John Wiley and Sons Ltd
Identifiers: 991005540037607891
Copyright: © 2003 John Wiley & Sons, Ltd.
Murdoch Affiliation: State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration
Citation topics: 2 Chemistry; 2.211 Mass Spectrometry; 2.211.304 Mass Spectrometry Advances
Web Of Science research areas: Biochemical Research Methods; Chemistry, Analytical; Spectroscopy
ESI research areas: Chemistry