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Hum Mutat. 2002 Jul;20(1):57-64.

Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry.

Author information

1
GSF-National Research Center for Environment and Health, Institute of Epidemiology, Neuherberg, Germany.

Abstract

One of the major challenges in the near future is the identification of genes that contribute to complex disorders. Large scale association studies that utilize a dense map of single nucleotide polymorphisms (SNPs) have been considered as a valuable tool for this purpose. However, genome-wide screens are limited by costs of genotyping thousands of SNPs in a large number of individuals. Here we present a pooling strategy that enables high-throughput SNP validation and determination of allele frequencies in case and control populations. Quantitative analysis of allele frequencies of SNPs in DNA pools is based on matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry of primer extension assays. We demonstrate the accuracy and reliability of this approach on pools of eight previously genotyped individuals with an allele frequency representation in the range of 0.1 to 0.9. The accuracy of measured allele frequencies was shown in DNA pools of 142 to 186 individuals using additional markers. Allele frequencies determined from the pooled samples deviate from the real frequencies by about 3%. The described method reduces costs and time and enables genotyping of up to thousands of samples by taking advantage of the high-throughput MALDI-TOF technology.

PMID:
12112658
DOI:
10.1002/humu.10094
[Indexed for MEDLINE]

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