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Large‐scale determination of SNP allele frequencies in DNA pools using MALDI‐TOF mass spectrometry
Author(s) -
Werner Monika,
Sych Michael,
Herbon Nicole,
Illig Thomas,
König Inke R.,
Wjst Matthias
Publication year - 2002
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.10094
Subject(s) - biology , genotyping , snp genotyping , single nucleotide polymorphism , allele frequency , genetics , allele , computational biology , genotype , gene
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. © 2002 Wiley‐Liss, Inc.