High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools

Abstract

To facilitate positional cloning of complex trait susceptibility loci, we are investigating methods to reduce the effort required to identify trait-associated alleles. We examined primer extension analysis by matrix-assisted laser desorption͞ionization time-offlight mass spectrometry to screen single-nucleotide polymorphisms (SNPs) for association by using DNA pools. We tested whether this method can accurately estimate allele frequency differences between pools while maintaining the high-throughput nature of assay design, sample handling, and scoring. We follow up interesting allele frequency differences in pools by genotyping individuals. We tested DNA pools of 182, 228, and 499 individuals using 16 SNPs with minor allele frequencies 0.026 -0.486 and allele frequency differences 0.001-0.108 that we had genotyped previously on individuals and 381 SNPs that we had not. Precision, as measured by the average standard deviation among 16 semidependent replicates, was 0.021 ؎ 0.011 for the 16 SNPs and 0.018 ؎ 0.008 for the 291͞381 SNPs used in further analysis. For the 16 SNPs, the average absolute error in predicting allele frequency differences between pools was 0.009; the largest errors were 0.031, 0.028, and 0.027. We determined that compensating for unequal peak heights in heterozygotes improved precision of allele frequency estimates but had only a very minor effect on accuracy of allele frequency differences between pools. Based on these data and assuming pools of 500 individuals, we conclude that at significance level 0.05 we would have 95% (82%) power to detect population allele frequency differences of 0.07 for control allele frequencies of 0.10 (0.50).A ssociation studies provide a powerful approach to identify the DNA variants underlying complex traits (1). Currently, association studies can be especially useful for narrowing a complex trait candidate interval identified by linkage analysis (2, 3), although improved genotyping technology and a map of single-nucleotide polymorphisms (SNPs) identifying the common haplotypes in the human genome may enable association studies of loci spanning the entire genome. A rate-limiting step for association studies is to obtain the large number of genotypes needed. Currently, a linkage region expected to contain a complex trait locus typically spans 10-20 Mb, and even with a priori knowledge of the linkage disequilibrium between DNA variants, thousands of densely spaced SNPs with a range of allele frequencies may need to be screened (4). In addition, sample sizes of hundreds or even thousands of individuals may be required to have sufficient power to detect loci with modest effect.A reliable screening method to identify SNPs associated with disease without genotyping all individuals would be efficient and economical. Screening SNPs by typing a limited number of DNA pools representing cases and controls in principle requires vastly fewer genotypes for each SNP, reducing labor and reagent costs. Genotyping cost becomes essentially independent of sample size, allowing lar...

Association between a variation in LRCH1 and knee osteoarthritis: A genome‐wide single‐nucleotide polymorphism association study using DNA pooling

“…The basic design was a 2-group study of subjects with and without OA of the knee. To facilitate the screening of such a large number of SNPs, we utilized a high-throughput approach using DNA pools, chip-based mass spectrometry (24)(25)(26), and a 3-step SNP selection strategy (27). In the first step, we performed a single PCR and primer extension reaction for each SNP on 2 DNA pools consisting of equimolar amounts of DNA from each subject in each study group (knee OA and control).…”

A whole genome association study of neuroticism using DNA pooling

“…DNA pooling allows substantial savings in genotyping costs (see, for example, references [44][45][46] ) and there have been successes using DNA pooling in the analysis of a relatively small number of markers, for example, in schizophrenia 47,48 multiple sclerosis, 49 and serum high-density lipoprotein cholesterol levels. 50,51 However, in the two cases where whole genome association has been attempted (that is, in memory 52 and mild mental impairment 53 ), the yields have been low, that is, in both cases only one locus was considered significant.…”

Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry

“…The accuracy and precision of this approach have been studied extensively for estimating allele frequencies in DNA pools by primer extension and MALDI-TOF MS (21)(22)(23)(24)(25). The mass spectrometric analytical challenge is actually less demanding for methylation analysis.…”