DNA Pooling: a tool for large-scale association studies

Key Points DNA pooling is an effective way of reducing the cost of genotyping in large-scale association studies. DNA pools should be constituted with care to ensure that equal amounts of DNA are contributed by the individuals that make up a pool. Accurate quantitative genotyping assays are available for use on pooled DNA. Differential amplification occurs for many single-nucleotide polymorphisms, and this bias should be corrected in the estimation of allele frequency from pooled DNA. A two-stage design, in which positive marker loci from pooling studies are followed by confirmatory individual genotyping, might represent the best trade-off between the cost savings of pooling and the full information that is provided by individual genotyping. Random experimental errors in the constitution of DNA pools and in the measurement of allele frequencies from pooled DNA should be taken into account in statistical analysis. Sophisticated pooling designs are being developed that can take account of hidden population stratification, confounders and interactions, and that allow the analysis of haplotypes. DNA pooling is a practical way to reduce the cost of large-scale association studies to identify susceptibility loci for common diseases. Pooling allows allele frequencies in groups of individuals to be measured using far fewer PCR reactions and genotyping assays than are used when genotyping individuals. Here, we discuss recent developments in quantitative genotyping assays and in the design and analysis of pooling studies. Sophisticated pooling designs are being developed that can take account of hidden population stratification, confounders and inter-loci interactions, and that allow the analysis of haplotypes.