Evidence is mounting that multiple genes are involved in complex traits and that these each account for very small proportions of the overall phenotypic variance. Association studies of many markers in 1000s of individuals will be required to identify such genes. A number of large twin cohorts have already been collected and provide a valuable resource for carrying out studies that are robust to the effect of population stratification. Technologies based on microarrays will soon allow 1,000,000 SNPs to be typed at one time, however financial considerations prevent most researchers from using these approaches to genotype all individuals. Recently, microarrays have been shown to give accurate allele frequency measurements in pooled DNA samples and provide a simple way to select the best markers for individual genotyping. This drastically reduces the cost and workload of large scale association studies. One limitation of this methodology relates to the analytical procedures which have only been developed to allow comparison of two pools e.g. case/control pools. In this paper we use meta-regression to analyze pooled DNA data allowing the allele frequency in each pool to be related to the average quantitative phenotypic measure of the individuals whose DNA were used to construct the pools. Alongside this we describe a technique that can be used to determine the power for such studies. We present results from some preliminary investigations of different pooling strategies that can be applied to large twin samples and demonstrate that the method retains a large proportion of the power available from individual genotyping.