DNA pooling for genomic scanning - Application to an association study

We are undertaking an association study to look for genes involved in general cognitive ability (see also L. Hill et al. poster, this conference). We intend to study approximately 3,500 SSR markers to scan the entire genome (average interval between markers is approximately 1 cM) to identify QTL. A pooling approach will be used to greatly reduce the amount of genotyping required [Daniels et al., 1998]. This involves pooling DNA from 51 high IQ (136) individuals and the separate pooling of DNA from 51 mid IQ (103) individuals (IQ mean = 100, 1 s.d. = 16), and amplification of each pool with fluorescently labelled SSR markers. The PCR products are electrophoresed using ABI 377 or 373 DNA fragment analyzer so that differences in allele image patterns (Δ-AIP) between the two groups can be compared. In this poster we describe adaptations for a large scale genome scan, and include results for 154 markers on chromosome 4 (213 cM). With very little optimization (a maximum of two PCR conditions was used per marker), 119 gave Δ-AIPs that were reproducible within pools. These Δ-AIP scores were analyzed for differences in amplification patterns between high and mid IQ pools. Eight Δ-AIPs indicated significant differences between the populations (P < 0.05), whilst three Δ-AIPs showed very significant values (P < 0.01). The putatively significant markers are being tested for replication in independent samples of even more extremely selected subjects (mid pool IQ = 101, high pool IQ = 160). Markers yielding replicated positive results will be used to genotype individuals to determine how differences in amplification profiles of pools of individuals relate to differences in allele frequencies.