After completion of fatSNP stage 2, we aimed to identify SNPs within the wider genomic regions not targeted by the exon-focussed de novo discovery phase. This was performed using 60 cases drawn randomly from the Cardiff Full sample. From these, we generated 6 pooled samples each containing DNA from ten samples. PCR primers were designed to span 381,988 bp of the genomic sequence in and around ZNF804A (figure 1). Long range PCRs were generated using the Roche Expand long template PCR system. The PCR products were gel purified after electrophoresis, and sent to Illumina Inc (SanDiego) for sequencing using Solexa technology. The resultant single-end reads were assembled and analysed for putative SNPs using both DNAStar (http://www.dnastar.com) and MAQ (http://maq.sourceforge.net). We used the default parameters for DNAStar analysis. The MAQ output was filtered using previously published thresholds(18).
