Linkage disequilibrium mapping of chromosome 22 in schizophrenia using DNA pooling on Chinese and Scottish populations

There is good evidence from linkage analysis that there are several genetic loci for schizophrenia, including on chromosomes 6, 13q, 8p, and 22q. However, linkage alone has poor power to precisely localize the underlying susceptibility genes. Using chromosome 22 as a starting point, we have attempted to confirm and fine-map linked loci using linkage disequilibrium analysis of the entire chromosome with approximately 70 microsatellite markers (average spacing ∼500 Kb). Two clinical samples of schizophrenic patients were used, consisting of 180 family trios and 80 sibling pairs from Chengdu, SW China (n = 860), and 400 cases and 400 controls from the Highland and Grampian regions of Scotland (N = 800). To reduce the amount of genotyping to a practical level, DNA samples were pooled at equimolar concentration, using fluorescent quantification of the DNA. This resulted in three separate matched sets of pools from the Chinese parents and offspring, derived from 100 trios, 80 trios, and 80 sibling-pairs, and two sets of case-control pools from the Scottish sample. Fluorescently labelled markers were initially genotyped in one pooled sample set from each ethnic group (100 trios and 200 cases and controls) on the capillary polymer-based ABI 310 genetic analyzer. The integrated peak areas of allele traces from fluorograms were compared between parents and offspring or case-controls to detect potential differences in allele frequency or allele transmission. The majority of traces were very similar between the pairs of pools, and those markers which showed differences were genotyped in the additional pools, followed by individual genotyping of the samples for transmission disequilibrium or chi-square analysis to pinpoint areas of significant linkage disequilibrium.