Screening a large reference sample to identify very low frequency sequencevariants: comparisons between two genes

Most human sequence variation is in the form of single-nucleotide polymorph isms(1-3) (SNPs). It has been proposed that coding-region SNPs (cSNPs) be u sed for direct association studies to determine the genetic basis of comple x traits(4,5). The success of such studies depends on the frequency of dise ase-associated alleles, and their distribution in different ethnic populati ons(6,7). If disease-associated alleles are frequent in most populations, t hen direct genotyping of candidate variants could show robust associations in manageable study samples(6). This approach is less feasible if the genet ic risk from a given candidate gene is due to many infrequent alleles. Prev ious studies of several genes demonstrated that most variants are relativel y infrequent(2,3) (<0.05). These surveys genotyped small samples (n<75) and thus had limited ability to identify rare alleles. Here we evaluate the pr evalence and distribution of such rare alleles by genotyping an ethnically diverse reference sample that is more than six times larger than those used in previous studies(8) (n=450). We screened for variants in the complete c oding sequence and intron-exon junctions of two candidate genes for neurops ychiatric phenotypes: SLC6A4, encoding the serotonin transporter; and SLC18 A2, encoding the vesicular monoamine transporter(9,10). Both genes have uni que roles in neuronal transmission, and variants in either gene might be as sociated with neurobehavioral phenotypes(11-13).