Genotyping of three single nucleotide polymorphisms following whole genome preamplification of DNA collected from buccal cells.

Collection of genomic DNA from buccal cells is a simple and convenient procedure for genotyping individuals. One disadvantage is that the amount of genomic DNA may be inadequate for genotyping projects that require a large number of determinations per sample. Primer Extension Preamplification (PEP) methods that can amplify the entire genome 100-fold or more offer a potential solution to this problem. To test whether the preamplified DNA product retains the original allelic distribution of the genomic DNA sample from which it was derived, we compared PEP buccal DNA with genomic buccal DNA from 94 pairs of monozygotic twins. Using the 5' nuclease (Taqman) method, we genotyped three SNPs that are of wide interest in behavioral and psychiatric genetic studies. The percent agreement between allele calls using PEP DNA samples and those using genomic DNA samples ranged between 99% and 100% depending on SNP assay. These data complement our earlier findings with respect to microsatellite markers and variable number tandem repeat (VNTR) polymorphisms and indicate that whole-genome preamplification is an appropriate method for providing DNA for SNP genotyping these and possibly other loci.