Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome ampli®ed DNA

Whole genome ampli®cation (WGA) procedures such as primer extension preampli®cation (PEP) or multiple displacement ampli®cation (MDA) have the potential to provide an unlimited source of DNA for large-scale genetic studies. We have performed a quantitative evaluation of PEP and MDA for genotyping single nucleotide polymorphisms (SNPs) using multiplex, four-color ̄uorescent minisequencing in a microarray format. Forty-®ve SNPs were genotyped and the WGA methods were evaluated with respect to genotyping success, signal-to-noise ratios, power of genotype discrimination, yield and imbalanced ampli®cation of alleles in the MDA product. Both PEP and MDA products provided genotyping results with a high concordance to genomic DNA. For PEP products the power of genotype discrimination was lower than for MDA due to a 2-fold lower signal-to-noise ratio. MDA products were indistinguishable from genomic DNA in all aspects studied. To obtain faithful representation of the SNP alleles at least 0.3 ng DNA should be used per MDA reaction. We conclude that the use of WGA, and MDA in particular, is a highly promising procedure for producing DNA in suf®cient amounts even for genome wide SNP mapping studies.