Comparing Whole-Genome Amplification Methods and Sources of Biological Samples for Single-Nucleotide Polymorphism Genotyping

High-throughput genotyping systems promise to be an efficient means of identifying susceptibility genes involved in the etiology of non-Mendelian disorders. Adequate amounts of high-quality DNA are essential, however, for large-scale genotyping studies (1). The supply of genomic DNA is frequently limited, and the quality of DNA obtained from oral buccal swabs or Guthrie cards has not been thoroughly evaluated for high-throughput single-nucleotide polymorphism (SNP) genotyping (2)(3). Whole-genome amplification (WGA) technologies offer the opportunity to expand DNA from depleted biological samples. The first generation of WGA strategies (i.e., PCR-based methods) (4)(5), however, was limited by substantial amplification bias and incomplete coverage of genetic markers (6)(7). Recently, new strategies for WGA, such as multiple displacement amplification (MDA) or OmniPlex® WGA technology (Rubicon Genomics) have been developed. MDA is an isothermal amplification with the bacteriophage φ29 DNA polymerase (6)(8), whereas OmniPlex uses in vitro libraries with fragmented DNA (∼1.5 kb) to amplify the entire genome by PCR (9).To apply WGA technology to BeadArray™ genotyping (Illumina), the utility of MDA and/or OmniPlex on DNA samples derived from lymphoblast cells has been evaluated (9)(10). In this study, we determined the genotyping success rate and reliability of 2 MDA variants (8)(11) and OmniPlex with and without 7-deaza-dGTP, using buccal swabs, whole blood, dried blood spots, and sheared genomic DNA on 1260- and 1228-SNP BeadArray panels. The 7-deaza-dGTP nucleotide analog was included in an attempt to ensure amplification of GC-rich DNA.After Institutional Review Board approval and informed consent were obtained, DNA samples were collected from participants in a study of oral clefts (12). Genomic DNA samples were prepared from peripheral blood by protein precipitation (13). Buccal cells were obtained by rubbing the inside of cheeks with a brush (Medical Packaging), and DNA …