In order to locate the disease variants involved in complex common disease it is now generally accepted that very large sample numbers will be required [1–4]. Not only do the sample collections need to provide high quality gDNA, for the purpose of accurate genotyping, they also need to be sustainable. If, for example, one million SNPs were to be genotyped in a whole genome association scan and only 1 ng were required per SNP genotype, 1 mg of DNA would be required from each clinical sample. Given that the gDNA yield from a typical blood sample of 8 ml is approximately 200 μg, and that the typical yield from a mouth-swab is just 10 μg, there is clearly a short-fall in available quantities unless other means are employed to amplify the DNA resource. Moreover, many existing and effectively irreplaceable DNA sample collections, which have been used in previous studies and are now depleted, may consist of only nanogram quantities of gDNA.
At present, the gold standard method for generating gDNA from whole blood samples is through the process of immortalisation by transformation of the peripheral blood lymphocytes with Epstein-Barr Virus (EBV) . Although this method of transfecting EBV creates an unlimited resource of gDNA, the procedure is costly, lengthy and not applicable to existing collections for which the gDNA has already been extracted. If there was a reliable method to enzymatically amplify the whole genome from nanogram-levels of gDNA and directly from clinical samples to microgram amounts then this would enable the use of archived gDNA in future studies, as well as providing an accelerated route to full use of newly collected clinical samples for high-throughput genotyping.
Molecular Staging, Inc. (MSI) (New Haven, CT, USA) have developed a method for whole genome amplification by Φ29 polymerase Multiple Displacement Amplification (MDA). It has been reported by the company that this method can reliably amplify the whole genome from gDNA, whole blood and other clinical samples [6–8]. Each DNA sample should give similar yields of product in all reactions with little dependency on the quantity of starting template [6, 7]. Moreover, the MDA reaction should give complete coverage of the genome with little regional bias , which is critical when the product is to be used for high-throughput SNP genotyping. We set up a series of experiments with MSI in order to validate their claims that MDA product from gDNA is a viable alternative template to un-manipulated gDNA in SNP genotyping.
Recent studies have been conducted using MDA product from Amersham [9, 10], and report the high level of accuracy achieved when these products are genotyped using TaqMan or multiplex, four-colour fluorescent minisequencing with six and 45 SNPs, respectively. However, without DNA resource limitations, a genotyping bottleneck exists mostly as a result of time- and assay set-up costs and hence, in order to achieve large-scale genotyping, highly multiplexed assays are required. In such multiplexed assays, there is greater potential for erosion of genotyping quality, due to reduced substrate integrity. The validation of the use of amplified DNA resources with such highly multiplexed methods is, therefore, essential.
The BeadArray genotyping platform of Illumina™ Inc. (San Diego, CA, USA) offers a high-throughput, highly multiplexed and highly automated genotyping service facility . The BeadArray platform is highly miniaturised, using fibre optic bundles as a substrate for a high-density microarray . It is the combination of this miniaturisation with an ability to multiplex up to 1,536 SNP assays  that makes BeadArray an attractive potential solution to the genotyping bottleneck. A recent study by Barker and colleagues, with 2,320 SNPs and five samples, found 99.86% concordance between MSI MDA product and gDNA . However, since only five samples were studied it was not possible to evaluate accurately the efficacy of BeadArray on MDA product template, including estimation of sample exclusion and failure rates. In the present report we have, therefore, studied 86 MDA product samples and 384 SNPs using BeadArray, allowing comparison with the single-plex methods TaqMan® (Assays-by-DesignSM, Applied Biosystems, Foster City, CA, USA) and Invader® (Third Wave Technologies, Inc., Madison, WI, USA) with gDNA.