Abstract
The evolution of genomic technologies is occurring rapidly and often requires large amounts of source DNA. There is an expanded desire to analyze smaller numbers of cells for higher resolution studies as well as to take advantage of large numbers of archived samples (eg. FFPE, serum, etc.). To provide enough material for the latest genomic technologies, whole genome amplification (WGA) has reemerged as an important and necessary technique. The GVRG has evaluated several new WGA products, assessing the quantity and quality of generated samples as well as sample performance on particular current genomic assay platforms.
The GVRG has completed a benchmarking study evaluation of several commercially available WGA kits using different genotyping assays. The WGA kits were tested on six different samples following the manufacturer's protocols. The samples included Coriell DNA from a trio of CEPH individuals, 2 FFPE DNAs, both from the same individual but one newly extracted and the other extracted two years ago, and one sample from the Coriell trio that was fragmented prior to amplification. The WGA kits were from Sigma, NuGen, Qiagen and GE Life Sciences. The six samples were amplified as blind duplicates at several GVRG member lab sites resulting in a total of 78 amplified products.
Quality metrics were performed on the 78 amplified products using several different techniques in order to provide measurements on yield, fragment size, and concentration. Several widely used genotyping methods were used to evaluate the amplification products, including Illumina Human Omni1 Quad Beadchip, TaqMan copy number and SNP genotyping assays, and STR genotyping. Data will be presented on genotyping concordance and loss of heterozygosity checks across the different platforms where possible. Additional data is being presented here as the study conclusion on new FFPE processing kits utilized for Illumina Infinium Beadchips.