GVRG 2011-2012 Research Study Conclusion: Evaluation of DNA Whole Genome Amplification Technologies for Genotyping
Year: 2012
Type: article
Abstract: The evolution of genomic technologies is occurring rapidly and often requires large amounts of source DNA. There is also 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 newest genomic technologies, whole genome amplification (WGA) has reemerged as an important and necessary technique. With some new WGA products on the market, we have evaluated the quantity and quality of WGA products generated as well their performance on some of the current genomic applications. The GVRG has completed a benchmarking study evaluation of 6 commercially available WGA kits using several genotyping assays. Utilizing 6 samples, the different WGA kits were tested following the manufacturer's protocols. The samples included Coriell DNA from a trio of CEPH individuals, 2 FFPE DNAs, both from the same individual (1 newly extracted and the other extracted 2 years ago), and 1 sample from the Coriell trio that was fragmented prior to amplification for a total of 6 samples tested. The WGA kits included those from Sigma, NuGen, Qiagen and GE Life Sciences. The 6 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.
Source: Europe PMC (PubMed Central)
Authors: Dagnall, Casey, Blake, Sean, Nicolet, Charles, Rosato, Caprice, Grills, George, Hutchinson, Amy
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2139901635