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Please use this identifier to cite or link to this item: http://hdl.handle.net/10397/5160

Title: Genotyping performance assessment of whole genome amplified DNA with respect to multiplexing level of assay and its period of storage
Authors: Ho, Daniel W. H.
Yiu, Wai Chi
Yap, Keng-hung Maurice
Fung, Wai Yan
Ng, Po Wah
Yip, Shea-ping
Issue Date: 11-Oct-2011
Publisher: Public Library of Science (PLoS)
Citation: PLoS ONE, Oct. 2011, v. 6, no. 10, e26119, p. 1-7.
Abstract: Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at −70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy) of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex) of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy) due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy.
Description: DOI: 10.1371/journal.pone.0026119
Rights: Copyright: ©2011 Ho et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Type: Journal/Magazine Article
URI: http://hdl.handle.net/10397/5160
ISSN: 1932-6203 (online)
Appears in Collections:HTI Journal/Magazine Articles
SO Journal/Magazine Articles

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