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Article: Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

TitleGenotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage
Authors
Issue Date2011
Citation
PLoS ONE, 2011, v. 6, n. 10, p. e26119 How to Cite?
AbstractWhole 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. © 2011 Ho et al.
Persistent Identifierhttp://hdl.handle.net/10722/214736
ISSN
2015 Impact Factor: 3.057
2015 SCImago Journal Rankings: 1.395

 

DC FieldValueLanguage
dc.contributor.authorHo, DWH-
dc.contributor.authorYiu, WC-
dc.contributor.authorYap, MKH-
dc.contributor.authorFung, WY-
dc.contributor.authorNg, PW-
dc.contributor.authorYip, SP-
dc.date.accessioned2015-08-21T11:53:38Z-
dc.date.available2015-08-21T11:53:38Z-
dc.date.issued2011-
dc.identifier.citationPLoS ONE, 2011, v. 6, n. 10, p. e26119-
dc.identifier.issn1932-6203-
dc.identifier.urihttp://hdl.handle.net/10722/214736-
dc.description.abstractWhole 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. © 2011 Ho et al.-
dc.languageeng-
dc.relation.ispartofPLoS ONE-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleGenotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage-
dc.typeArticle-
dc.identifier.emailHo, DWH: dwhho@hku.hk-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1371/journal.pone.0026119-
dc.identifier.pmid22022531-
dc.identifier.scopuseid_2-s2.0-80053984289-
dc.identifier.hkuros248526-
dc.identifier.volume6-
dc.identifier.spagee26119-
dc.identifier.epagee26119-

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