Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage
| Autor: | Maurice Yap, Po Wah Ng, Daniel W.H. Ho, Wai Yan Fung, Shea Ping Yip, Wai Chi Yiu |
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| Rok vydání: | 2011 |
| Předmět: |
Quality Control
Heredity Time Factors Genotyping Techniques Science Genotypes Preservation Biological Gene Identification and Analysis Biology Polymorphism Single Nucleotide law.invention Molecular Genetics law Genetics Humans Genetic Testing Genotyping Genetic Association Studies Polymerase chain reaction Whole Genome Amplification Multidisciplinary Complex Traits Genome Human Human Genetics DNA Nucleic acid amplification technique Trait Locus DNA extraction Molecular biology genomic DNA Genetic Polymorphism Medicine Biological Assay Human genome Nucleic Acid Amplification Techniques Population Genetics Research Article |
| Zdroj: | PLoS ONE PLoS ONE, Vol 6, Iss 10, p e26119 (2011) |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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