A comparison of DNA pools constructed following whole genome amplification for two-stage SNP genotyping designs

Zhao, Zhen Zhen, Nyholt, Dale R., James, Michael R., Mayne, Renee, Treloar, Susan A. and Montgomery, Grant W. (2005) A comparison of DNA pools constructed following whole genome amplification for two-stage SNP genotyping designs. Twin Research and Human Genetics, 8 4: 353-361.


Author Zhao, Zhen Zhen
Nyholt, Dale R.
James, Michael R.
Mayne, Renee
Treloar, Susan A.
Montgomery, Grant W.
Title A comparison of DNA pools constructed following whole genome amplification for two-stage SNP genotyping designs
Journal name Twin Research and Human Genetics   Check publisher's open access policy
ISSN 1832-4274
Publication date 2005-08
Sub-type Article (original research)
DOI 10.1375/1832427054936718
Volume 8
Issue 4
Start page 353
End page 361
Total pages 9
Place of publication Bowen Hills, Qld
Publisher Australian Academic Press for the ISTS
Language eng
Subject 111799 Public Health and Health Services not elsewhere classified
Abstract Genotyping in DNA pools reduces the cost and the time required to complete large genotyping projects. The aim of the present study was to evaluate pooling as part of a strategy for fine mapping in regions of significant linkage. Thirty-nine single nucleotide polymorphisms (SNPs) were analyzed in two genomic DNA pools of 384 individuals each and results compared with data after typing all individuals used in the pools. There were no significant differences using data from either 2 or 8 heterozygous individuals to correct frequency estimates for unequal allelic amplification. After correction, the mean difference between estimates from the genomic pool and individual allele frequencies was .033. A major limitation of the use of DNA pools is the time and effort required to carefully adjust the concentration of each individual DNA sample before mixing aliquots. Pools were also constructed by combining DNA after Multiple Displacement Amplification (MDA). The MDA pools gave similar results to pools constructed after careful DNA quantitation (mean difference from individual genotyping .040) and MDA provides a rapid method to generate pools suitable for some applications. Pools provide a rapid and cost-effective screen to eliminate SNPs that are not polymorphic in a test population and can detect minor allele frequencies as low as 1% in the pooled samples. With current levels of accuracy, pooling is best suited to an initial screen in the SNP validation process that can provide high-throughput comparisons between cases and controls to prioritize SNPs for subsequent individual genotyping.
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Population Health Publications
 
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