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http://dx.doi.org/10.5351/CKSS.2009.16.6.1037

Comparison of Methods for Detecting and Quantifying Variation in Copy Numbers of Duplicated Genes  

Jeon, Jin-Tae (Division of Animal Life Science, Gyeongsang National University)
Ahn, Sung-Jin (Department of Information Statistics, RICIC and RINS, Gyeongsang National University)
Publication Information
Communications for Statistical Applications and Methods / v.16, no.6, 2009 , pp. 1037-1046 More about this Journal
Abstract
Copy number variations(CNVs) are known as one of the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing real-time polymerase chain reaction(PCR), invader assays and other techniques have been used to detect CNVs. However, the higher the copy number in a genome, the more difficult it is to resolve the copies, so a more accurate method for measuring CNVs and assigning genotype is needed. PCR followed by a quantitative oligonucleotide ligation assay(qOLA) was developed for quantifying CNVs. The aim of this study was to compare the two methods for detecting and quantifying the CNVs of duplicated gene: the published pyrosequencing assay(pyro_CNV) and the newly developed qOLA_CNV. The accuracy and precision of the assay were evaluated for porcine KIT, which was selected as a model locus. Overall, the root mean squares(RMSs) of bias and standard deviation of qOLA_CNV were 2.09 and 0.45, respectively. These values are less than half of those of pyro CNV.
Keywords
Copy number variation; quantitative oligonucleotide ligation assay; pyrosequencing assay; root mean square;
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