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

Abstract

Copy number variations(CNVs) are known as one of the most important factors in susceptibility to genetic disorders because they a ect 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 di cult 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.