An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay

Bo-Young Seo¹ , Eung-Woo Park² , Sung-Jin Ahn³ , Sang-Ho Lee¹ , Jae-Hwan Kim¹ , Hyun-Tae Im¹ , Jun-Heon Lee⁴ , In-Cheol Cho⁵ , Il-Keun Kong¹ and Jin-Tae Jeon¹

¹Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Korea

²Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea

³Division of Mathematics and Information Statistics, Member of RICIC, Gyeongsang National University, Jinju 660-701, Korea

⁴Division of Animal Science and Resources, Research Center for Transgenic Cloned Pigs, Chungnam National University, Daejeon 305-764, Korea

⁵Department of Animal Science, National Institute of Subtropical Agriculture, Rural Development Administration, Jeju 690-150, Korea

author email corresponding author email

BMC Genetics 2007, 8:81doi:10.1186/1471-2156-8-81


Published:	23 November 2007

Abstract

Background

Aside from single nucleotide polymorphisms, copy number variations (CNVs) are the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing, real-time 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.

Results

PCR followed by a quantitative oligonucleotide ligation assay (qOLA) was developed for quantifying CNVs. The accuracy and precision of the assay were evaluated for porcine KIT, which was selected as a model locus. Overall, the root mean squares of bias and standard deviation of qOLA were 2.09 and 0.45, respectively. These values are less than half of those in the published pyrosequencing assay for analyzing CNV in porcine KIT. Using a combined method of qOLA and another pyrosequencing for quantitative analysis of KIT copies with spliced forms, we confirmed the segregation of KIT alleles in 145 F₁animals with pedigree information and verified the correct assignment of genotypes. In a diagnostic test on 100 randomly sampled commercial pigs, there was perfect agreement between the genotypes obtained by grouping observations on a scatter plot and by clustering using the nearest centroid sorting method implemented in PROC FASTCLUS of the SAS package. In a test on 159 Large White pigs, there were only two discrepancies between genotypes assigned by the two clustering methods (98.7% agreement), confirming that the quantitative ligation assay established here makes genotyping possible through the accurate measurement of high KIT copy numbers (>4 per diploid genome). Moreover, the assay is sensitive enough for use on DNA from hair follicles, indicating that DNA from various sources could be used.

Conclusion

We have established a high resolution quantification method using an oligonucleotide ligation assay to measure CNVs, and verified the reliability of genotype assignment for random animal samples using the nearest centroid sorting method. This new method will make it more practical to determine KIT CNV and to genotype the complicated Dominant White/KIT locus in pigs. This procedure could have wide applications for studying gene or segment CNVs in other species.