Open Access Methodology article

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*

Author Affiliations

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

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

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

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

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

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

Published: 23 November 2007

Additional files

Additional file 1:

Verification of the specificity of PCR primers used for amplifying breakpoints of KIT CNV using a porcine × rodent somatic cell hybrid panel. (a) The results from the primer set (KITBPF and KIT1BPR) for the normal copy. (b) The results from the primer set (KITBPF and KIT2BPR) for the duplicated copy. M, 100-bp size standard; numbers are positive clone numbers.

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Additional file 2:

Standard curves for qOLA_CNV and Pyro_CNV. A serial dilution from 0% to 100% duplicated copy vs normal copy (PCR-amplified and cloned) was used for the estimation. (a) A curve estimated using peak height values from qOLA_CNV (correlation coefficient = 0.999). (b) A curve estimated using peak area values from qOLA_CNV (correlation coefficient = 0.999). (c) A curve estimated using Pyro_CNV (correlation coefficient = 0.995). (d) A comparison of the three curves by root mean square (RMS) of the bias to reference values and standard deviations. The qOLA_CNV using peak height measurements is the most accurate and precise of the three.

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Additional file 3:

Typical coat colors of parental and F1 animals. (a) A Korean native boar (Black). (b) A Landrace sow (White). (c) An F1 littermate produced by a cross between a Korean native boar (i/i) and a Landrace sow (I1/i); four white pigs were genotyped as I1/i and three colored ones as i/i.

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Additional file 4:

Comparison of genotyping results for 159 Large White pigs by the two genotyping methods. The genotypes for the clustering measurements on the plot are in the first column, and the numbers of class centroid for the statistical analysis are given in the first row. The two discrepancies between the assignment methods are indicated by italic and bold numbers.

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