A Sensitive Method for Detecting Variation in Copy Numbers of Duplicated Genes

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  • Gene duplications are common in the vertebrate genome, and duplicated loci often show a variation in copy number that may have important phenotypic effects. Here we describe a powerful method for quantification of duplicated copies based on pyrosequencing. A reliable quantification was obtained by amplification of the duplication break-point and a corresponding nonduplicated sequence in a competitive PCR assay. A comparison with an independent method for quantification based on the Invader technology revealed an excellent correlation between the two methods. The pyrosequencing-based method was evaluated by analyzing variation in copy number at the duplicated KIT/Dominant white locus in pigs. We were able to distinguish haplotypes at this locus by combining the duplication breakpoint test with a diagnostic test for a functionally important splice mutation in the duplicated gene. An extensive allelic variation, including the presence of a new allele carrying a single KIT copy expected to encode a truncated KIT receptor, was revealed when analyzing white pigs from commercial lines.

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    Article (Published)
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    Attribution-NonCommercial 4.0 International
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  • Citation for previous publication
    • Pielberg G., Day A.E., Plastow G.S., and Andersson L. 2003. A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res. 13, 2171-2177.
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