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A sensitive method for detecting variation in copy numbers of duplicatedgenes
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- Pielberg, Gerli (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
- Day, A E (author)
- Plastow, G S (author)
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- (creator_code:org_t)
- 2003-09-02
- 2003
- English.
- In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 13:9, s. 2171-2177
- Journal article (peer-reviewed)
Abstract
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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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- Pielberg, Gerli
- Day, A E
- Plastow, G S
- Andersson, Leif
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