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A sensitive method for detecting variation in copy numbers of duplicatedgenes
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
2003 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 13, no 9, 2171-2177 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2003. Vol. 13, no 9, 2171-2177 p.
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-64807DOI: 10.1101/gr.1188203PubMedID: 12952884OAI: oai:DiVA.org:uu-64807DiVA: diva2:92718
Available from: 2008-10-17 Created: 2008-10-17 Last updated: 2017-11-30Bibliographically approved

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Pielberg, Gerli

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