A sensitive method for detecting variation in copy numbers of duplicated genes

Abstract

Gene duplications are common in the vertebrate genome, and duplicated loci often show a variation ill 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 breakpoint and a corresponding nonduplicated sequence in a competitive PCR assay. A comparison with all independent method for quantification based on the Invader technology revealed all 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 lilies

Published in

Genome Research
2003, Volume: 13, number: 9, pages: 2171-2177 Publisher: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT

SLU Authors

• Andersson, Leif

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Pielberg, Gerli

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Animal and Dairy Science
Veterinary Science


Publication identifier

DOI: https://doi.org/10.1101/gr.1188203

Permanent link to this page (URI)

https://res.slu.se/id/publ/1725