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

• Author(s) / Creator(s)

  • Day, Andy E.
  • Andersson, Leif
  • Plastow, Graham S.
  • Pielberg, Gerli

• 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.

• Date created

  2003

• Subjects / Keywords

  • COAT COLOR
  • KIT
  • DOMINANT WHITE COLOR
  • CYP2D6 GENE
  • DNA POOLS
  • DOMESTIC PIG
  • Mutations
  • SIGNAL AMPLIFICATION REACTION
  • SINGLE NUCLEOTIDE POLYMORPHISMS
  • Alleles

• Type of Item

  Article (Published)

• DOI

  https://doi.org/10.7939/R3MC07

• License

  Attribution-NonCommercial 4.0 International