title: Determination of beta-defensin genomic copy number in different populations: a comparison of three methods.
abstract: BACKGROUND
  There have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and β-defensins and Crohn's disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with disease. At present, real-time quantitative PCR (QPCR) is the most commonly used method to determine gene copy number, however the Paralogue Ratio Test (PRT) is being used in more and more laboratories.
  
  
  RESULTS
  In this study we compare a Pyrosequencing-based Paralogue Ratio Test (PPRT) for determining beta-defensin gene copy number with two currently used methods for gene copy number determination, QPCR and triplex PRT by typing five different cohorts (UK, Danish, Portuguese, Ghanaian and Czech) of DNA from a total of 576 healthy individuals. We found a systematic measurement bias between DNA cohorts revealed by QPCR, but not by the PRT-based methods. Using PRT, copy number ranged from 2 to 9 copies, with a modal copy number of 4 in all populations.
  
  
  CONCLUSIONS
  QPCR is very sensitive to quality of the template DNA, generating systematic biases that could produce false-positive or negative disease associations. Both triplex PRT and PPRT do not show this systematic bias, and type copy number within the correct range, although triplex PRT appears to be a more precise and accurate method to type beta-defensin copy number.
authors.affiliation: Department for Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: Peder
authors.initials: P
authors.lastname: Fode
authors.forename: Cathrine
authors.initials: C
authors.lastname: Jespersgaard
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Hardwick
authors.forename: Helen
authors.initials: H
authors.lastname: Bogle
authors.forename: Michael
authors.initials: M
authors.lastname: Theisen
authors.forename: Daniel
authors.initials: D
authors.lastname: Dodoo
authors.forename: Martin
authors.initials: M
authors.lastname: Lenicek
authors.forename: Libor
authors.initials: L
authors.lastname: Vitek
authors.forename: Ana
authors.initials: A
authors.lastname: Vieira
authors.forename: Joao
authors.initials: J
authors.lastname: Freitas
authors.forename: Paal Skytt
authors.initials: PS
authors.lastname: Andersen
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Hollox
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D015331:Cohort Studies; D018153:Czech Republic; D003718:Denmark; D018628:Gene Dosage; D020022:Genetic Predisposition to Disease; D005828:Genetics, Population / Q000379:methods*; D015894:Genome, Human / Q000235:genetics; D005869:Ghana; D006801:Humans; D008969:Molecular Sequence Data; D011153:Population; D011174:Portugal; D006113:United Kingdom; D023083:beta-Defensins / Q000235:genetics*
chemical_list: D023083:beta-Defensins