title: Accurate measurement of gene copy number for human alpha-defensin DEFA1A3.
abstract: BACKGROUND
  Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing.
  
  
  RESULTS
  In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples.
  
  
  CONCLUSIONS
  We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn's disease, type I diabetes, HIV progression and multiple sclerosis.
authors.forename: Fayeza F
authors.initials: FF
authors.lastname: Khan
authors.forename: Danielle
authors.initials: D
authors.lastname: Carpenter
authors.forename: Laura
authors.initials: L
authors.lastname: Mitchell
authors.forename: Omniah
authors.initials: O
authors.lastname: Mansouri
authors.forename: Holly A
authors.initials: HA
authors.lastname: Black
authors.forename: Jess
authors.initials: J
authors.lastname: Tyson
authors.affiliation: School of Biology, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK. john.armour@nottingham.ac.uk.
authors.forename: John A L
authors.initials: JA
authors.lastname: Armour
mesh_terms: D000483:Alleles; D002898:Chromosomes, Human, Pair 8; D004171:Diploidy; D018628:Gene Dosage; D055106:Genome-Wide Association Study; D005838:Genotype; D060005:Genotyping Techniques; D006239:Haplotypes; D006801:Humans; D005810:Multigene Family; D010456:Peptides, Cyclic / Q000032:analysis* / Q000235:genetics; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D023084:alpha-Defensins / Q000032:analysis* / Q000235:genetics
chemical_list: C429483:DEFA1A3 protein, human; D010456:Peptides, Cyclic; D023084:alpha-Defensins