Narrowing down the distal border of the copy number variable beta-defensin gene cluster on human 8p23

BMC Res Notes. 2014 Feb 19;7:93. doi: 10.1186/1756-0500-7-93.

Abstract

Background: Copy number variation (CNV) in the range from 2 to 12 per diploid genome is an outstanding feature of the beta-defensin gene (DEFB) cluster on human chromosome 8p23.1 numerously demonstrated by different methods. So far, CNV was proven for a 115 kb region between DEFB4 and 21 kb proximal of DEFB107 but the borders for the entire CNV repeat unit are still unknown. Our study aimed to narrow down the distal border of the DEFB cluster.

Results: We established tests for length polymorphisms based on amplification and capillary electrophoresis with laser-induced fluorescence (CE-LIF) analysis of seven insertion/deletion (indel) containing regions spread over the entire cluster. The tests were carried out with 25 genomic DNAs with different previously determined cluster copy numbers. CNV was demonstrated for six indels between ~1 kb distal of DEFB108P and 10 kb proximal of DEFB107. In contrast, the most distal indel is not affected by CNV.

Conclusion: Our analysis fixes the minimal length of proven CNV to 157 kb including DEFB108P but excluding DEFB109P. The distal border between CNV and non-CNV part of the DEF cluster is located in the 59 kb interval chr8:7,171,082-7,230,128.

MeSH terms

  • Chromosome Mapping
  • Chromosomes, Human, Pair 8 / genetics*
  • DNA Copy Number Variations*
  • Electrophoresis, Capillary / methods
  • Fluorescence
  • Gene Dosage*
  • Gene Order
  • Humans
  • INDEL Mutation
  • Introns / genetics
  • Multigene Family*
  • Polymorphism, Genetic
  • Protein Isoforms / genetics
  • Pseudogenes / genetics
  • beta-Defensins / genetics*

Substances

  • Protein Isoforms
  • beta-Defensins