Abstract
BackgroundCopy 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.ResultsWe 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.ConclusionOur 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.
Highlights
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
In order to confirm or exclude CNV at multiple sites spread over DEF cluster b, namely distal and proximal of the outermost ones with proven CNV, we identified indels in the DEF cluster b by two approaches
Because we demonstrated the lack of CNV for indel 1 and the DEFB109P pseudogene, the distal border that separates the unique, copy number (CN) invariable from the CN variable part of the DEF cluster must be located in the interval between both indels
Summary
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. Ten genes and pseudogenes (DEFB109P, DEFB108P, DEFB4, HSPD1P, DEFB103, SPAG11, DEFB104, DEFB106, DEFB105 and DEFB107) are organized in a cluster of ~218 kb embedded in different types of low copy repeats (LCR) originating from segmental duplications. The DEF cluster b is embedded in one of two complex segmental duplications, REPD and REPP, involved in polymorphic inversions [1,2,3]. In these regions CNV for the FAM90A gene class was shown [4]. For 7 genes (DEFB4, DEFB103, SPAG11, DEFB104, DEFB106, DEFB105 and DEFB107), the probes hybridize to regions with no other paralogs than the DEF cluster b copies on 8p23.1 (Figure 1B). The MLPA results for DEFB108P were not reproducible and the probe was removed from the kit when changing to kit version P139-B1 in June 2009
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