Narrowing down the distal border of the copy number variable beta-defensin gene cluster on human 8p23Reportar como inadecuado




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BMC Research Notes

, 7:93

First Online: 19 February 2014Received: 07 February 2014Accepted: 10 February 2014DOI: 10.1186-1756-0500-7-93

Cite this article as: Taudien, S., Huse, K., Groth, M. et al. BMC Res Notes 2014 7: 93. doi:10.1186-1756-0500-7-93

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.

KeywordsDefensin CNV borders Length polymorphism Paralog ratio test Indel DEFB108P DEFB109P AbbreviationsBACBacterial Artificial Chromosome

CE-LIFCapillary Electrophoresis with Laser-Induced Fluorescence

CNCopy Number

CNVCopy Number Variationl

DEFDefensin

MLPAMultiplex Ligation Dependent Probe Amplification

PRTParalog Ratio Test

SNPSingle Nucleotide Polymorphism.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-7-93 contains supplementary material, which is available to authorized users.

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Autor: Stefan Taudien - Klaus Huse - Marco Groth - Matthias Platzer

Fuente: https://link.springer.com/







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