title: Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing.
abstract: BACKGROUND
  In highly copy number variable (CNV) regions such as the human defensin gene locus, comprehensive assessment of sequence variations is challenging. PCR approaches are practically restricted to tiny fractions, and next-generation sequencing (NGS) approaches of whole individual genomes e.g. by the 1000 Genomes Project is confined by an affordable sequence depth. Combining target enrichment with NGS may represent a feasible approach.
  
  
  RESULTS
  As a proof of principle, we enriched a ~850 kb section comprising the CNV defensin gene cluster DEFB, the invariable DEFA part and 11 control regions from two genomes by sequence capture and sequenced it by 454 technology. 6,651 differences to the human reference genome were found. Comparison to HapMap genotypes revealed sensitivities and specificities in the range of 94% to 99% for the identification of variations.Using error probabilities for rigorous filtering revealed 2,886 unique single nucleotide variations (SNVs) including 358 putative novel ones. DEFB CN determinations by haplotype ratios were in agreement with alternative methods.
  
  
  CONCLUSIONS
  Although currently labor extensive and having high costs, target enriched NGS provides a powerful tool for the comprehensive assessment of SNVs in highly polymorphic CNV regions of individual genomes. Furthermore, it reveals considerable amounts of putative novel variations and simultaneously allows CN estimation.
authors: Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany. stau@fli-leibniz.de
authors: Stefan
authors: S
authors: Taudien
authors: Karol
authors: K
authors: Szafranski
authors: Marius
authors: M
authors: Felder
authors: Marco
authors: M
authors: Groth
authors: Klaus
authors: K
authors: Huse
authors: Francesca
authors: F
authors: Raffaelli
authors: Andreas
authors: A
authors: Petzold
authors: Xinmin
authors: X
authors: Zhang
authors: Philip
authors: P
authors: Rosenstiel
authors: Jochen
authors: J
authors: Hampe
authors: Stefan
authors: S
authors: Schreiber
authors: Matthias
authors: M
authors: Platzer
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