Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing

BMC Genomics

Research Article

Jochen Hampe¹  Philip Rosenstiel²  Stefan Schreiber³  Marius Felder⁴  Andreas Petzold⁴  Marco Groth⁴  Francesca Raffaelli⁴  Matthias Platzer⁴  Stefan Taudien⁴  Klaus Huse⁴  Karol Szafranski⁴  Xinmin Zhang⁵ 

[1] Dept. of General Intermal Medicine, Christian-Albrechts-University Kiel, Germany;Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Germany;Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Germany;Dept. of General Intermal Medicine, Christian-Albrechts-University Kiel, Germany;Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany;Roche NimbleGen, Inc., Madison, WI, USA;

关键词: Sequence Depth;    Diploid Genome;    Sequence Capture;    Copy Number Estimation;    Hg18 Reference;   

DOI  :  10.1186/1471-2164-12-243

 received in 2011-01-27, accepted in 2011-05-18,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundIn 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.ResultsAs 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.ConclusionAlthough 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.

【 授权许可】

CC BY   
© Taudien et al; licensee BioMed Central Ltd. 2011