Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
作者: Stefan TaudienPetra GalgoczyKlaus HuseKathrin ReichwaldMarkus SchilhabelKarol SzafranskiAtsushi ShimizuShuichi AsakawaAdam FrankishIvan F LoncarevicNobuyoshi ShimizuRoman SiddiquiMatthias Platzer
作者单位: 1Genomanalyse, Institut für Molekulare Biotechnologie, Beutenbergstr. 11, D-07745, Jena, Germany
2Keio University School of Medicine, 35 Shinanomachi, 160-8582, Shinjuku-ku, Tokyo, Japan
3Wellcome Trust Sanger Institute, CB10 1SA, Cambridge, Hinxton, UK
4Institut für Humangenetik und Anthropologie, Friedrich-Schiller-Universität Jena, Kollegiengasse 10, D-07743, Jena, Germany
刊名: BMC Genomics, 2004, Vol.5 (1), pp.345-354
来源数据库: Springer Nature Journal
DOI: 10.1186/1471-2164-5-92
关键词: Segmental DuplicationWhole Genome ShotgunHg16 AssemblyComplete Hydatidiform MoleMultiplex Amplifiable Probe Hybridisation
英文摘要: Abstract(#br)Background(#br)Defensins are important components of innate immunity to combat bacterial and viral infections, and can even elicit antitumor responses. Clusters of defensin (DEF) genes are located in a 2 Mb range of the human chromosome 8p23.1. This DEF locus, however, represents one of the regions in the euchromatic part of the final human genome sequence which contains segmental duplications, and recalcitrant gaps indicating high structural dynamics. Results(#br)We find that inter- and intraindividual genetic variations within this locus prevent a correct automatic assembly of the human reference genome (NCBI Build 34) which currently even contains misassemblies. Manual clone-by-clone alignment and gene annotation as well as repeat and SNP/haplotype analyses result in an...
全文获取路径: Springer Nature  (合作)
影响因子:4.397 (2012)