title: A novel framework for the identification and analysis of duplicons between human and chimpanzee.
abstract: Human and other primate genomes consist of many segmental duplications (SDs) due to fixation of copy number variations (CNVs). Structure of these duplications within the human genome has been shown to be a complex mosaic composed of juxtaposed subunits (called duplicons). These duplicons are difficult to be uncovered from the mosaic repeat structure. In addition, the distribution and evolution of duplicons among primates are still poorly investigated. In this paper, we develop a statistical framework for discovering duplicons via integration of a Hidden Markov Model (HMM) and a permutation test. Our comparative analysis indicates that the mosaic structure of duplicons is common in CNV/SD regions of both human and chimpanzee genomes, and a subset of core duplicons is shared by the majority of CNVs/SDs. Phylogenetic analyses using duplicons suggested that most CNVs/SDs share common duplication ancestry. Many human/chimpanzee duplicons flank both ends of CNVs, which may be hotspots of nonallelic homologous recombination.
authors.affiliation: Genomics Research Center, Academia Sinica, Taipei, Taiwan.
authors.forename: Trees-Juen
authors.initials: TJ
authors.lastname: Chuang
authors.forename: Shian-Zu
authors.initials: SZ
authors.lastname: Wu
authors.forename: Yao-Ting
authors.initials: YT
authors.lastname: Huang
mesh_terms: D000818:Animals; D033481:Chromosomes, Mammalian / Q000235:genetics; D016000:Cluster Analysis; D056915:DNA Copy Number Variations; D059765:Homologous Recombination / Q000235:genetics; D006801:Humans; D008390:Markov Chains; D058977:Molecular Sequence Annotation; D009030:Mosaicism; D002679:Pan troglodytes / Q000235:genetics*; D010802:Phylogeny; D056916:Segmental Duplications, Genomic / Q000235:genetics*; D013045:Species Specificity