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BioMed Research International
Volume 2013 (2013), Article ID 264532, 12 pages
http://dx.doi.org/10.1155/2013/264532
Methodology Report

A Novel Framework for the Identification and Analysis of Duplicons between Human and Chimpanzee

1Genomics Research Center, Academia Sinica, Taipei, Taiwan
2Department of Computer Science and Information Engineering, National Chung Cheng University, No.168 University Road Chiayi, Taiwan

Received 24 April 2013; Revised 25 June 2013; Accepted 10 July 2013

Academic Editor: Che-Lun Hung

Copyright © 2013 Trees-Juen Chuang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.