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BioMed Research International
Volume 2013 (2013), Article ID 264532, 12 pages
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.
- A. J. Sharp, D. P. Locke, S. D. McGrath et al., “Segmental duplications and copy-number variation in the human genome,” American Journal of Human Genetics, vol. 77, no. 1, pp. 78–88, 2005.
- J. A. Bailey, Z. Gu, R. A. Clark et al., “Recent segmental duplications in the human genome,” Science, vol. 297, no. 5583, pp. 1003–1007, 2002.
- X. She, Z. Jiang, R. A. Clark et al., “Shotgun sequence assembly and recent segmental duplications within the human genome,” Nature, vol. 431, no. 7011, pp. 927–930, 2004.
- L. Feuk, A. R. Carson, and S. W. Scherer, “Structural variation in the human genome,” Nature Reviews Genetics, vol. 7, no. 2, pp. 85–97, 2006.
- T. J. Aitman, R. Dong, T. J. Vyse et al., “Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans,” Nature, vol. 439, no. 7078, pp. 851–855, 2006.
- E. Gonzalez, H. Kulkarni, H. Bolivar et al., “The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility,” Science, vol. 307, no. 5714, pp. 1434–1440, 2005.
- A. B. Singleton, M. Farrer, J. Johnson et al., “α-synuclein locus triplication causes Parkinson's disease,” Science, vol. 302, no. 5646, p. 841, 2003.
- A. Rovelet-Lecrux, D. Hannequin, G. Raux et al., “APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy,” Nature Genetics, vol. 38, no. 1, pp. 24–26, 2006.
- Z. Jiang, R. Hubley, A. Smit, and E. E. Eichler, “DupMasker: a tool for annotating primate segmental duplications,” Genome Research, vol. 18, no. 8, pp. 1362–1368, 2008.
- Z. Cheng, M. Ventura, X. She et al., “A genome-wide comparison of recent chimpanzee and human segmental duplications,” Nature, vol. 437, no. 7055, pp. 88–93, 2005.
- X. She, Z. Cheng, S. Zöllner, D. M. Church, and E. E. Eichler, “Mouse segmental duplication and copy number variation,” Nature Genetics, vol. 40, no. 7, pp. 909–914, 2008.
- A. S. Lee, M. Gutiérrez-Arcelus, G. H. Perry et al., “Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies,” Human Molecular Genetics, vol. 17, no. 8, pp. 1127–1136, 2008.
- T. J. Nicholas, Z. Cheng, M. Ventura, K. Mealey, E. E. Eichler, and J. M. Akey, “The genomic architecture of segmental duplications and associated copy number variants in dogs,” Genome Research, vol. 19, no. 3, pp. 491–499, 2009.
- F.-C. Chen, Y.-Z. Chen, and T.-J. Chuang, “CNVVdb: a database of copy number variations across vertebrate genomes,” Bioinformatics, vol. 25, no. 11, pp. 1419–1421, 2009.
- R. Redon, S. Ishikawa, K. R. Fitch et al., “Global variation in copy number in the human genome,” Nature, vol. 444, no. 7118, pp. 444–454, 2006.
- G. H. Perry, J. Tchinda, S. D. McGrath et al., “Hotspots for copy number variation in chimpanzees and humans,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 21, pp. 8006–8011, 2006.
- G. H. Perry, F. Yang, T. Marques-Bonet et al., “Copy number variation and evolution in humans and chimpanzees,” Genome Research, vol. 18, no. 11, pp. 1698–1710, 2008.
- D. Komura, F. Shen, S. Ishikawa et al., “Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays,” Genome Research, vol. 16, no. 12, pp. 1575–1584, 2006.
- T. S. Price, R. Regan, R. Mott et al., “SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data,” Nucleic Acids Research, vol. 33, no. 11, pp. 3455–3464, 2005.
- K. Chen, J. W. Wallis, M. D. McLellan et al., “BreakDancer: an algorithm for high-resolution mapping of genomic structural variation,” Nature Methods, vol. 6, no. 9, pp. 677–681, 2009.
- J. Sebat, B. Lakshmi, J. Troge et al., “Large-scale copy number polymorphism in the human genome,” Science, vol. 305, no. 5683, pp. 525–528, 2004.
- A. J. Sharp, Z. Cheng, and E. E. Eichler, “Structural variation of the human genome,” Annual Review of Genomics and Human Genetics, vol. 7, pp. 407–442, 2006.
- H. Xiao, N. Jiang, E. Schaffner, E. J. Stockinger, and E. Van Der Knaap, “A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit,” Science, vol. 319, no. 5869, pp. 1527–1530, 2008.
- Z. Jiang, H. Tang, M. Ventura et al., “Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution,” Nature Genetics, vol. 39, no. 11, pp. 1361–1368, 2007.
- C. L. Kahn and B. J. Raphael, “A parsimony approach to analysis of human segmental duplications,” Pacific Symposium on Biocomputing, vol. 14, pp. 126–137, 2009.
- J. A. Bailey and E. E. Eichler, “Primate segmental duplications: crucibles of evolution, diversity and disease,” Nature Reviews Genetics, vol. 7, no. 7, pp. 552–564, 2006.
- E. E. Eichler, M. L. Budarf, M. Rocchi et al., “Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity,” Human Molecular Genetics, vol. 6, no. 7, pp. 991–1002, 1997.
- P. A. Pevzner, H. Tang, and G. Tesler, “De novo repeat classification and fragment assembly,” Genome Research, vol. 14, no. 9, pp. 1786–1796, 2004.
- P. M. Kim, H. Y. K. Lam, A. E. Urban et al., “Analysis of copy number variants and segmental duplications in the human genome: evidence for a change in the process of formation in recent evolutionary history,” Genome Research, vol. 18, no. 12, pp. 1865–1874, 2008.
- S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990.
- Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, “A greedy algorithm for aligning DNA sequences,” Journal of Computational Biology, vol. 7, no. 1-2, pp. 203–214, 2000.
- L. R. Rabiner, “Tutorial on hidden Markov models and selected applications in speech recognition,” Proceedings of the IEEE, vol. 77, no. 2, pp. 257–286, 1989.
- M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007.
- S. A. McCarroll and D. M. Altshuler, “Copy-number variation and association studies of human disease,” Nature Genetics, vol. 39, no. 1, pp. S37–S42, 2007.