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Science 9 August 2002:
Vol. 297. no. 5583, pp. 1003 - 1007
DOI: 10.1126/science.1072047
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Reports

Recent Segmental Duplications in the Human Genome

Jeffrey A. Bailey,1 Zhiping Gu,2 Royden A. Clark,1 Knut Reinert,2 Rhea V. Samonte,1 Stuart Schwartz,1 Mark D. Adams,2 Eugene W. Myers,2 Peter W. Li,2 Evan E. Eichler1*

Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.

1 Department of Genetics, Center for Computational Genomics, and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA.
2 Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.
*   To whom correspondence should be addressed. E-mail: eee{at}cwru.edu

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Segmental trisomy of chromosome 17: A mouse model of human aneuploidy syndromes.
T. Vacik, M. Ort, S. Gregorova, P. Strnad, R. Blatny, N. Conte, A. Bradley, J. Bures, and J. Forejt (2005)
PNAS 102, 4500-4505
   Abstract »    Full Text »    PDF »
Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling.
Y. Zhou and B. Mishra (2005)
PNAS 102, 4051-4056
   Abstract »    Full Text »    PDF »
The Influence of CCL3L1 Gene-Containing Segmental Duplications on HIV-1/AIDS Susceptibility.
E. Gonzalez, H. Kulkarni, H. Bolivar, A. Mangano, R. Sanchez, G. Catano, R. J. Nibbs, B. I. Freedman, M. P. Quinones, M. J. Bamshad, et al. (2005)
Science 307, 1434-1440
   Abstract »    Full Text »    PDF »
Complex genomic rearrangements lead to novel primate gene function.
F. D. Ciccarelli, C. von Mering, M. Suyama, E. D. Harrington, E. Izaurralde, and P. Bork (2005)
Genome Res. 15, 343-351
   Abstract »    Full Text »    PDF »
Evolutionary History of Chromosome 20.
D. Misceo, M. F. Cardone, L. Carbone, P. D'Addabbo, P. J. de Jong, M. Rocchi, and N. Archidiacono (2005)
Mol. Biol. Evol. 22, 360-366
   Abstract »    Full Text »    PDF »
Patterns of Segmental Duplication in the Human Genome.
L. Zhang, H. H. S. Lu, W.-y. Chung, J. Yang, and W.-H. Li (2005)
Mol. Biol. Evol. 22, 135-141
   Abstract »    Full Text »    PDF »


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