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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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Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes.
P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand, and G. Benson (2004)
Genome Res. 14, 1861-1869
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Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing.
T. S. Furey, M. Diekhans, Y. Lu, T. A. Graves, L. Oddy, J. Randall-Maher, L. W. Hillier, R. K. Wilson, and D. Haussler (2004)
Genome Res. 14, 2034-2040
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Human chromosome 7 circa 2004: a model for structural and functional studies of the human genome.
S. W. Scherer and E. D. Green (2004)
Hum. Mol. Genet. 13, R303-R313
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Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse.
A.-M. Mallon, L. Wilming, J. Weekes, J. G.R. Gilbert, J. Ashurst, S. Peyrefitte, L. Matthews, M. Cadman, R. McKeone, C. A. Sellick, et al. (2004)
Genome Res. 14, 1888-1901
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Recurrent Sites for New Centromere Seeding.
M. Ventura, S. Weigl, L. Carbone, M. F. Cardone, D. Misceo, M. Teti, P. D'Addabbo, A. Wandall, E. Bjorck, P. J. de Jong, et al. (2004)
Genome Res. 14, 1696-1703
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Duplicative and Conservative Transpositions of Larval serum protein 1 Genes in the Genus Drosophila.
J. Gonzalez, F. Casals, and A. Ruiz (2004)
Genetics 168, 253-264
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Evolution of Beta Satellite DNA Sequences: Evidence for Duplication-Mediated Repeat Amplification and Spreading.
M. F. Cardone, L. Ballarati, M. Ventura, M. Rocchi, A. Marozzi, E. Ginelli, and R. Meneveri (2004)
Mol. Biol. Evol. 21, 1792-1799
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