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Science 23 July 2004:
Vol. 305. no. 5683, pp. 525 - 528
DOI: 10.1126/science.1098918
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Reports

Large-Scale Copy Number Polymorphism in the Human Genome

Jonathan Sebat,1 B. Lakshmi,1 Jennifer Troge,1 Joan Alexander,1 Janet Young,2 Pär Lundin,3 Susanne Månér,3 Hillary Massa,2 Megan Walker,2 Maoyen Chi,1 Nicholas Navin,1 Robert Lucito,1 John Healy,1 James Hicks,1 Kenny Ye,4 Andrew Reiner,1 T. Conrad Gilliam,5 Barbara Trask,2 Nick Patterson,6 Anders Zetterberg,3 Michael Wigler1*

The extent to which large duplications and deletions contribute to human genetic variation and diversity is unknown. Here, we show that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans. Representational oligonucleotide microarray analysis of 20 individuals revealed a total of 221 copy number differences representing 76 unique CNPs. On average, individuals differed by 11 CNPs, and the average length of a CNP interval was 465 kilobases. We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease.

1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
2 Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
3 Karolinska Institute, Stockholm SE-17176, Sweden.
4 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA.
5 Columbia Genome Center, Columbia University, New York, NY 10032, USA.
6 Broad Institute, Cambridge, MA 02139, USA.

* To whom correspondence should be addressed. E-mail: wigler{at}cshl.edu

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B. Mosch, M. Morawski, A. Mittag, D. Lenz, A. Tarnok, and T. Arendt (2007)
J. Neurosci. 27, 6859-6867
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Copy Number Variation in the Human Genome and Its Implications for Cardiovascular Disease.
R. L. Pollex and R. A. Hegele (2007)
Circulation 115, 3130-3138
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Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.
J. O. Korbel, A. E. Urban, F. Grubert, J. Du, T. E. Royce, P. Starr, G. Zhong, B. S. Emanuel, S. M. Weissman, M. Snyder, et al. (2007)
PNAS 104, 10110-10115
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What is a gene, post-ENCODE? History and updated definition.
M. B. Gerstein, C. Bruce, J. S. Rozowsky, D. Zheng, J. Du, J. O. Korbel, O. Emanuelsson, Z. D. Zhang, S. Weissman, and M. Snyder (2007)
Genome Res. 17, 669-681
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Association Studies of BMI and Type 2 Diabetes in the Neuropeptide Y Pathway: A Possible Role for NPY2R as a Candidate Gene for Type 2 Diabetes in Men.
C. D. Campbell, H. N. Lyon, J. Nemesh, J. A. Drake, T. Tuomi, D. Gaudet, X. Zhu, R. S. Cooper, K. G. Ardlie, L. C. Groop, et al. (2007)
Diabetes 56, 1460-1467
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