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Abstract

Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalog the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene “mountains” and a much larger number of gene “hills” that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.

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Supplementary Material

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References and Notes

1
B. Vogelstein, K. W. Kinzler, Nat. Med.10, 789 (2004).
2
P. A. Futrealet al., Nat. Rev. Cancer4, 177 (2004).
3
A. Bardelli, V. E. Velculescu, Curr. Opin. Genet. Dev.15, 5 (2005).
4
C. Greenmanet al., Nature446, 153 (2007).
5
T. Sjöblomet al., Science314, 268 (2006).
6
K. D. Pruitt, T. Tatusova, D. R. Maglott, Nucleic Acids Res.35, D61 (2007).
7
See supporting material on Science Online.
8
M. Cargillet al., Nat. Genet.22, 231 (1999).
9
M. K. Halushkaet al., Nat. Genet.22, 239 (1999).
10
P. Stephenset al., Nat. Genet.37, 590 (2005).
11
J. V. Chamary, J. L. Parmley, L. D. Hurst, Nat. Rev. Genet.7, 98 (2006).
12
R. Karchin, Structural models of mutants identified in breast cancers; http://karchinlab.org/RefSeqMutants/breast.html.
13
R. Karchin, Structural models of mutants identified in colorectal cancers. http://karchinlab.org/RefSeqMutants/colorectal.html.
14
R. Karchinet al., Bioinformatics21, 2814 (2005).
15
S. Bolket al., Proc. Natl. Acad. Sci. U.S.A.97, 268 (2000).
16
L. F. Onuchicet al., Am. J. Hum. Genet.70, 1305 (2002).
17
A. I. den Hollanderet al., Nat. Genet.23, 217 (1999).
18
Y. Samuelset al., Science304, 554 (2004).
19
K. E. Bachmanet al., Cancer Biol. Ther.3, 772 (2004).
20
D. K. Brodericket al., Cancer Res.64, 5048 (2004).
21
J. W. Leeet al., Oncogene24, 1477 (2005).
22
A. Bagchiet al., Cell128, 459 (2007).
23
J. S. Boehmet al., Cell129, 1065 (2007).
24
M. Satpathyet al., Cancer Res.67, 7194 (2007).
25
V. Theodorouet al., Nat. Genet.39, 759 (2007).
26
N. Beerenwinkelet al., PLoS Comput. Biol.3, e225 (2007).
27
A. Bardelliet al., Science300, 949 (2003).
28
D. W. Parsonset al., Nature436, 792 (2005).
29
R. K. Thomaset al., Nat. Genet.39, 347 (2007).
30
C. M. Annunziataet al., Cancer Cell12, 115 (2007).
31
J. J. Keatset al., Cancer Cell12, 131 (2007).
32
F. Diehl, L. A. Diaz Jr., Curr. Opin. Oncol.19, 36 (2007).
33
R. Sanchez, A. Sali, Proc. Natl. Acad. Sci. U.S.A.95, 13597 (1998).
34
E. F. Pettersenet al., J. Comput. Chem.25, 1605 (2004).
35
We thank J. Lutterbaugh, E. Lawrence, and L. Beard for assistance with cell culture and DNA preparation; K. Makowski and the Agencourt sequencing team for assistance with automated sequencing; C.-S. Liu and the SoftGenetics team for their assistance with mutation detection analyses; and D. H. Nguyen of the Johns Hopkins Department of Art as Applied to Medicine for the artwork in Fig. 3. Supported by The Virginia and D. K. Ludwig Fund for Cancer Research; NIH grants CA121113, CA 43460, CA 57345, CA62924, GM07309, RR017698, P30-CA43703, CA109274, GM070219, and CA112828; NCI Division of Cancer Prevention contract HHSN261200433002C; Department of Defense grant DAMD17-03-1-0241; NSF grant DMS034211; The Pew Charitable Trusts; The Palmetto Health Foundation; The Maryland Cigarette Restitution Fund; The State of Ohio Biomedical Research and Technology Transfer Commission; The Clayton Fund; The Blaustein Foundation; The National Colorectal Cancer Research Alliance; the Strang Cancer Prevention Center; the Division of Cancer Prevention of the National Cancer Institute; the Avon Foundation; The Flight Attendant's Medical Research Institute; the V Foundation for Cancer Research; the Summer Running Fund; and The Palmetto Health Foundation. Under separate licensing agreements between the Johns Hopkins University and Genzyme Corporation and Exact Sciences Corporation, K.W.K., B.V., and V.E.V. are entitled to a share of royalties received by the University on sales of products related to research described in this paper. These authors and the University own Genzyme stock, which is subject to certain restrictions under University policy. The terms of these arrangements are managed by the Johns Hopkins University in accordance with its conflict-of-interest policies.

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Information & Authors

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Published In

Science
Volume 318 | Issue 5853
16 November 2007

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Submission history

Received: 29 May 2007
Accepted: 1 October 2007
Published in print: 16 November 2007

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Notes

Supporting Online Material
www.sciencemag.org/cgi/content/full/1145720/DC1
Materials and Methods
Statistical Analysis Package
Fig. S1
Tables S1 to S6
References

Authors

Affiliations

Laura D. Wood*
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
D. Williams Parsons*
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Siân Jones*
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Jimmy Lin*
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Tobias Sjöblom*,†
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Rebecca J. Leary
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Dong Shen
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Simina M. Boca
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Department of Biostatistics, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA.
Thomas Barber
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Janine Ptak
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Natalie Silliman
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Steve Szabo
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Zoltan Dezso
GeneGo, St. Joseph, MI 49085, USA.
Vadim Ustyanksky
GeneGo, St. Joseph, MI 49085, USA.
Tatiana Nikolskaya
GeneGo, St. Joseph, MI 49085, USA.
Vavilov Institute of General Genetics, Moscow, Russia.
Yuri Nikolsky
GeneGo, St. Joseph, MI 49085, USA.
Rachel Karchin
Department of Biomedical Engineering, Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.
Paul A. Wilson
Department of Biomedical Engineering, Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.
Joshua S. Kaminker
Department of Bioinformatics, Genentech, San Francisco, CA 94080, USA.
Zemin Zhang
Department of Bioinformatics, Genentech, San Francisco, CA 94080, USA.
Randal Croshaw
Department of Pathology and Microbiology, The Center for Colon Cancer Research, and The South Carolina Cancer Center, Division of Basic Research, The University of South Carolina, School of Medicine, Columbia, SC 29229, USA.
Joseph Willis
Department of Pathology and Ireland Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106, USA.
Dawn Dawson
Department of Pathology and Ireland Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106, USA.
Michail Shipitsin
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
James K. V. Willson
Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.
Saraswati Sukumar
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA.
Kornelia Polyak
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
Ben Ho Park
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA.
Charit L. Pethiyagoda
Perlegen Sciences, Mountain View, CA 94043, USA.
P. V. Krishna Pant
Perlegen Sciences, Mountain View, CA 94043, USA.
Dennis G. Ballinger
Perlegen Sciences, Mountain View, CA 94043, USA.
Andrew B. Sparks§
Perlegen Sciences, Mountain View, CA 94043, USA.
James Hartigan
Agencourt Bioscience Corporation, Beverly, MA 01915, USA.
Douglas R. Smith
Agencourt Bioscience Corporation, Beverly, MA 01915, USA.
Erick Suh
Agencourt Bioscience Corporation, Beverly, MA 01915, USA.
Nickolas Papadopoulos
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Phillip Buckhaults
Department of Pathology and Microbiology, The Center for Colon Cancer Research, and The South Carolina Cancer Center, Division of Basic Research, The University of South Carolina, School of Medicine, Columbia, SC 29229, USA.
Sanford D. Markowitz
Department of Medicine and Ireland Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, and Howard Hughes Medical Institute, Cleveland, OH 44106, USA.
Giovanni Parmigiani [email protected]
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Kenneth W. Kinzler [email protected]
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Victor E. Velculescu [email protected]
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Bert Vogelstein [email protected]
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.

Notes

To whom correspondence should be addressed. E-mail: [email protected] (G.P.); [email protected] (K.W.K.); [email protected] (V.E.V.); [email protected] (B.V.)

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