An integrated genomic analysis of human glioblastoma multiforme

Science

Volumn 321, Issue 5897, 2008, Pages 1807-1812

  Parsons, D Williams ^a,b   Jones, Siân ^a   Zhang, Xiaosong ^a   Lin, Jimmy Cheng Ho ^a   Leary, Rebecca J ^a   Angenendt, Philipp ^a   Mankoo, Parminder ^c   Carter, Hannah ^c   Siu, I Mei ^c   Gallia, Gary L ^c   Olivi, Alessandro ^c   McLendon, Roger ^d   Rasheed, B Ahmed ^d   Keir, Stephen ^d   Nikolskaya, Tatiana ^e   Nikolsky, Yuri ^f   Busam, Dana A ^g   Tekleab, Hanna ^g   Diaz Jr , Luis A ^a   Hartigan, James ^h   Smith, Doug R ^h   Strausberg, Robert L ^g   Marie, Suely Kazue Nagahashi ⁱ   Shinjo, Sueli Mieko Oba ⁱ   Yan, Hai ^d   Riggins, Gregory J ^c   Bigner, Darell D ^d   Karchin, Rachel ^c   Papadopoulos, Nick ^a   Parmigiani, Giovanni ^a   Vogelstein, Bert ^a   Velculescu, Victor E ^a   Kinzler, Kenneth W ^a   more..

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c DEPARTMENT OF PATHOLOGY   (United States)

^d DUKE UNIVERSITY MEDICAL CENTER   (United States)

^e VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

^f GeneGo bioinformatics software Inc   (United States)

^g J CRAIG VENTER INSTITUTE   (United States)

^h Agencourt Bioscience Corporation   (United States)

ⁱ UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ISOCITRATE DEHYDROGENASE;

BRAIN; CANCER; CLASSIFICATION; DISEASE TREATMENT; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ANALYSIS;

ARTICLE; DNA MICROARRAY; GENE AMPLIFICATION; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOMICS; GLIOBLASTOMA; HUMAN; POINT MUTATION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ADULT; BRAIN NEOPLASMS; FEMALE; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; GLIOBLASTOMA; HUMANS; ISOCITRATE DEHYDROGENASE; MALE; MIDDLE AGED; MUTATION; MUTATION, MISSENSE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION; SURVIVAL RATE;

EID: 52949127312     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1164382     Document Type: Article

References (51)

1. D. N. Louis et al., Acta Neuropathol. 114, 97 (2007).
2. R. Stupp et al., N. Engl. J. Med. 352, 987 (2005).
3. H. Scherer, Am. J. Cancer 40, 159 (1940).
4. P. Kleihues, H. Ohgaki, Neuro-oncol. 1, 44 (1999).
5. H. Ohgaki, P. Kleihues, Am. J. Pathol. 170, 1445 (2007).
6. H. Ohgaki et al., Cancer Res. 64, 6892 (2004).
7. I. K. Mellinghoff et al., N. Engl. J. Med. 353, 2012 (2005).
8. E. A. Maher et al., Cancer Res. 66, 11502 (2006).
9. C. L. Tso et al., Cancer Res. 66, 159 (2006).
10. T. Sjöblom et al., Science 314, 268 (2006).
11. L. D. Wood et al., Science 318, 1108 (2007).
12. Materials and methods are available as supporting material on Science Online.
13. D. P. Cahill et al., Clin. Cancer Res. 13, 2038 (2007).
14. C. Hunter et al., Cancer Res. 66, 3987 (2006).
15. J. M. Winter, J. R. Brody, S. E. Kern, Cancer Biol. Ther. 5, 360 (2006).
16. S. Jones et al., Proc. Natl. Acad. Sci. U.S.A. 105, 4283 (2008).
17. S. Jones et al., Science 321, 1801 (2008).
18. R. Kraus-Ruppert, J. Laissue, H. Burki, N. Odartchenko, J. Comp. Neurol. 148, 211 (1973).
19. P. C. Ng, S. Henikoff, Nucleic Acids Res. 31, 3812 (2003).
20. R. Karchin, Structural models of mutants identified in glioblastomas (2008); http://karchinlab.org/Mutants/CAN-genes/brain/GBM.html
21. F. J. Steemers et al., Nat. Methods 3, 31 (2006).
22. R. J. Leary et al., Proc. Natl. Acad. Sci. U.S.A., in press.
23. P. Cairns et al., Nat. Genet. 11, 210 (1995).
24. J. M. Nigro et al., Nature 342, 705 (1989).
25. J. Li et al., Science 275, 1943 (1997).
26. K. Ueki et al., Cancer Res. 56, 150 (1996).
27. A. J. Wong et al., Proc. Natl. Acad. Sci. U.S.A. 84, 6899 (1987).
28. M. Mizoguchi, C. L. Nutt, G. Mohapatra, D. N. Louis, Brain Pathol. 14, 372 (2004).
29. L. Frederick, X. Y. Wang, G. Eley, C. D. James, Cancer Res. 60, 1383 (2000).
30. Y. Li et al., Cell 69, 275 (1992).
31. G. Thiel et al., Anticancer Res. 15, 2495 (1995).
32. Y. Samuels et al., Science 304, 554 (2004).
33. D. K. Broderick et al., Cancer Res. 64, 5048 (2004).
34. G. L. Gallia et al., Mol. Cancer Res. 4, 709 (2006).
35. S. Ekins, Y. Nikolsky, A. Bugrim, E. Kirillov, T. Nikolskaya, Methods Mol. Biol. 356, 319 (2007).
36. J. Lin et al., Genome Res. 17, 1304 (2007).
37. V. E. Velculescu, L. Zhang, B. Vogelstein, K. W. Kinzler, Science 270, 484 (1995).
38. S. Saha et al., Nat. Biotechnol. 20, 508 (2002).
39. M. Sultan et al., Science 321, 956 (2008).
40. R. Lister et al., Cell 133, 523 (2008).
41. A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, B. Wold, Nat. Methods 5, 621 (2008).
42. R. Morin et al., Biotechniques 45, 81 (2008).
43. B. V. Geisbrecht, S. J. Gould, J. Biol. Chem. 274, 30527 (1999).
44. X. Xu et al., J. Biol. Chem. 279, 33946 (2004).
45. S. M. Lee et al., Free Radic. Biol. Med. 32, 1185 (2002).
46. S. Y. Kim et al., Mol. Cell. Biochem. 302, 27 (2007).
47. A. Nekrutenko, D. M. Hillis, J. C. Patton, R. D. Bradley, R. J. Baker, Mol. Biol. Evol. 15, 1674 (1998).
48. G. T. Jennings, K. I. Minard, L. McAlister-Henn, Biochemistry 36, 13743 (1997).
49. I. S. Kil, S. Y. Kim, S. J. Lee, J. W. Park, Free Radic. Biol. Med. 43, 1197 (2007).
50. E. F. Pettersen et al., J. Comput. Chem. 25, 1605 (2004).
51. Contact information for the authors who directed the major components of this project is as follows: H. Yan, G. J. Riggins (clinical and sample coordination), yan00002@mc.duke.edu, griggin1@jhmi.edu; D. D. Bigner (pathological and clinical review), bigne001@mc.duke. edu; R. Karchin (bioinformatic analysis), karchin@jhu. edu; N. Papadopoulos (gene expression analysis), npapado1@jhmi.edu; G. Parmigiani (statistical analysis), gp@jhu.edu; B. Vogelstein, V. E. Velculescu, K. W. Kinzler (sequencing and copy number analysis), bertvog@gmail. com, velculescu@jhmi.edu, kinzlke@jhmi.edu. We thank N. Silliman, J. Ptak, L. Dobbyn, and M. Whalen for assistance with PCR amplification; D. Lister, L. J. Ehinger, D. L. Satterfield, J. D. Funkhouser, and P. Killela for assistance with DNA purification; T. Sjöblom for assistance with database management; the Agencourt sequencing team for assistance with automated sequencing; and C.-S. Liu and the SoftGenetics team for their assistance with mutation detection analyses. This project was carried out under the auspices of the Ludwig Brain Tumor Initiative and was supported by the Virginia and D. K. Ludwig Fund for Cancer Research, NIH grants CA121113, NS052507, CA43460, CA57345, CA62924, CA09547, 5P50-NS-20023, CA108786, and CA11898, the Pew Charitable Trusts, the Pediatric Brain Tumor Foundation Institute, the Hirschhorn Foundation, Alex's Lemonade Stand Foundation, the American Brain Tumor Association, the American Society of Clinical Oncology, the Brain Tumor Research Fund and Beckman Coulter Corporation. Under separate licensing agreements between the Johns Hopkins University and Genzyme, Beckman Coulter, and Exact Sciences Corporations, B.V., V.E.V., and K.W.K. 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 and Exact Sciences 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.