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| Scientific Publications
All data generated by The Cancer Genome Atlas (TCGA) Research Network are made open to the public through the Data Coordinating Center and the TCGA Data Portal. The following is a growing list of publications from the TCGA Research Network (designated with an *) and from other investigators who have successfully leveraged the TCGA data for their own work.
Yadav, A.K., Renfrow, J.J., Scholtens, D.M., Xie, H., Duran, G.E., Bredel, C., Vogel, H., Chandler, J.P., Chakravarti, A., Robe, P.A., et al. (2009). Monosomy of Chromosome 10 Associated With Dysregulation of Epidermal Growth Factor Signaling in Glioblastomas. JAMA 302, 276-289. View PubMed abstract
Yip, S., Miao, J., Cahill, D.P., Iafrate, A.J., Aldape, K., Nutt, C.L., and Louis, D.N. (2009). MSH6 mutations arise in glioblastomas during temozolomide therapy and mediate temozolomide resistance. Clin Cancer Res 15, 4622-4629. View PubMed abstract
Bredel, M., Scholtens, D.M., Harsh, G.R., Bredel, C., Chandler, J.P., Renfrow, J.J., Yadav, A.K., Vogel, H., Scheck, A.C., Tibshirani, R., et al. (2009). A Network Model of a Cooperative Genetic Landscape in Brain Tumors. JAMA 302, 261-275. View PubMed abstract
Wrensch, M., Jenkins, R. B., Chang, J. S., Yeh, R., Xiao, Y., Decker, P. A., Ballman, K. V., Berger, M., Buckner, J. C., Chang, S., et al (2009). Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nature Genetics 41, 905-908. View PubMed abstract
Shete, S., Hosking, F. J., Robertson, L. B., Dobbins, S. E., Sanson, M., Malmer, B., Simon, M., Marie, Y., Boisselier, B., Delattre, J., et al (2009). Genome-wide association study identifies five susceptibility loci for glioma. Nature Genetics 41, 899-904. View PubMed abstract
Veeriah, S., Brennan, C., Meng, S., Singh, B., Fagin, J.A., Solit, D.B., Paty, P.B., Rohle, D., Vivanco, I., Chmielecki, J., et al. (2009). The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci U S A 106, 9435-9440. View PubMed abstract
Bengtsson, H., Ray, A., Spellman, P., and Speed, T.P. (2009). A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. Bioinformatics 25, 861-867. View PubMed abstract
Li, A., Walling, J., Ahn, S., Kotliarov, Y., Su, Q., Quezado, M., Oberholtzer, J.C., Park, J., Zenklusen, J.C., and Fine, H.A. (2009). Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res 69, 2091-2099. View PubMed abstract
Hampton, O.A., Den Hollander, P., Miller, C.A., Delgado, D.A., Li, J., Coarfa, C., Harris, R.A., Richards, S., Scherer, S.E., Muzny, D.M., et al. (2009). A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res 19, 167-177. View PubMed abstract
Chiang, D.Y., Getz, G., Jaffe, D. B., O’Kelly, M.J., Zhao, X., Carter, S.L., Russ, C., Nusbaum, C., Meyerson, M., and Lander, E.S. (2009). High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6, 99-103. View PubMed abstract
Freire, P., Vilela, M., Deus, H., Kim, Y.-W., Koul, D., Colman, H., Aldape, K.D., Bogler, O., Yung, W.K.A., Coombes, K., et al. (2008). Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme. PLoS One 3, Article No.: e4076. View PubMed abstract
Zheng, H., Ying, H., Yan, H., Kimmelman, A.C., Hiller, D.J., Chen, A.J., Perry, S.R., Tonon, G., Chu, G.C., Ding, Z., et al. (2008). p53 and Pten control neural and glioma stem/progenitor cell renewal and differentiation. Nature 455, 1129-1133. View PubMed abstract
*The Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068.
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