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Genome Analysis Publications

Selected Publications for Which the Genome Analysis Core Has Made Significant Contributions

(2011). Cancer genetics: Teasing apart cancer’s influences. Nature 470, 143-143.

Bauer, J., Curtin, J.A., Pinkel, D., and Bastian, B.C. (2007). Congenital melanocytic nevi frequently harbor NRAS mutations but no BRAF mutations. J Invest Dermatol 127, 179-182.

Kitagawa, M., Lee, S.H., and McCormick, F. (2008). Skp2 suppresses p53-dependent apoptosis by inhibiting p300. Mol Cell 29, 217-231.

Mao, J.H., Kim, I.J., Wu, D., Climent, J., Kang, H.C., DelRosario, R., and Balmain, A. (2008). FBXW7 targets mTOR for degradation and cooperates with PTEN in tumor suppression. Science 321, 1499-1502. PMCID: PMC2849753.

Mirzoeva, O.K., Das, D., Heiser, L.M., Bhattacharya, S., Siwak, D., Gendelman, R., Bayani, N., Wang, N.J., Neve, R.M., Guan, Y., Hu, Z., Knight, Z.,

Feiler, H.S., Gascard, P., Parvin, B., Spellman, P.T., Shokat, K.M., Wyrobek, A.J., Bissell, M.J., McCormick, F., Kuo, W.L., Mills, G.B., Gray, J.W., and

Korn, W.M. (2009). Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition. Cancer Res 69, 565-572. PMCID: PMC2737189.

North, J.P., Kageshita, T., Pinkel, D., LeBoit, P.E., and Bastian, B.C. (2008). Distribution and significance of occult intraepidermal tumor cells surrounding primary melanoma. J Invest Dermatol 128, 2024-2030. PMCID: PMC2825251.

Quigley, D.A., To, M.D., Kim, I.J., Lin, K.K., Albertson, D.G., Sjolund, J., Perez-Losada, J., and Balmain, A. (2011). Network analysis of skin tumor progression identifies a rewired genetic architecture affecting inflammation and tumor susceptibility. Genome Biol 12, R5.

Quigley, D.A., To, M.D., Perez-Losada, J., Pelorosso, F.G., Mao, J.H., Nagase, H., Ginzinger, D.G., and Balmain, A. (2009). Genetic architecture of mouse skin inflammation and tumour susceptibility. Nature 458, 505-508.

To, M.D., Wong, C.E., Karnezis, A.N., Del Rosario, R., Di Lauro, R., and Balmain, A. (2008). Kras regulatory elements and exon 4A determine mutation specificity in lung cancer. Nat Genet 40, 1240-1244. PMCID: PMC2654781.

Van Raamsdonk, C.D., Bezrookove, V., Green, G., Bauer, J., Gaugler, L., O’Brien, J.M., Simpson, E.M., Barsh, G.S., and Bastian, B.C. (2009). Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi. Nature 457, 599-602. PMCID: PMC2696133.

Van Raamsdonk, C.D., Griewank, K.G., Crosby, M.B., Garrido, M.C., Vemula, S., Wiesner, T., Obenauf, A.C., Wackernagel, W., Green, G., Bouvier, N.,

Sozen, M.M., Baimukanova, G., Roy, R., Heguy, A., Dolgalev, I., Khanin, R., Busam, K., Speicher, M.R., O’Brien, J., and Bastian, B.C. (2010). Mutations in GNA11 in uveal melanoma. N Engl J Med 363, 2191-2199. PMCID: PMC3107972.

Wakabayashi, Y., Mao, J.H., Brown, K., Girardi, M., and Balmain, A. (2007). Promotion of Hras-induced squamous carcinomas by a polymorphic variant of the Patched gene in FVB mice. Nature 445, 761-765.

Cadieux B, Ching TT, VandenBerg SR, Costello JF. 2006. Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, MTHFR allele status and increased proliferation. Cancer Research 66:8469-76.

Cleaver JE, Feeney L, Tang JY, and Tuttle P. 2007. Xeroderma pigmentosum group C in an isolated region of guatemala J Invest Dermatol 127: 493-496.

Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, Kutzner H, Cho KH, Aiba S, Brocker EB, LeBoit PE, Pinkel D, Bastian BC. 2005. Distinct sets of genetic alterations in melanoma. N Engl J Med 353:2135-47.

Curtin JA, Stark MS, Pinkel D, Hayward NK, Bastian BC. 2006. P13-kinase subunits are infrequent somatic targets in melanoma. J Invest Dermatol 126:1660-63.

Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. 2006. DNA motifs associated with aberrant CpG island methylation. Genomics 87:572-79.

Fridlyand J, Snijders A, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler

H, Gray JW, Waldman F, Pinkel D, Albertson DG. 2006. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer6 96.

Haas-Kogan DA, Prados MD, Tihan T, Eberhard DA, Jelluma N, Arvold ND, Baumer R, Lamborn KR, Kapadia A, Malec M, Berger MS, Stokoe D. 2005. Epidermal growth factor receptor, protein kinase B/Akt, and glioma response to erlotinib. J NCI 97:880-87.

Hodgson JG, Malek T, Bornstein S, Hariono S, Ginzinger DG, Muller WJ, Gray JW. 2005. Copy Number Aberrations in Mouse Breast Tumors Reveal Loci and Genes Important in Tumorigenic Receptor Tyrosine Kinase Signaling. Cancer Res 65:9695-9704.

Kitigawa, M, Lee SH, McCormick F. 2008. Skp2 suppresses p53-dependent apoptosis by Inhibiting p300. Mol Cell 29: 217-231.

Lacher MD, Tiirikainen MI, Saunier EF, Christian C, Anders M, Oft M, Balmain A, Akhurst RJ, Korn WM. 2006. Transforming growth factor-beta receptor inhibition enhances adenoviral infectability of carcinoma cells via up-regulation of Coxsackie and Adenovirus Receptor in conjunction with reversal of epithelial-mesenchymal transition. Cancer Res 66:1648-57.

Lee SH, McCormick F. 2005. Downregulation of Skp2 and p27/Kip1 synergistically induces apoptosis in G98G glioblastoma cells. J Mol Med 83:296-307.

Macrae M, Neve RM, Rodriguez-Viciana P, Haqq C, Yeh J, Chen C, Gray JW, McCormick F. 2005. A conditional feedback loop regulates Ras activity through EphA2. Cancer Cell 8:111-18.

Oda K, Stokoe D, Taketani Y, McCormick F. 2005. High frequency of co-existent mutations of PIK3CA and PTEN genes in endometrial carcinoma. Cancer Research 65:10669-73.

O’Shea C, Choi S, Bagus B, McCormick F. 2005. Heat shock phenocopies E1B-55K late functions and selectively sensitizes refractory tumor cells to ONYX-015 oncolytic viral therapy. Cancer Cell 8:61-74.

O’Shea C, Klupsch K, Choi S, Bagus B, Soria C, Shen J, McCormick F, Stokoe D. 2005. Adenoviral proteins mimic nutrient/growth signals to activate the mTOR pathway for viral replication. EMBO J 24:1211-21.

Rodriguez-Viciana P, Oses-Prieto J, Burlingame A, Fried M, McCormick F. 2006. A phosphate holoenzyme comprised of shoc2/sur8 and the catalytic subunit of pp1 functions as an M-Ras effector to modulate Raf activity. Molecular Cell 22:217-30.

Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. 2005. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res 15:302-11.

Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RCK, Albertson DG. 2005. Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. Oncogene 24:4232-442.

Tominaga Y, Meyer T, Kolesnichenko M, Bilanges B, Stokoe D. 2005. Translational deregulation in PDK-1 embryonic stem cells. Mol Cell Biol 25:8465-75.

Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Jurnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, De Jong PJ, Pevzner P, Collins C. 2006. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res 16:394-404.


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