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Ragazzon, B., Assié, G., and Bertherat, J. (2011). Transcriptome analysis of adrenocortical cancers: from molecular classification to the identification of new treatments. Endocr. Relat. Cancer 18, R15–27.


Ayoub, C., Wasylyk, C., Li, Y., Thomas, E., Marisa, L., Robé, A., Roux, M., Abecassis, J., de Reyniès, A., and Wasylyk, B. (2010). ANO1 amplification and expression in HNSCC with a high propensity for future distant metastasis and its functions in HNSCC cell lines. Br. J. Cancer 103, 715–726.

Banneau, G., Guedj, M., MacGrogan, G., de Mascarel, I., Velasco, V., Schiappa, R., Bonadona, V., David, A., Dugast, C., Gilbert-Dussardier, B., et al. (2010). Molecular apocrine differentiation is a common feature of breast cancer in patients with germline PTEN mutations. Breast Cancer Res. 12, R63.

Bryant, C.M., Albertus, D.L., Kim, S., Chen, G., Brambilla, C., Guedj, M., Arima, C., Travis, W.D., Yatabe, Y., Takahashi, T., et al. (2010). Clinically relevant characterization of lung adenocarcinoma subtypes based on cellular pathways: an international validation study. PLoS ONE 5, e11712.

Burnichon, N., Brière, J.-J., Libé, R., Vescovo, L., Rivière, J., Tissier, F., Jouanno, E., Jeunemaitre, X., Bénit, P., Tzagoloff, A., et al. (2010). SDHA is a tumor suppressor gene causing paraganglioma. Hum. Mol. Genet. 19, 3011–3020.

Cairo, S., Wang, Y., de Reyniès, A., Duroure, K., Dahan, J., Redon, M.-J., Fabre, M., McClelland, M., Wang, X.W., Croce, C.M., et al. (2010). Stem cell-like micro-RNA signature driven by Myc in aggressive liver cancer. Proc. Natl. Acad. Sci. U.S.A. 107, 20471–20476.

Chibon, F., Lagarde, P., Salas, S., Pérot, G., Brouste, V., Tirode, F., Lucchesi, C., de Reyniès, A., Kauffmann, A., Bui, B., et al. (2010). Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity. Nat. Med. 16, 781–787.

Cizkova M, Cizeron-Clairac G, Vacher S, Susini A, Andrieu C, Lidereau R, Bièche I (2010). Gene expression profiling reveals new aspects of PIK3CA mutation in ERalpha-positive breast cancer: major implication of the Wnt signaling pathway. PLoS One. 5(12), e15647.

Ducray, F., de Reyniès, A., Chinot, O., Idbaih, A., Figarella-Branger, D., Colin, C., Karayan-Tapon, L., Chneiweiss, H., Wager, M., Vallette, F., et al. (2010). An ANOCEF genomic and transcriptomic microarray study of the response to radiotherapy or to alkylating first-line chemotherapy in glioblastoma patients. Mol. Cancer 9, 234.

Huang, Y., de Reyniès, A., de Leval, L., Ghazi, B., Martin-Garcia, N., Travert, M., Bosq, J., Brière, J., Petit, B., Thomas, E., et al. (2010). Gene expression profiling identifies emerging oncogenic pathways operating in extranodal NK/T-cell lymphoma, nasal type. Blood 115, 1226–1237.

Jardin, F., Jais, J.-P., Molina, T.-J., Parmentier, F., Picquenot, J.-M., Ruminy, P., Tilly, H., Bastard, C., Salles, G.-A., Feugier, P., et al. (2010). Diffuse large B-cell lymphomas with CDKN2A deletion have a distinct gene expression signature and a poor prognosis under R-CHOP treatment: a GELA study. Blood 116, 1092–1104.

Jeanmougin, M., de Reyniès, A., Marisa, L., Paccard, C., Nuel, G., and Guedj, M. (2010). Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies. PLoS ONE 5, e12336.

Job B, Bernheim A, Beau-Faller M, Camilleri-Broët S, Girard P, Hofman P, Mazières J, Toujani S, Lacroix L, Laffaire J, Dessen P, Fouret P; LG Investigators. Genomic aberrations in lung adenocarcinoma in never smokers. PLoS One. 2010 Dec 6;5(12):e15145.

Jung, A.C., Briolat, J., Millon, R., de Reyniès, A., Rickman, D., Thomas, E., Abecassis, J., Clavel, C., and Wasylyk, B. (2010). Biological and clinical relevance of transcriptionally active human papillomavirus (HPV) infection in oropharynx squamous cell carcinoma. Int. J. Cancer 126, 1882–1894.

Perkins, G., Lièvre, A., Ramacci, C., Méatchi, T., de Reyniès, A., Emile, J.-F., Boige, V., Tomasic, G., Bachet, J.-B., Bibeau, F., et al. (2010). Additional value of EGFR downstream signaling phosphoprotein expression to KRAS status for response to anti-EGFR antibodies in colorectal cancer. Int. J. Cancer 127, 1321–1331.

Ragazzon, B., Libé, R., Gaujoux, S., Assié, G., Fratticci, A., Launay, P., Clauser, E., Bertagna, X., Tissier, F., de Reyniès, A., et al. (2010). Transcriptome analysis reveals that p53 and {beta}-catenin alterations occur in a group of aggressive adrenocortical cancers. Cancer Res. 70, 8276–8281.

Salas, S., Chibon, F., Noguchi, T., Terrier, P., Ranchere-Vince, D., Lagarde, P., Benard, J., Forget, S., Blanchard, C., Dômont, J., et al. (2010). Molecular characterization by array comparative genomic hybridization and DNA sequencing of 194 desmoid tumors. Genes Chromosomes Cancer 49, 560–568.

Williamson, D., Missiaglia, E., de Reyniès, A., Pierron, G., Thuille, B., Palenzuela, G., Thway, K., Orbach, D., Laé, M., Fréneaux, P., et al. (2010). Fusion gene-negative alveolar rhabdomyosarcoma is clinically and molecularly indistinguishable from embryonal rhabdomyosarcoma. J. Clin. Oncol. 28, 2151–2158.


Corbin, M., de Reyniès, A., Rickman, D.S., Berrebi, D., Boccon-Gibod, L., Cohen-Gogo, S., Fabre, M., Jaubert, F., Faussillon, M., Yilmaz, F., et al. (2009). WNT/beta-catenin pathway activation in Wilms tumors: a unifying mechanism with multiple entries? Genes Chromosomes Cancer 48, 816–827.

Favier, J., Brière, J.-J., Burnichon, N., Rivière, J., Vescovo, L., Benit, P., Giscos-Douriez, I., de Reyniès, A., Bertherat, J., Badoual, C., et al. (2009). The Warburg Effect Is Genetically Determined in Inherited Pheochromocytomas. PLoS ONE 4, e7094.

Pérot, G., Derré, J., Coindre, J.-M., Tirode, F., Lucchesi, C., Mariani, O., Gibault, L., Guillou, L., Terrier, P., and Aurias, A. (2009). Strong smooth muscle differentiation is dependent on myocardin gene amplification in most human retroperitoneal leiomyosarcomas. Cancer Res. 69, 2269–2278.

Rebouissou, S., Amessou, M., Couchy, G., Poussin, K., Imbeaud, S., Pilati, C., Izard, T., Balabaud, C., Bioulac-Sage, P., and Zucman-Rossi, J. (2009). Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Nature 457, 200–204.

de Reyniès, A., Assié, G., Rickman, D.S., Tissier, F., Groussin, L., René-Corail, F., Dousset, B., Bertagna, X., Clauser, E., and Bertherat, J. (2009). Gene expression profiling reveals a new classification of adrenocortical tumors and identifies molecular predictors of malignancy and survival. J. Clin. Oncol. 27, 1108–1115.

Zagani, R., Hamzaoui, N., Cacheux, W., de Reyniès, A., Terris, B., Chaussade, S., Romagnolo, B., Perret, C., and Lamarque, D. (2009). Cyclooxygenase-2 inhibitors down-regulate osteopontin and Nr4A2-new therapeutic targets for colorectal cancers. Gastroenterology 137, 1358–1366.e1–3.


Cairo, S., Armengol, C., de Reyniès, A., Wei, Y., Thomas, E., Renard, C.-A., Goga, A., Balakrishnan, A., Semeraro, M., Gresh, L., et al. (2008). Hepatic stem-like phenotype and interplay of Wnt/beta-catenin and Myc signaling in aggressive childhood liver cancer. Cancer Cell 14, 471–484.

Decaens, T., Godard, C., de Reyniès, A., Rickman, D.S., Tronche, F., Couty, J.-P., Perret, C., and Colnot, S. (2008). Stabilization of beta-catenin affects mouse embryonic liver growth and hepatoblast fate. Hepatology 47, 247–258.

Ducray, F., Idbaih, A., de Reyniès, A., Bièche, I., Thillet, J., Mokhtari, K., Lair, S., Marie, Y., Paris, S., Vidaud, M., et al. (2008). Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile. Mol. Cancer 7, 41.

Hacein-Bey-Abina, S., Garrigue, A., Wang, G.P., Soulier, J., Lim, A., Morillon, E., Clappier, E., Caccavelli, L., Delabesse, E., Beldjord, K., et al. (2008). Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J. Clin. Invest. 118, 3132–3142.

Idbaih, A., Marie, Y., Lucchesi, C., Pierron, G., Manié, E., Raynal, V., Mosseri, V., Hoang-Xuan, K., Kujas, M., Brito, I., et al. (2008). BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas. Int. J. Cancer 122, 1778–1786.

Idbaih, A., Paris, S., Boisselier, B., Marie, Y., Sanson, M., Thillet, J., Hoang-Xuan, K., and Delattre, J.-Y. (2008b). Mutational analysis of Rac2 in gliomas. J. Neurooncol. 87, 365–366.

Jais, J.-P., Haioun, C., Molina, T.J., Rickman, D.S., de Reyniès, A., Berger, F., Gisselbrecht, C., Brière, J., Reyes, F., Gaulard, P., et al. (2008). The expression of 16 genes related to the cell of origin and immune response predicts survival in elderly patients with diffuse large B-cell lymphoma treated with CHOP and rituximab. Leukemia 22, 1917–1924.

Janoueix-Lerosey, I., Lequin, D., Brugières, L., Ribeiro, A., de Pontual, L., Combaret, V., Raynal, V., Puisieux, A., Schleiermacher, G., Pierron, G., et al. (2008). Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 455, 967–970.

Ladeiro, Y., Couchy, G., Balabaud, C., Bioulac-Sage, P., Pelletier, L., Rebouissou, S., and Zucman-Rossi, J. (2008). MicroRNA profiling in hepatocellular tumors is associated with clinical features and oncogene/tumor suppressor gene mutations. Hepatology 47, 1955–1963.

de Reyniès, A., Boige, V., Milano, G., Faivre, J., and Laurent-Puig, P. (2008). KRAS mutation signature in colorectal tumors significantly overlaps with the cetuximab response signature. J. Clin. Oncol. 26, 2228–2230; author reply 2230–2231.

Rickman, D.S., Millon, R., de Reyniès, A., Thomas, E., Wasylyk, C., Muller, D., Abecassis, J., and Wasylyk, B. (2008). Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays. Oncogene 27, 6607–6622.


Bertheau, P., Turpin, E., Rickman, D.S., Espié, M., de Reyniès, A., Feugeas, J.-P., Plassa, L.-F., Soliman, H., Varna, M., de Roquancourt, A., et al. (2007). Exquisite sensitivity of TP53 mutant and basal breast cancers to a dose-dense epirubicin-cyclophosphamide regimen. PLoS Med. 4, e90.

Boyault, S., Rickman, D.S., de Reyniès, A., Balabaud, C., Rebouissou, S., Jeannot, E., Hérault, A., Saric, J., Belghiti, J., Franco, D., et al. (2007). Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatology 45, 42–52.

Clappier, E., Cuccuini, W., Kalota, A., Crinquette, A., Cayuela, J.-M., Dik, W.A., Langerak, A.W., Montpellier, B., Nadel, B., Walrafen, P., et al. (2007). The C-MYB locus is involved in chromosomal translocation and genomic duplications in human T-cell acute leukemia (T-ALL), the translocation defining a new T-ALL subtype in very young children. Blood 110, 1251–1261.

Condomines, M., Hose, D., Raynaud, P., Hundemer, M., De Vos, J., Baudard, M., Moehler, T., Pantesco, V., Moos, M., Schved, J.-F., et al. (2007). Cancer/testis genes in multiple myeloma: expression patterns and prognosis value determined by microarray analysis. J. Immunol. 178, 3307–3315.

Fasseu, M., Aplan, P.D., Chopin, M., Boissel, N., Bories, J.-C., Soulier, J., von Boehmer, H., Sigaux, F., and Regnault, A. (2007). p16INK4A tumor suppressor gene expression and CD3epsilon deficiency but not pre-TCR deficiency inhibit TAL1-linked T-lineage leukemogenesis. Blood 110, 2610–2619.

Idbaih, A., Boisselier, B., Sanson, M., Crinière, E., Liva, S., Marie, Y., Carpentier, C., Paris, S., Laigle-Donadey, F., Mokhtari, K., et al. (2007). Tumor genomic profiling and TP53 germline mutation analysis of first-degree relative familial gliomas. Cancer Genet. Cytogenet. 176, 121–126.

Lamant, L., de Reyniès, A., Duplantier, M.-M., Rickman, D.S., Sabourdy, F., Giuriato, S., Brugières, L., Gaulard, P., Espinos, E., and Delsol, G. (2007). Gene-expression profiling of systemic anaplastic large-cell lymphoma reveals differences based on ALK status and two distinct morphologic ALK+ subtypes. Blood 109, 2156–2164.

de Leval, L., Rickman, D.S., Thielen, C., de Reyniès, A. de, Huang, Y.-L., Delsol, G., Lamant, L., Leroy, K., Brière, J., Molina, T., et al. (2007). The gene expression profile of nodal peripheral T-cell lymphoma demonstrates a molecular link between angioimmunoblastic T-cell lymphoma (AITL) and follicular helper T (TFH) cells. Blood 109, 4952–4963.

Mahtouk, K., Hose, D., Raynaud, P., Hundemer, M., Jourdan, M., Jourdan, E., Pantesco, V., Baudard, M., De Vos, J., Larroque, M., et al. (2007). Heparanase influences expression and shedding of syndecan-1, and its expression by the bone marrow environment is a bad prognostic factor in multiple myeloma. Blood 109, 4914–4923.

Mariani, O., Brennetot, C., Coindre, J.-M., Gruel, N., Ganem, C., Delattre, O., Stern, M.-H., and Aurias, A. (2007). JUN oncogene amplification and overexpression block adipocytic differentiation in highly aggressive sarcomas. Cancer Cell 11, 361–374.

Renard, C.-A., Labalette, C., Armengol, C., Cougot, D., Wei, Y., Cairo, S., Pineau, P., Neuveut, C., de Reyniès, A., Dejean, A., et al. (2007). Tbx3 is a downstream target of the Wnt/beta-catenin pathway and a critical mediator of beta-catenin survival functions in liver cancer. Cancer Res. 67, 901–910.

Rocques, N., Abou Zeid, N., Sii-Felice, K., Lecoin, L., Felder-Schmittbuhl, M.-P., Eychène, A., and Pouponnot, C. (2007). GSK-3-mediated phosphorylation enhances Maf-transforming activity. Mol. Cell 28, 584–597.

dos Santos, N.R., Rickman, D.S., de Reyniès, A., Cormier, F., Williame, M., Blanchard, C., Stern, M.-H., and Ghysdael, J. (2007). Pre-TCR expression cooperates with TEL-JAK2 to transform immature thymocytes and induce T-cell leukemia. Blood 109, 3972–3981.

Tirode, F., Laud-Duval, K., Prieur, A., Delorme, B., Charbord, P., and Delattre, O. (2007). Mesenchymal stem cell features of Ewing tumors. Cancer Cell 11, 421–429.

Vincent-Salomon, A., Ganem-Elbaz, C., Manié, E., Raynal, V., Sastre-Garau, X., Stoppa-Lyonnet, D., Stern, M.-H., and Heard, E. (2007). X inactive-specific transcript RNA coating and genetic instability of the X chromosome in BRCA1 breast tumors. Cancer Res. 67, 5134–5140.


Benhamouche, S., Decaens, T., Godard, C., Chambrey, R., Rickman, D.S., Moinard, C., Vasseur-Cognet, M., Kuo, C.J., Kahn, A., Perret, C., et al. (2006). Apc tumor suppressor gene is the “zonation-keeper” of mouse liver. Dev. Cell 10, 759–770.

Clappier, E., Cuccuini, W., Cayuela, J.M., Vecchione, D., Baruchel, A., Dombret, H., Sigaux, F., and Soulier, J. (2006). Cyclin D2 dysregulation by chromosomal translocations to TCR loci in T-cell acute lymphoblastic leukemias. Leukemia 20, 82–86.

Duplantier, M.M., Lamant, L., Sabourdy, F., de Reyniès, A., Delsol, G., and Espinos, E. (2006). Serpin A1 is overexpressed in ALK+ anaplastic large cell lymphoma and its expression correlates with extranodal dissemination. Leukemia 20, 1848–1854.

Moreaux, J., Hose, D., Reme, T., Jourdan, E., Hundemer, M., Legouffe, E., Moine, P., Bourin, P., Moos, M., Corre, J., et al. (2006). CD200 is a new prognostic factor in multiple myeloma. Blood 108, 4194–4197.

Palomero, T., Lim, W.K., Odom, D.T., Sulis, M.L., Real, P.J., Margolin, A., Barnes, K.C., O’Neil, J., Neuberg, D., Weng, A.P., et al. (2006). NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc. Natl. Acad. Sci. U.S.A. 103, 18261–18266.

de Reyniès, A., Geromin, D., Cayuela, J.-M., Petel, F., Dessen, P., Sigaux, F., and Rickman, D.S. (2006). Comparison of the latest commercial short and long oligonucleotide microarray technologies. BMC Genomics 7, 51.

Vert, J.-P., Foveau, N., Lajaunie, C., and Vandenbrouck, Y. (2006). An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics 7, 520.


de Fraipont, F., El Atifi, M., Cherradi, N., Le Moigne, G., Defaye, G., Houlgatte, R., Bertherat, J., Bertagna, X., Plouin, P.-F., Baudin, E., et al. (2005). Gene expression profiling of human adrenocortical tumors using complementary deoxyribonucleic Acid microarrays identifies several candidate genes as markers of malignancy. J. Clin. Endocrinol. Metab. 90, 1819–1829.

Janoueix-Lerosey, I., Hupé, P., Maciorowski, Z., La Rosa, P., Schleiermacher, G., Pierron, G., Liva, S., Barillot, E., and Delattre, O. (2005). Preferential occurrence of chromosome breakpoints within early replicating regions in neuroblastoma. Cell Cycle 4, 1842–1846.

Schaack, B., Reboud, J., Combe, S., Fouqué, B., Berger, F., Boccard, S., Filhol-Cochet, O., and Chatelain, F. (2005). A “DropChip” cell array for DNA and siRNA transfection combined with drug screening. NanoBiotechnology 1, 183-189.

Soulier, J., Clappier, E., Cayuela, J.-M., Regnault, A., García-Peydró, M., Dombret, H., Baruchel, A., Toribio, M.-L., and Sigaux, F. (2005). HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL). Blood 106, 274–286.


Chibon, F., Mariani, O., Derré, J., Mairal, A., Coindre, J.-M., Guillou, L., Sastre, X., Pédeutour, F., and Aurias, A. (2004). ASK1 (MAP3K5) as a potential therapeutic target in malignant fibrous histiocytomas with 12q14-q15 and 6q23 amplifications. Genes Chromosomes Cancer 40, 32–37.

Orsetti, B., Nugoli, M., Cervera, N., Lasorsa, L., Chuchana, P., Ursule, L., Nguyen, C., Redon, R., du Manoir, S., Rodriguez, C., et al. (2004). Genomic and expression profiling of chromosome 17 in breast cancer reveals complex patterns of alterations and novel candidate genes. Cancer Res. 64, 6453–6460.


Redon, R., Hussenet, T., Bour, G., Caulee, K., Jost, B., Muller, D., Abecassis, J., and du Manoir, S. (2002). Amplicon mapping and transcriptional analysis pinpoint cyclin L as a candidate oncogene in head and neck cancer. Cancer Res. 62, 6211–6217.