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1. Full Text Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer
by Robertson, A. Gordon and Kim, Jaegil and Al-Ahmadie, Hikmat and Bellmunt, Joaquim and Guo, Guangwu and Cherniack, Andrew D and Hinoue, Toshinori and Laird, Peter W and Hoadley, Katherine A and Akbani, Rehan and Castro, Patricia and Castro, Mauro A.A and Gibb, Ewan A and Kanchi, Rupa S and Gordenin, Dmitry A and Shukla, Sachet A and Sanchez-Vega, Francisco and Hansel, Donna E and Czerniak, Bogdan A and Reuter, Victor E and Su, Xiaoping and de Sa Carvalho, Benilton and Chagas, Vinicius S and Mungall, Andrew J and Mungall, Karen L and Sadeghi, Sara and Pedamallu, Chandra Sekhar and Lu, Yiling and Klimczak, Leszek J and Zhang, Jiashan (Julia) and Zhang, Jiexin and Choo, Caleb and Ojesina, Akinyemi I and Bullman, Susan and Leraas, Kristen M and Lichtenberg, Tara M and Wu, Ye and Wu, Catherine J and Schultz, Nikolaus and Schultz, Nicholaus and Getz, Gad and Meyerson, Matthew and Mills, Gordon B and McConkey, David J and Albert, Monique and Alexopoulou, Iakovina and Ally, Adrian and Antic, Tatjana and Aron, Manju and Balasundaram, Miruna and Bartlett, John and Baylin, Stephen B and Beaver, Allison and Birol, Inanc and Boice, Lori and Bootwalla, Moiz S and Bowen, Jay and Bowlby, Reanne and Brooks, Denise and Broom, Bradley M and Bshara, Wiam and Burks, Eric and Cárcano, Flavio M and Carlsen, Rebecca and Carvalho, Benilton S and Carvalho, Andre L and Castle, Eric P and Catto, James W and Chesla, David W and Chuah, Eric and Chudamani, Sudha and Cortessis, Victoria K and Cottingham, Sandra L and Crain, Daniel and Curley, Erin and Daneshmand, Siamak and Demchok, John A and Dhalla, Noreen and Djaladat, Hooman and Eckman, John and Egea, Sophie C and Engel, Jay and Felau, Ina and Ferguson, Martin L and Gardner, Johanna and Gastier-Foster, Julie M and Gerken, Mark and Gomez-Fernandez, Carmen R and Harr, Jodi and Hartmann, Arndt and Herbert, Lynn M and Ho, Thai H and Holt, Robert A and Hutter, Carolyn M and Jones, Steven J.M and Jorda, Merce and Kahnoski, Richard J and Kasaian, Katayoon and Kwiatkowski, David J and Lai, Phillip H and ... and TCGA Res Network and TCGA Research Network
Cell, ISSN 0092-8674, 10/2017, Volume 171, Issue 3, pp. 540 - 556.e25
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were... 
neoantigen | lncRNA transcriptome | luminal mRNA subtype | muscle-invasive bladder cancer | basal mRNA subtype | DNA methylation | regulon | microRNA | APOBEC mutation | neuronal subtype | PHASE PROTEIN ARRAY | LUMINAL SUBTYPES | ACCURATE | UROTHELIAL CARCINOMA | QUANTIFICATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | RECEPTOR | SOMATIC ERCC2 MUTATIONS | EXPRESSION | GENETIC ALTERATIONS | BASAL | CELL BIOLOGY | Humans | Middle Aged | RNA, Long Noncoding - genetics | Urinary Bladder - pathology | DNA Methylation | Urinary Bladder Neoplasms - genetics | Urinary Bladder Neoplasms - therapy | Survival Analysis | Urinary Bladder Neoplasms - pathology | Aged | MicroRNAs - genetics | Muscle, Smooth - pathology | Urinary Bladder Neoplasms - epidemiology | Cluster Analysis | MicroRNA | Bladder cancer | Analysis | Stem cells | Index Medicus
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2. Full Text The Molecular Taxonomy of Primary Prostate Cancer
by Abeshouse, Adam and Ahn, Jaeil and Akbani, Rehan and Ally, Adrian and Amin, Samirkumar and Andry, Christopher D and Annala, Matti and Aprikian, Armen and Armenia, Joshua and Arora, Arshi and Auman, J. Todd and Balasundaram, Miruna and Balu, Saianand and Barbieri, Christopher E and Bauer, Thomas and Benz, Christopher C and Bergeron, Alain and Beroukhim, Rameen and Berrios, Mario and Bivol, Adrian and Bodenheimer, Tom and Boice, Lori and Bootwalla, Moiz S and Borges dos Reis, Rodolfo and Boutros, Paul C and Bowen, Jay and Bowlby, Reanne and Boyd, Jeffrey and Bradley, Robert K and Breggia, Anne and Brimo, Fadi and Bristow, Christopher A and Brooks, Denise and Broom, Bradley M and Bryce, Alan H and Bubley, Glenn and Burks, Eric and Butterfield, Yaron S.N and Button, Michael and Canes, David and Carlotti, Carlos G and Carlsen, Rebecca and Carmel, Michel and Carroll, Peter R and Carter, Scott L and Cartun, Richard and Carver, Brett S and Chan, June M and Chang, Matthew T and Chen, Yu and Cherniack, Andrew D and Chevalier, Simone and Chin, Lynda and Cho, Juok and Chu, Andy and Chuah, Eric and Chudamani, Sudha and Cibulskis, Kristian and Ciriello, Giovanni and Clarke, Amanda and Cooperberg, Matthew R and Corcoran, Niall M and Costello, Anthony J and Cowan, Janet and Crain, Daniel and Curley, Erin and David, Kerstin and Demchok, John A and Demichelis, Francesca and Dhalla, Noreen and Dhir, Rajiv and Doueik, Alexandre and Drake, Bettina and Dvinge, Heidi and Dyakova, Natalya and Felau, Ina and Ferguson, Martin L and Frazer, Scott and Freedland, Stephen and Fu, Yao and Gabriel, Stacey B and Gao, Jianjiong and Gardner, Johanna and Gastier-Foster, Julie M and Gehlenborg, Nils and Gerken, Mark and Gerstein, Mark B and Getz, Gad and Godwin, Andrew K and Gopalan, Anuradha and Graefen, Markus and Graim, Kiley and Gribbin, Thomas and Guin, Ranabir and Gupta, Manaswi and Hadjipanayis, Angela and Haider, Syed and Hamel, Lucie and Hayes, D. Neil and Heiman, David I and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell, ISSN 0092-8674, 11/2015, Volume 163, Issue 4, pp. 1011 - 1025
There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part... 
ACTIVE ANDROGEN RECEPTOR | WHOLE-GENOME | DNA METHYLATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | SPOP | GENOMIC ABERRATIONS | RADICAL PROSTATECTOMY | RECURRENCE | EXPRESSION PROFILES | MUTATIONS | ETS GENE FUSIONS | CELL BIOLOGY | Prostatic Neoplasms - metabolism | Prostatic Neoplasms - pathology | Signal Transduction | Epigenesis, Genetic | Humans | Receptors, Androgen - metabolism | Gene Expression Regulation, Neoplastic | ras Proteins - metabolism | Gene Fusion | Male | Phosphatidylinositol 3-Kinases - metabolism | Neoplasm Metastasis - genetics | Prostatic Neoplasms - genetics | DNA Repair | Mutation | Epigenetic inheritance | Prostate cancer | Analysis | Genomics | Index Medicus
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3. Full Text Comprehensive molecular characterization of urothelial bladder carcinoma
by Weinstein, John N and Akbani, Rehan and Broom, Bradley M and Wang, Wenyi and Verhaak, Roeland G. W and McConkey, David and Lerner, Seth and Morgan, Margaret and Creighton, Chad J and Smith, Carolyn and Cherniack, Andrew D and Kim, Jaegil and Pedamallu, Chandra Sekhar and Noble, Michael S and Al-Ahmadie, Hikmat A and Reuter, Victor E and Rosenberg, Jonathan E and F.Bajorin, Dean and Bochner, Bernard H and Solit, David B and Koppie, Theresa and Robinson, Brian and Gordenin, Dmitry A and Fargo, David and Klimczak, Leszek J and Roberts, Steven A and Au, Jessie and Laird, Peter W and Hinoue, Toshinori and Schultz, Nikolaus and Ramirez, Ricardo and Hansel, Donna and Hoadley, Katherine A and Kim, William Y and Damrauer, Jeffrey S and Baylin, Stephen B and Mungall, Andrew J and Robertson, A. Gordon and Chu, Andy and Kwiatkowski, David J and Sougnez, Carrie and Cibulskis, Kristian and Lichtenstein, Lee and Sivachenko, Andrey and Stewart, Chip and Lawrence, Michael S and Getz, Gad and Lander, Eric and Gabrie, Stacey B and Donehower, Lawrence and Carter, Scott L and Saksena, Gordon and Schumacher, Steven E and Freeman, Samuel S and Jung, Joonil and Bhatt, Ami S and Pugh, Trevor and Beroukhim, Rameen and Meyerson, Matthew and Ally, Adrian and Balasundaram, Miruna and Butterfield, Yaron S. N and Dhalla, Noreen and Hirst, Carrie and Holt, Robert A and Jones, Steven J. M and Lee, Darlene and Li, Haiyan I and Marra, Marco A and Mayo, Michael and Moore, Richard A and Schein, Jacqueline E and Sipahimalani, Payal and Tam, Angela and Thiessen, Nina and Wong, Tina and Wye, Natasja and Bowlby, Reanne and Chuah, Eric and Guin, Ranabir and Shen, Hui and Bootwalla, Moiz S and Triche Jr, Timothy and Lai, Phillip H and Van Den Berg, David J and Weisenberger, Daniel J and Balu, Saianand and Bodenheimer, Tom and Hoyle, Alan P and Jefferys, Stuart R and Meng, Shaowu and Mose, Lisle E and Simons, Janae V and Soloway, Mathew G and Wu, Junyuan and Parker, Joel S and Hayes, D. Neil and Roach, Jeffrey and Buda, Elizabeth and Jones, Corbin D and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and The Cancer Genome Atlas Research Network
Nature, ISSN 0028-0836, 2014, Volume 507, Issue 7492, pp. 315 - 322
Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents... 
GENE FUSIONS | GENOMES | MULTIDISCIPLINARY SCIENCES | KINASE | MUTATIONS | CANCER | FGFR | Protein Kinases - metabolism | Cell Cycle - genetics | Virus Integration - genetics | Protein Kinases - genetics | TOR Serine-Threonine Kinases - metabolism | Humans | RNA, Messenger - genetics | Oxidative Stress - genetics | MicroRNAs - metabolism | Chromatin - virology | Phosphatidylinositol 3-Kinases - metabolism | Signal Transduction - genetics | Urinary Bladder Neoplasms - drug therapy | Molecular Targeted Therapy | RNA, Messenger - metabolism | Down-Regulation - genetics | Urinary Bladder Neoplasms - virology | Urinary Bladder Neoplasms - genetics | Urinary Bladder Neoplasms - pathology | MicroRNAs - genetics | Proto-Oncogene Proteins c-akt - metabolism | Chromatin - genetics | Gene Expression Regulation, Neoplastic - genetics | Physiological aspects | Research | Molecular biology | Bladder cancer | Oncology, Experimental | Cancer | DNA methylation | Mutation | Kinases | Genes | Index Medicus
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4. Full Text Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
by Ley, Timothy J and Miller, Christopher and Ding, Li and Raphael, Benjamin J and Mungall, Andrew J and Robertson, Gordon and Hoadley, Katherine and Triche Jr, Timothy J and Laird, Peter W and Baty, Jack D and Fulton, Lucinda L and Fulton, Robert and Heath, Sharon E and Kalicki-Veizer, Joelle and Kandoth, Cyriac and Klco, Jeffery M and Koboldt, Daniel C and Kanchi, Krishna-Latha and Kulkarni, Shashikant and Lamprecht, Tamara L and Larson, David E and Lin, G and Lu, Charles and McLellan, Michael D and McMichael, Joshua F and Payton, Jacqueline and Schmidt, Heather and Spencer, David H and Tomasson, Michael H and Wallis, John W and Wartman, Lukas D and Watson, Mark A and Welch, John and Wendl, Michael C and Ally, Adrian and Balasundaram, Miruna and Birol, Inanc and Butterfield, Yaron and Chiu, Readman and Chu, Andy and Chuah, Eric and Chun, Hye-Jung and Corbett, Richard and Dhalla, Noreen and Guin, Ranabir and He, An and Hirst, Carrie and Hirst, Martin and Holt, Robert A and Jones, Steven and Karsan, Aly and Lee, Darlene and Li, Haiyan I and Marra, Marco A and Mayo, Michael and Moore, Richard A and Mungall, Karen and Parker, Jeremy and Pleasance, Erin and Plettner, Patrick and Schein, Jacquie and Stoll, Dominik and Swanson, Lucas and Tam, Angela and Thiessen, Nina and Varhol, Richard and Wye, Natasja and Zhao, Yongjun and Gabriel, Stacey and Getz, Gad and Sougnez, Carrie and Zou, Lihua and Leiserson, Mark D. M and Vandin, Fabio and Wu, Hsin-Ta and Applebaum, Frederick and Baylin, Stephen B and Akbani, Rehan and Broom, Bradley M and Chen, Ken and Motter, Thomas C and Nguyen, Khanh and Weinstein, John N and Zhang, Nianziang and Ferguson, Martin L and Adams, Christopher and Black, Aaron and Bowen, Jay and Gastier-Foster, Julie and Grossman, Thomas and Lichtenberg, Tara and Wise, Lisa and Davidsen, Tanja and Demchok, John A and Mills Shaw, Kenna R and Sheth, Margi and Sofia, Heidi J and Yang, Liming and Downing, James R and Eley, Greg and ... and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
The New England Journal of Medicine, ISSN 0028-4793, 05/2013, Volume 368, Issue 22, pp. 2059 - 2074
More than 25% of patients with AML carry no mutations in genes known to be associated with leukemia. Analyses of genomes, transcriptomes, and methylomes of AML... 
MEDICINE, GENERAL & INTERNAL | COPY NUMBER ALTERATIONS | HYPERMETHYLATION | EVOLUTION | GENE | TRANSCRIPTION | MONOSOMAL KARYOTYPE | EXPRESSION PROFILES | MUTATIONS | MICRORNA EXPRESSION | CANCER | Gene Expression | Epigenomics | Humans | Middle Aged | Gene Fusion | Male | DNA Methylation | CpG Islands | Adult | Female | MicroRNAs - genetics | Mutation | Genome, Human | Sequence Analysis, DNA - methods | Leukemia, Myeloid, Acute - classification | Leukemia, Myeloid, Acute - genetics | Gene mutations | Research | Chromatin | Phenotypes | Myeloid leukemia | Pathogenesis | MiRNA | Genomes | Algorithms | Consolidation | Classification | DNA methylation | Tumor suppressor genes | Cohesin | Methylation | Acute myeloid leukemia | DNA sequencing | Index Medicus | Abridged Index Medicus
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5. Full Text Comprehensive molecular portraits of human breast tumours
by Koboldt, Daniel C and Fulton, Robert S and McLellan, Michael D and Schmidt, Heather and Kalicki-Veizer, Joelle and McMichael, Joshua F and Fulton, Lucinda L and Dooling, David J and Ding, Li and Mardis, Elaine R and Wilson, Richard K and Ally, Adrian and Balasundaram, Miruna and Butterfield, Yaron S. N and Carlsen, Rebecca and Carter, Candace and Chu, Andy and Chuah, Eric and Chun, Hye-Jung E and Coope, Robin J. N and Dhalla, Noreen and Guin, Ranabir and Hirst, Carrie and Hirst, Martin and Holt, Robert A and Lee, Darlene and Li, Haiyan I and Mayo, Michael and Moore, Richard A and Mungall, Andrew J and Pleasance, Erin and Robertson, A. Gordon and Schein, Jacqueline E and Shafiei, Arash and Sipahimalani, Payal and Slobodan, Jared R and Stoll, Dominik and Tam, Angela and Thiessen, Nina and Varhol, Richard J and Wye, Natasja and Zeng, Thomas and Zhao, Yongjun and Birol, Inanc and Jones, Steven J. M and Marra, Marco A and Cherniack, Andrew D and Saksena, Gordon and Onofrio, Robert C and Pho, Nam H and Carter, Scott L and Schumacher, Steven E and Tabak, Barbara and Hernandez, Bryan and Gentry, Jeff and Nguyen, Huy and Crenshaw, Andrew and Ardlie, Kristin and Beroukhim, Rameen and Winckler, Wendy and Getz, Gad and Gabriel, Stacey B and Meyerson, Matthew and Chin, Lynda and Kucherlapati, Raju and Hoadley, Katherine A and Auman, J. Todd and Fan, Cheng and Turman, Yidi J and Shi, Yan and Li, Ling and Topal, Michael D and He, Xiaping and Chao, Hann-Hsiang and Prat, Aleix and Silva, Grace O and Iglesia, Michael D and Zhao, Wei and Usary, Jerry and Berg, Jonathan S and Adams, Michael and Booker, Jessica and Wu, Junyuan and Gulabani, Anisha and Bodenheimer, Tom and Hoyle, Alan P and Simons, Janae V and Soloway, Matthew G and Mose, Lisle E and Jefferys, Stuart R and Balu, Saianand and Parker, Joel S and Hayes, D. Neil and Perou, Charles M and Malik, Simeen and Mahurkar, Swapna and Shen, Hui and Weisenberger, Daniel J and Triche Jr, Timothy and Lai, Phillip H and ... and Canc Genome Atlas Network and Cancer Genome Atlas Network and The Cancer Genome Atlas Network
Nature, ISSN 0028-0836, 10/2012, Volume 490, Issue 7418, pp. 61 - 70
We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and... 
PATHWAYS | TARGET | BASAL-LIKE | SUPPRESSOR | PIK3CA GENE | SUBTYPES | MULTIDISCIPLINARY SCIENCES | HIGH-FREQUENCY | LUMINAL-B | CANCER | MUTATIONAL EVOLUTION | GATA3 Transcription Factor - genetics | Receptors, Estrogen - metabolism | Oligonucleotide Array Sequence Analysis | Genomics | Humans | Gene Expression Regulation, Neoplastic | Ovarian Neoplasms - pathology | Gene Expression Profiling | Breast Neoplasms - metabolism | Ovarian Neoplasms - genetics | DNA Methylation | DNA Mutational Analysis | Female | Genes, BRCA1 | Genes, Neoplasm - genetics | Breast Neoplasms - classification | RNA, Messenger - genetics | Retinoblastoma Protein - metabolism | DNA Copy Number Variations - genetics | Genes, p53 - genetics | Mutation - genetics | Genetic Heterogeneity | Genome, Human - genetics | Phosphatidylinositol 3-Kinases - genetics | Exome - genetics | Breast Neoplasms - genetics | Class I Phosphatidylinositol 3-Kinases | Breast Neoplasms - pathology | Retinoblastoma Protein - genetics | Genes, erbB-2 - genetics | Proteomics | Protein Array Analysis | RNA, Neoplasm - genetics | MAP Kinase Kinase Kinase 1 - genetics | MicroRNAs - genetics | Breast tumors | Gene mutations | Oncology, Experimental | Genetic aspects | Research | Identification and classification | Cancer | Proteins | DNA methylation | Genetics | Breast cancer | Mutation | Index Medicus | Càncer de mama | Oncologia | Oncology | Gene expression | Expressió gènica | Genòmica
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