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5. Establishment of a patient-specific avatar organoid model derived from EUS-guided fine-needle biopsy for timely clinical application in pancreatic ductal adenocarcinoma (with video)

Author

Kim, Hyemin, Jang, Jinho, Choi, Jin Ho, Song, Joo Hye, Lee, Su Hyun, Park, Jiho, Ryoo, Si Kyong, Lee, Eun Mi, Jeong, Hyoung-oh, Kim, Seunghoon, Lee, Se-Hoon, Lee, Kwang Hyuck, Lee, Kyu Taek, Kim, Kyoung Mee, Jang, Kee-Taek, Lee, Hyunsook, Lee, Semin, Lee, Jong Kyun, and Park, Joo Kyung

Published
2024
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13. PWWP2B promotes DNA end resection and homologous recombination

Author

Ju, Min Kyung, Lee, Joo Rak, Choi, Yeonsong, Park, Seon Young, Sul, Hee Jung, Chung, Hee Jin, An, Soyeong, Lee, Semin, Jung, Eunyoung, Kim, Bohyun, Choi, Bo Youn, Kim, Bum Jun, Kim, Hyeong Su, Lim, Hyun, Kang, Ho Suk, Soh, Jae Seung, Myung, Kyungjae, Kim, Kab Choong, Cho, Ji Woong, Seo, Jinwon, Kim, Tae Moon, Lee, Ja Yil, Kim, Yonghwan, Kim, Hongtae, and Zang, Dae Young

Published
2022
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14. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

Author

Robertson, A Gordon, Shih, Juliann, Yau, Christina, Gibb, Ewan A, Oba, Junna, Mungall, Karen L, Hess, Julian M, Uzunangelov, Vladislav, Walter, Vonn, Danilova, Ludmila, Lichtenberg, Tara M, Kucherlapati, Melanie, Kimes, Patrick K, Tang, Ming, Penson, Alexander, Babur, Ozgun, Akbani, Rehan, Bristow, Christopher A, Hoadley, Katherine A, Iype, Lisa, Chang, Matthew T, Network, TCGA Research, Abdel-Rahman, Mohamed H, Ally, Adrian, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Benz, Christopher, Beroukhim, Rameen, Birol, Inanc, Bodenheimer, Tom, Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Cebulla, Colleen M, Cherniack, Andrew D, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cibulskis, Kristian, Cope, Leslie, Coupland, Sarah E, Defreitas, Timothy, Demchok, John A, Desjardins, Laurence, Dhalla, Noreen, Esmaeli, Bita, Felau, Ina, Ferguson, Martin L, Frazer, Scott, Gabriel, Stacey B, Gastier-Foster, Julie M, Gehlenborg, Nils, Gerken, Mark, Gershenwald, Jeffrey E, Getz, Gad, Griewank, Klaus G, Grimm, Elizabeth A, Hayes, D Neil, Hegde, Apurva M, Heiman, David I, Helsel, Carmen, Hobensack, Shital, Holt, Robert A, Hoyle, Alan P, Hu, Xin, Hutter, Carolyn M, Jager, Martine J, Jefferys, Stuart R, Jones, Corbin D, Jones, Steven JM, Kandoth, Cyriac, Kasaian, Katayoon, Kim, Jaegil, Kucherlapati, Raju, Lander, Eric, Lawrence, Michael S, Lazar, Alexander J, Lee, Semin, Leraas, Kristen M, Lin, Pei, Liu, Jia, Liu, Wenbin, Lolla, Laxmi, and Lu, Yiling

Subjects
Eye Disease and Disorders of Vision, Cancer, Human Genome, Rare Diseases, Genetics, Biomarkers, Tumor, DNA Copy Number Variations, DNA Methylation, Eukaryotic Initiation Factor-1, Gene Expression Regulation, Neoplastic, Humans, Melanoma, Monosomy, Mutation, Phosphoproteins, Prognosis, RNA Splicing Factors, Serine-Arginine Splicing Factors, Tumor Suppressor Proteins, Ubiquitin Thiolesterase, Uveal Neoplasms, TCGA Research Network, EIF1AX, GNA11, GNAQ, SF3B1, SRSF2, TCGA, molecular subtypes, monosomy 3, noncoding RNA, uveal melanoma, Neurosciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations. Within D3-UM, EIF1AX- and SRSF2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, providing insight into the biology of these low- versus intermediate-risk clinical mutation subtypes.

Published
2017

15. Integrated genomic and molecular characterization of cervical cancer

Author

Burk, Robert D, Chen, Zigui, Saller, Charles, Tarvin, Katherine, Carvalho, Andre L, Scapulatempo-Neto, Cristovam, Silveira, Henrique C, Fregnani, José H, Creighton, Chad J, Anderson, Matthew L, Castro, Patricia, Wang, Sophia S, Yau, Christina, Benz, Christopher, Robertson, A Gordon, Mungall, Karen, Lim, Lynette, Bowlby, Reanne, Sadeghi, Sara, Brooks, Denise, Sipahimalani, Payal, Mar, Richard, Ally, Adrian, Clarke, Amanda, Mungall, Andrew J, Tam, Angela, Lee, Darlene, Chuah, Eric, Schein, Jacqueline E, Tse, Kane, Kasaian, Katayoon, Ma, Yussanne, Marra, Marco A, Mayo, Michael, Balasundaram, Miruna, Thiessen, Nina, Dhalla, Noreen, Carlsen, Rebecca, Moore, Richard A, Holt, Robert A, Jones, Steven JM, Wong, Tina, Pantazi, Angeliki, Parfenov, Michael, Kucherlapati, Raju, Hadjipanayis, Angela, Seidman, Jonathan, Kucherlapati, Melanie, Ren, Xiaojia, Xu, Andrew W, Yang, Lixing, Park, Peter J, Lee, Semin, Rabeno, Brenda, Huelsenbeck-Dill, Lori, Borowsky, Mark, Cadungog, Mark, Iacocca, Mary, Petrelli, Nicholas, Swanson, Patricia, Ojesina, Akinyemi I, Le, Xuan, Sandusky, George, Adebamowo, Sally N, Akeredolu, Teniola, Adebamowo, Clement, Reynolds, Sheila M, Shmulevich, Ilya, Shelton, Candace, Crain, Daniel, Mallery, David, Curley, Erin, Gardner, Johanna, Penny, Robert, Morris, Scott, Shelton, Troy, Liu, Jia, Lolla, Laxmi, Chudamani, Sudha, Wu, Ye, Birrer, Michael, McLellan, Michael D, Bailey, Matthew H, Miller, Christopher A, Wyczalkowski, Matthew A, Fulton, Robert S, Fronick, Catrina C, Lu, Charles, Mardis, Elaine R, Appelbaum, Elizabeth L, Schmidt, Heather K, Fulton, Lucinda A, Cordes, Matthew G, Li, Tiandao, Ding, Li, Wilson, Richard K, Rader, Janet S, Behmaram, Behnaz, Uyar, Denise, and Bradley, William

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cervical Cancer, Cancer, Clinical Research, Human Genome, Sexually Transmitted Infections, Biotechnology, Genetics, 2.1 Biological and endogenous factors, Aetiology, APOBEC-1 Deaminase, Adenocarcinoma, B7-H1 Antigen, Carcinoma, Squamous Cell, Caspase 8, DNA-Binding Proteins, Female, Genomics, HLA-A Antigens, Human papillomavirus 16, Humans, Keratins, Mitogen-Activated Protein Kinase Kinases, Molecular Targeted Therapy, Mutation, Nuclear Proteins, PTEN Phosphohydrolase, Phosphatidylinositol 3-Kinases, Programmed Cell Death 1 Ligand 2 Protein, Protein Serine-Threonine Kinases, Proteomics, Proto-Oncogene Proteins p21(ras), RNA, Long Noncoding, Receptor, ErbB-3, Receptor, Transforming Growth Factor-beta Type II, Receptors, Transforming Growth Factor beta, Signal Transduction, Transcription Factors, Uterine Cervical Neoplasms, Virus Integration, Cancer Genome Atlas Research Network, Albert Einstein College of Medicine, Analytical Biological Services, Barretos Cancer Hospital, Baylor College of Medicine, Beckman Research Institute of City of Hope, Buck Institute for Research on Aging, Canada's Michael Smith Genome Sciences Centre, Harvard Medical School, Helen F. Graham Cancer Center &Research Institute at Christiana Care Health Services, HudsonAlpha Institute for Biotechnology, ILSbio, LLC, Indiana University School of Medicine, Institute of Human Virology, Institute for Systems Biology, International Genomics Consortium, Leidos Biomedical, Massachusetts General Hospital, McDonnell Genome Institute at Washington University, Medical College of Wisconsin, Medical University of South Carolina, Memorial Sloan Kettering Cancer Center, Montefiore Medical Center, NantOmics, National Cancer Institute, National Hospital, Abuja, Nigeria, National Human Genome Research Institute, National Institute of Environmental Health Sciences, National Institute on Deafness &Other Communication Disorders, Ontario Tumour Bank, London Health Sciences Centre, Ontario Tumour Bank, Ontario Institute for Cancer Research, Ontario Tumour Bank, The Ottawa Hospital, Oregon Health &Science University, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, SRA International, St Joseph's Candler Health System, Eli &Edythe L. Broad Institute of Massachusetts Institute of Technology &Harvard University, Research Institute at Nationwide Children's Hospital, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, University of Bergen, University of Texas MD Anderson Cancer Center, University of Abuja Teaching Hospital, University of Alabama at Birmingham, University of California, Irvine, University of California Santa Cruz, University of Kansas Medical Center, University of Lausanne, University of New Mexico Health Sciences Center, University of North Carolina at Chapel Hill, University of Oklahoma Health Sciences Center, University of Pittsburgh, University of São Paulo, Ribeir ão Preto Medical School, University of Southern California, University of Washington, University of Wisconsin School of Medicine &Public Health, Van Andel Research Institute, Washington University in St Louis, Receptor, erbB-3, General Science & Technology
Abstract

Cervical cancer remains one of the leading causes of cancer-related deaths worldwide. Here we report the extensive molecular characterization of 228 primary cervical cancers, one of the largest comprehensive genomic studies of cervical cancer to date. We observed notable APOBEC mutagenesis patterns and identified SHKBP1, ERBB3, CASP8, HLA-A and TGFBR2 as novel significantly mutated genes in cervical cancer. We also discovered amplifications in immune targets CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2), and the BCAR4 long non-coding RNA, which has been associated with response to lapatinib. Integration of human papilloma virus (HPV) was observed in all HPV18-related samples and 76% of HPV16-related samples, and was associated with structural aberrations and increased target-gene expression. We identified a unique set of endometrial-like cervical cancers, comprised predominantly of HPV-negative tumours with relatively high frequencies of KRAS, ARID1A and PTEN mutations. Integrative clustering of 178 samples identified keratin-low squamous, keratin-high squamous and adenocarcinoma-rich subgroups. These molecular analyses reveal new potential therapeutic targets for cervical cancers.

Published
2017

18. Establishment of a patient-specific avatar organoid model derived from endoscopic ultrasonography-guided fine needle biopsy for timely clinical application in pancreatic ductal adenocarcinoma

Author

Kim, Hyemin, primary, Jang, Jinho, additional, Choi, Jin Ho, additional, Song, Joo Hye, additional, Lee, Su Hyun, additional, Park, Jiho, additional, Ryoo, Si Kyong, additional, Lee, Eun Mi, additional, Jeong, Hyoung-oh, additional, Kim, Seunghoon, additional, Lee, Se-Hoon, additional, Lee, Kwang Hyuck, additional, Lee, Kyu Taek, additional, Kim, Kyoung Mee, additional, Jang, Kee-Taek, additional, Lee, Hyunsook, additional, Lee, Semin, additional, Lee, Jong Kyun, additional, and Park, Joo Kyung, additional

Published
2024
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20. Multiregional Single-Cell Transcriptomics Reveals an Association between Partial Emt and Immunosuppressive States in Oral Squamous Cell Carcinoma

Author

Kim, Seunghoon, primary, Kee, Hyun Jung, additional, Kim, Dahee, additional, Jang, Jinho, additional, Jeong, Hyoung-oh, additional, Sim, Nam Suk, additional, Hwang, Tae, additional, Choi, David Whee-Young, additional, Lee, Kyoung Jun, additional, Lee, Jaewoong, additional, Park, Young Min, additional, Lee, Semin, additional, and Koh, Yoon Woo, additional

Published
2024
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21. Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

Author

Jeon, Sungwon, primary, Choi, Hansol, additional, Jeon, Yeonsu, additional, Choi, Whan-Hyuk, additional, Choi, Hyunjoo, additional, An, Kyungwhan, additional, Ryu, Hyojung, additional, Bhak, Jihun, additional, Lee, Hyeonjae, additional, Kwon, Yoonsung, additional, Ha, Sukyeon, additional, Kim, Yeo Jin, additional, Blazyte, Asta, additional, Kim, Changjae, additional, Kim, Yeonkyung, additional, Kang, Younghui, additional, Woo, Yeong Ju, additional, Lee, Chanyoung, additional, Seo, Jeongwoo, additional, Yoon, Changhan, additional, Bolser, Dan, additional, Biro, Orsolya, additional, Shin, Eun-Seok, additional, Kim, Byung Chul, additional, Kim, Seon-Young, additional, Park, Ji-Hwan, additional, Jeon, Jongbum, additional, Jung, Dooyoung, additional, Lee, Semin, additional, and Bhak, Jong, additional

Published
2024
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23. Decoding a highly mixed Kazakh genome

Author

Seidualy, Madina, Blazyte, Asta, Jeon, Sungwon, Bhak, Youngjune, Jeon, Yeonsu, Kim, Jungeun, Eriksson, Anders, Bolser, Dan, Yoon, Changhan, Manica, Andrea, Lee, Semin, and Bhak, Jong

Published
2020
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24. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Author

Alioto, Tyler S, Buchhalter, Ivo, Derdak, Sophia, Hutter, Barbara, Eldridge, Matthew D, Hovig, Eivind, Heisler, Lawrence E, Beck, Timothy A, Simpson, Jared T, Tonon, Laurie, Sertier, Anne-Sophie, Patch, Ann-Marie, Jäger, Natalie, Ginsbach, Philip, Drews, Ruben, Paramasivam, Nagarajan, Kabbe, Rolf, Chotewutmontri, Sasithorn, Diessl, Nicolle, Previti, Christopher, Schmidt, Sabine, Brors, Benedikt, Feuerbach, Lars, Heinold, Michael, Gröbner, Susanne, Korshunov, Andrey, Tarpey, Patrick S, Butler, Adam P, Hinton, Jonathan, Jones, David, Menzies, Andrew, Raine, Keiran, Shepherd, Rebecca, Stebbings, Lucy, Teague, Jon W, Ribeca, Paolo, Giner, Francesc Castro, Beltran, Sergi, Raineri, Emanuele, Dabad, Marc, Heath, Simon C, Gut, Marta, Denroche, Robert E, Harding, Nicholas J, Yamaguchi, Takafumi N, Fujimoto, Akihiro, Nakagawa, Hidewaki, Quesada, Víctor, Valdés-Mas, Rafael, Nakken, Sigve, Vodák, Daniel, Bower, Lawrence, Lynch, Andrew G, Anderson, Charlotte L, Waddell, Nicola, Pearson, John V, Grimmond, Sean M, Peto, Myron, Spellman, Paul, He, Minghui, Kandoth, Cyriac, Lee, Semin, Zhang, John, Létourneau, Louis, Ma, Singer, Seth, Sahil, Torrents, David, Xi, Liu, Wheeler, David A, López-Otín, Carlos, Campo, Elías, Campbell, Peter J, Boutros, Paul C, Puente, Xose S, Gerhard, Daniela S, Pfister, Stefan M, McPherson, John D, Hudson, Thomas J, Schlesner, Matthias, Lichter, Peter, Eils, Roland, Jones, David TW, and Gut, Ivo G

Subjects
Humans, Medulloblastoma, Mutation, Genome, Human, Leukemia, Lymphoid, High-Throughput Nucleotide Sequencing, Genome, Human, Leukemia, Lymphoid
Abstract

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.

Published
2015

25. Comprehensive genomic characterization of head and neck squamous cell carcinomas

Author

Lawrence, Michael S, Sougnez, Carrie, Lichtenstein, Lee, Cibulskis, Kristian, Lander, Eric, Gabriel, Stacey B, Getz, Gad, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Bowlby, Reanne, Brooks, Denise, Butterfield, Yaron SN, Carlsen, Rebecca, Cheng, Dean, Chu, Andy, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Gordon Robertson, A, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Protopopov, Alexei, Santoso, Netty, Lee, Semin, Parfenov, Michael, Zhang, Jianhua, Mahadeshwar, Harshad S, Tang, Jiabin, Ren, Xiaojia, Seth, Sahil, Haseley, Psalm, Zeng, Dong, Yang, Lixing, Xu, Andrew W, Song, Xingzhi, Pantazi, Angeliki, Bristow, Christopher A, Hadjipanayis, Angela, Seidman, Jonathan, Chin, Lynda, Park, Peter J, Kucherlapati, Raju, Akbani, Rehan, Casasent, Tod, Liu, Wenbin, Lu, Yiling, Mills, Gordon, Motter, Thomas, Weinstein, John, Diao, Lixia, Wang, Jing, Hong Fan, You, Liu, Jinze, Wang, Kai, Todd Auman, J, Balu, Saianand, Bodenheimer, Thomas, Buda, Elizabeth, Neil Hayes, D, Hoadley, Katherine A, Hoyle, Alan P, Jefferys, Stuart R, Jones, Corbin D, Kimes, Patrick K, Liu, Yufeng, Marron, JS, Meng, Shaowu, Mieczkowski, Piotr A, Mose, Lisle E, Parker, Joel S, Perou, Charles M, Prins, Jan F, Roach, Jeffrey, Shi, Yan, Simons, Janae V, Singh, Darshan, Soloway, Matthew G, Tan, Donghui, Veluvolu, Umadevi, Walter, Vonn, Waring, Scot, Wilkerson, Matthew D, Wu, Junyuan, Zhao, Ni, Cherniack, Andrew D, Hammerman, Peter S, Tward, Aaron D, Sekhar Pedamallu, Chandra, and Saksena, Gordon

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Human Genome, Biotechnology, Dental/Oral and Craniofacial Disease, Cancer, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Carcinoma, Squamous Cell, DNA Copy Number Variations, DNA, Neoplasm, Female, Gene Expression Regulation, Neoplastic, Genome, Human, Genomics, Head and Neck Neoplasms, Humans, Male, Molecular Targeted Therapy, Mutation, Oncogenes, RNA, Neoplasm, Signal Transduction, Squamous Cell Carcinoma of Head and Neck, Transcription Factors, Cancer Genome Atlas Network, General Science & Technology
Abstract

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.

Published
2015

26. Characterization of HPV and host genome interactions in primary head and neck cancers

Author

Parfenov, Michael, Pedamallu, Chandra Sekhar, Gehlenborg, Nils, Freeman, Samuel S, Danilova, Ludmila, Bristow, Christopher A, Lee, Semin, Hadjipanayis, Angela G, Ivanova, Elena V, Wilkerson, Matthew D, Protopopov, Alexei, Yang, Lixing, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Ren, Xiaojia, Zhang, Jianhua, Pantazi, Angeliki, Santoso, Netty, Xu, Andrew W, Mahadeshwar, Harshad, Wheeler, David A, Haddad, Robert I, Jung, Joonil, Ojesina, Akinyemi I, Issaeva, Natalia, Yarbrough, Wendell G, Hayes, D Neil, Grandis, Jennifer R, El-Naggar, Adel K, Meyerson, Matthew, Park, Peter J, Chin, Lynda, Seidman, JG, Hammerman, Peter S, Kucherlapati, Raju, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Bowlby, Reanne, Butterfield, Yaron SN, Carlsen, Rebecca, Cheng, Dean, Chu, Andy, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Robertson, A Gordon, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Mahadeshwar, Harshad S, Haseley, Psalm, Zeng, Dong, Bristow, Christopher, Hadjipanayis, Angela, Seidman, Jonathan, Akbani, Rehan, Casasent, Tod, Liu, Wenbin, Lu, Yiling, Mills, Gordon, Motter, Thomas, Weinstein, John, Diao, Lixia, Wang, Jing, Fan, You Hong, Liu, Jinze, Wang, Kai, Auman, J Todd, Balu, Saianand, Bodenheimer, Tom, Buda, Elizabeth, Hoadley, Katherine A, and Hoyle, Alan P

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Bioinformatics and Computational Biology, Genetics, Oncology and Carcinogenesis, Rare Diseases, Human Genome, Sexually Transmitted Infections, Cervical Cancer, Infectious Diseases, Dental/Oral and Craniofacial Disease, HIV/AIDS, Cancer, 2.2 Factors relating to the physical environment, Aetiology, 2.1 Biological and endogenous factors, Infection, Base Sequence, DNA Methylation, Gene Expression Regulation, Neoplastic, Genes, Neoplasm, Genome, Human, Head and Neck Neoplasms, Host-Pathogen Interactions, Humans, Molecular Sequence Data, Papillomaviridae, Virus Integration, cancer, head and neck, papilloma virus, genome rearrangement, integration sites, Cancer Genome Atlas Network
Abstract

Previous studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers display distinct biological and clinical features. HPV is known to drive cancer by the actions of the E6 and E7 oncoproteins, but the molecular architecture of HPV infection and its interaction with the host genome in head and neck cancers have not been comprehensively described. We profiled a cohort of 279 head and neck cancers with next generation RNA and DNA sequencing and show that 35 (12.5%) tumors displayed evidence of high-risk HPV types 16, 33, or 35. Twenty-five cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and both inter- and intrachromosomal rearrangements. Many of these events involved genes with documented roles in cancer. Cancers with integrated vs. nonintegrated HPV displayed different patterns of DNA methylation and both human and viral gene expressions. Together, these data provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viral oncogenesis.

Published
2014

27. Single-cell RNA Sequencing Reveals Novel Cellular Factors for Response to Immunosuppressive Therapy in Aplastic Anemia

Author

Jang, Jinho, primary, Kim, Hongtae, additional, Park, Sung-Soo, additional, Kim, Miok, additional, Min, Yong Ki, additional, Jeong, Hyoung-oh, additional, Kim, Seunghoon, additional, Hwang, Taejoo, additional, Choi, David Whee-Young, additional, Kim, Hee-Je, additional, Song, Sukgil, additional, Kim, Dong Oh, additional, Lee, Semin, additional, Lee, Chang Hoon, additional, and Lee, Jong Wook, additional

Published
2023
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28. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases

Author

Zhang, Yiqun, Yang, Lixing, Kucherlapati, Melanie, Chen, Fengju, Hadjipanayis, Angela, Pantazi, Angeliki, Bristow, Christopher A., Lee, Eunjung A., Mahadeshwar, Harshad S., Tang, Jiabin, Zhang, Jianhua, Seth, Sahil, Lee, Semin, Ren, Xiaojia, Song, Xingzhi, Sun, Huandong, Seidman, Jonathan, Luquette, Lovelace J., Xi, Ruibin, Chin, Lynda, Protopopov, Alexei, Li, Wei, Park, Peter J., Kucherlapati, Raju, and Creighton, Chad J.

Published
2018
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30. The Cancer Genome Atlas Pan-Cancer analysis project

Author

Chang, Kyle, Creighton, Chad J, Davis, Caleb, Donehower, Lawrence, Drummond, Jennifer, Wheeler, David, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron SN, Chu, Andy, Chuah, Eric, Chun, Hye-Jung E, Dhalla, Noreen, Guin, Ranabir, Hirst, Martin, Hirst, Carrie, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Robertson, A Gordon, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Varhol, Richard J, Beroukhim, Rameen, Bhatt, Ami S, Brooks, Angela N, Cherniack, Andrew D, Freeman, Samuel S, Gabriel, Stacey B, Helman, Elena, Jung, Joonil, Meyerson, Matthew, Ojesina, Akinyemi I, Pedamallu, Chandra Sekhar, Saksena, Gordon, Schumacher, Steven E, Tabak, Barbara, Zack, Travis, Lander, Eric S, Bristow, Christopher A, Hadjipanayis, Angela, Haseley, Psalm, Kucherlapati, Raju, Lee, Semin, Lee, Eunjung, Luquette, Lovelace J, Mahadeshwar, Harshad S, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J, Protopopov, Alexei, Ren, Xiaojia, Santoso, Netty, Seidman, Jonathan, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Xi, Ruibin, Xu, Andrew W, Yang, Lixing, Zeng, Dong, Auman, J Todd, Balu, Saianand, Buda, Elizabeth, Fan, Cheng, Hoadley, Katherine A, Jones, Corbin D, Meng, Shaowu, Mieczkowski, Piotr A, Parker, Joel S, Perou, Charles M, Roach, Jeffrey, Shi, Yan, Silva, Grace O, Tan, Donghui, Veluvolu, Umadevi, Waring, Scot, Wilkerson, Matthew D, Wu, Junyuan, Zhao, Wei, Bodenheimer, Tom, Hayes, D Neil, Hoyle, Alan P, Jeffreys, Stuart R, Mose, Lisle E, Simons, Janae V, Soloway, Mathew G, Baylin, Stephen B, Berman, Benjamin P, Bootwalla, Moiz S, Danilova, Ludmila, and Herman, James G

Subjects
Biological Sciences, Genetics, Cancer, Human Genome, Rare Diseases, Good Health and Well Being, Gene Expression Profiling, Genome, Humans, Neoplasms, Cancer Genome Atlas Research Network, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

Published
2013

31. The Somatic Genomic Landscape of Glioblastoma

Author

Brennan, Cameron W, Verhaak, Roel GW, McKenna, Aaron, Campos, Benito, Noushmehr, Houtan, Salama, Sofie R, Zheng, Siyuan, Chakravarty, Debyani, Sanborn, J Zachary, Berman, Samuel H, Beroukhim, Rameen, Bernard, Brady, Wu, Chang-Jiun, Genovese, Giannicola, Shmulevich, Ilya, Barnholtz-Sloan, Jill, Zou, Lihua, Vegesna, Rahulsimham, Shukla, Sachet A, Ciriello, Giovanni, Yung, WK, Zhang, Wei, Sougnez, Carrie, Mikkelsen, Tom, Aldape, Kenneth, Bigner, Darell D, Van Meir, Erwin G, Prados, Michael, Sloan, Andrew, Black, Keith L, Eschbacher, Jennifer, Finocchiaro, Gaetano, Friedman, William, Andrews, David W, Guha, Abhijit, Iacocca, Mary, O’Neill, Brian P, Foltz, Greg, Myers, Jerome, Weisenberger, Daniel J, Penny, Robert, Kucherlapati, Raju, Perou, Charles M, Hayes, D Neil, Gibbs, Richard, Marra, Marco, Mills, Gordon B, Lander, Eric, Spellman, Paul, Wilson, Richard, Sander, Chris, Weinstein, John, Meyerson, Matthew, Gabriel, Stacey, Laird, Peter W, Haussler, David, Getz, Gad, Chin, Lynda, Network, TCGA Research, Benz, Christopher, Barrett, Wendi, Ostrom, Quinn, Wolinsky, Yingli, Bose, Bikash, Boulos, Paul T, Boulos, Madgy, Brown, Jenn, Czerinski, Christine, Eppley, Matthew, Kempista, Thelma, Kitko, Teresa, Koyfman, Yakov, Rabeno, Brenda, Rastogi, Pawan, Sugarman, Michael, Swanson, Patricia, Yalamanchii, Kennedy, Otey, Ilana P, Liu, Yingchun Spring, Xiao, Yonghong, Auman, J Todd, Chen, Peng-Chieh, Hadjipanayis, Angela, Lee, Eunjung, Lee, Semin, Park, Peter J, Seidman, Jonathan, Yang, Lixing, Kalkanis, Steven, Poisson, Laila M, Raghunathan, Aditya, Scarpace, Lisa, Bressler, Ryan, and Eakin, Andrea

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Brain Cancer, Cancer, Brain Disorders, Rare Diseases, Cancer Genomics, Precision Medicine, Orphan Drug, Neurosciences, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies, 5.1 Pharmaceuticals, 4.2 Evaluation of markers and technologies, Brain Neoplasms, Female, Gene Expression Profiling, Gene Regulatory Networks, Glioblastoma, Humans, Male, Mutation, Proteome, Signal Transduction, TCGA Research Network, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.

Published
2013

32. Integrated genomic characterization of endometrial carcinoma

Author

Getz, Gad, Gabriel, Stacey B, Cibulskis, Kristian, Lander, Eric, Sivachenko, Andrey, Sougnez, Carrie, Lawrence, Mike, Kandoth, Cyriac, Dooling, David, Fulton, Robert, Fulton, Lucinda, Kalicki-Veizer, Joelle, McLellan, Michael D, O’Laughlin, Michelle, Schmidt, Heather, Wilson, Richard K, Ye, Kai, Ding, Li, Mardis, Elaine R, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron SN, Carlsen, Rebecca, Carter, Candace, Chu, Andy, Chuah, Eric, Chun, Hye-Jung E, Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Holt, Robert A, Jones, Steven JM, Lee, Darlene, Li, Haiyan I, Marra, Marco A, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Plettner, Patrick, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Varhol, Richard J, Gordon Robertson, A, Cherniack, Andrew D, Pashtan, Itai, Saksena, Gordon, Onofrio, Robert C, Schumacher, Steven E, Tabak, Barbara, Carter, Scott L, Hernandez, Bryan, Gentry, Jeff, Salvesen, Helga B, Ardlie, Kristin, Winckler, Wendy, Beroukhim, Rameen, Meyerson, Matthew, Hadjipanayis, Angela, Lee, Semin, Mahadeshwar, Harshad S, Park, Peter, Protopopov, Alexei, Ren, Xiaojia, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Xi, Ruibin, Yang, Lixing, Zeng, Dong, Kucherlapati, Raju, Chin, Lynda, Zhang, Jianhua, Todd Auman, J, Balu, Saianand, Bodenheimer, Tom, Buda, Elizabeth, Neil Hayes, D, Hoyle, Alan P, Jefferys, Stuart R, Jones, Corbin D, Meng, Shaowu, Mieczkowski, Piotr A, Mose, Lisle E, Parker, Joel S, Perou, Charles M, Roach, Jeff, Shi, Yan, Simons, Janae V, Soloway, Mathew G, Tan, Donghui, Topal, Michael D, Waring, Scot, Wu, Junyuan, Hoadley, Katherine A, Baylin, Stephen B, and Bootwalla, Moiz S

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Reproductive Medicine, Human Genome, Cancer, Uterine Cancer, Biotechnology, Breast Neoplasms, Chromosome Aberrations, DNA Copy Number Variations, DNA Mutational Analysis, DNA Polymerase II, DNA-Binding Proteins, Endometrial Neoplasms, Exome, Female, Gene Expression Regulation, Neoplastic, Genome, Human, Genomics, Humans, Ovarian Neoplasms, Poly-ADP-Ribose Binding Proteins, Signal Transduction, Transcription Factors, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.

Published
2013

34. Comprehensive genomic characterization of squamous cell lung cancers

Author

Hammerman, Peter S, Lawrence, Michael S, Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S, Gabriel, Stacey, Getz, Gad, Sougnez, Carrie, Imielinski, Marcin, Helman, Elena, Hernandez, Bryan, Pho, Nam H, Meyerson, Matthew, Chu, Andy, Chun, Hye-Jung E, Mungall, Andrew J, Pleasance, Erin, Gordon Robertson, A, Sipahimalani, Payal, Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron SN, Chuah, Eric, Coope, Robin JN, Corbett, Richard, Dhalla, Noreen, Guin, Ranabir, He, An, Hirst, Carrie, Hirst, Martin, Holt, Robert A, Lee, Darlene, Li, Haiyan I, Mayo, Michael, Moore, Richard A, Mungall, Karen, Ming Nip, Ka, Olshen, Adam, Schein, Jacqueline E, Slobodan, Jared R, Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven JM, Marra, Marco A, Saksena, Gordon, Cherniack, Andrew D, Schumacher, Stephen E, Tabak, Barbara, Carter, Scott L, Nguyen, Huy, Onofrio, Robert C, Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Protopopov, Alexei, Zhang, Jianhua, Hadjipanayis, Angela, Lee, Semin, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Lee, Eunjung, Chin, Lynda, Park, Peter J, Kucherlapati, Raju, Socci, Nicholas D, Liang, Yupu, Schultz, Nikolaus, Borsu, Laetitia, Lash, Alex E, Viale, Agnes, Sander, Chris, Ladanyi, Marc, Todd Auman, J, Hoadley, Katherine A, Wilkerson, Matthew D, Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J, Topal, Michael D, and Tan, Donghui

Subjects
Human Genome, Biotechnology, Genetics, Rare Diseases, Cancer, Lung Cancer, Lung, Aetiology, 2.1 Biological and endogenous factors, Adenocarcinoma, Adenocarcinoma of Lung, Carcinoma, Squamous Cell, DNA Mutational Analysis, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genes, p16, Genes, p53, Genome, Human, Genomics, Humans, Lung Neoplasms, Molecular Targeted Therapy, Mutation, Mutation Rate, Phosphatidylinositol 3-Kinases, Signal Transduction, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.

Published
2012

35. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

Author

Abdel-Rahman, Mohamed H., Akbani, Rehan, Ally, Adrian, Auman, J. Todd, Babur, Ozgun, Balasundaram, Miruna, Balu, Saianand, Benz, Christopher, Beroukhim, Rameen, Birol, Inanc, Bodenheimer, Tom, Bowen, Jay, Bowlby, Reanne, Bristow, Christopher A., Brooks, Denise, Carlsen, Rebecca, Cebulla, Colleen M., Chang, Matthew T., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cibulskis, Kristian, Cope, Leslie, Coupland, Sarah E., Danilova, Ludmila, Defreitas, Timothy, Demchok, John A., Desjardins, Laurence, Dhalla, Noreen, Esmaeli, Bita, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Gabriel, Stacey B., Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Gershenwald, Jeffrey E., Getz, Gad, Gibb, Ewan A., Griewank, Klaus G., Grimm, Elizabeth A., Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Helsel, Carmen, Hess, Julian M., Hoadley, Katherine A., Hobensack, Shital, Holt, Robert A., Hoyle, Alan P., Hu, Xin, Hutter, Carolyn M., Jager, Martine J., Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Kandoth, Cyriac, Kasaian, Katayoon, Kim, Jaegil, Kimes, Patrick K., Kucherlapati, Melanie, Kucherlapati, Raju, Lander, Eric, Lawrence, Michael S., Lazar, Alexander J., Lee, Semin, Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Jia, Liu, Wenbin, Lolla, Laxmi, Lu, Yiling, Iype, Lisa, Ma, Yussanne, Mahadeshwar, Harshad S., Mariani, Odette, Marra, Marco A., Mayo, Michael, Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Mungall, Karen L., Murray, Bradley A., Naresh, Rashi, Noble, Michael S., Oba, Junna, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Penson, Alexander, Perou, Charles M., Pihl, Todd, Pilarski, Robert, Protopopov, Alexei, Radenbaugh, Amie, Rai, Karan, Ramirez, Nilsa C., Ren, Xiaojia, Reynolds, Sheila M., Roach, Jeffrey, Robertson, A. Gordon, Roman-Roman, Sergio, Roszik, Jason, Sadeghi, Sara, Saksena, Gordon, Sastre, Xavier, Schadendorf, Dirk, Schein, Jacqueline E., Schoenfield, Lynn, Schumacher, Steven E., Seidman, Jonathan, Seth, Sahil, Sethi, Geetika, Sheth, Margi, Shi, Yan, Shields, Carol, Shih, Juliann, Shmulevich, Ilya, Simons, Janae V., Singh, Arun D., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi, Soloway, Matthew G., Song, Xingzhi, Stern, Marc-Henri, Stuart, Joshua, Sun, Qiang, Sun, Huandong, Tam, Angela, Tan, Donghui, Tang, Ming, Tang, Jiabin, Tarnuzzer, Roy, Taylor, Barry S., Thiessen, Nina, Thorsson, Vesteinn, Tse, Kane, Uzunangelov, Vladislav, Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, Walter, Vonn, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Wilkerson, Matthew D., Williams, Michelle D., Wise, Lisa, Woodman, Scott E., Wong, Tina, Wu, Ye, Yang, Liming, Yang, Lixing, Yau, Christina, Zenklusen, Jean C., Zhang, Jiashan, Zhang, Hailei, and Zmuda, Erik

Published
2017
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36. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations

Author

Zhang, Yiqun, Kwok-Shing Ng, Patrick, Kucherlapati, Melanie, Chen, Fengju, Liu, Yuexin, Tsang, Yiu Huen, de Velasco, Guillermo, Jeong, Kang Jin, Akbani, Rehan, Hadjipanayis, Angela, Pantazi, Angeliki, Bristow, Christopher A., Lee, Eunjung, Mahadeshwar, Harshad S., Tang, Jiabin, Zhang, Jianhua, Yang, Lixing, Seth, Sahil, Lee, Semin, Ren, Xiaojia, Song, Xingzhi, Sun, Huandong, Seidman, Jonathan, Luquette, Lovelace J., Xi, Ruibin, Chin, Lynda, Protopopov, Alexei, Westbrook, Thomas F., Shelley, Carl Simon, Choueiri, Toni K., Ittmann, Michael, Van Waes, Carter, Weinstein, John N., Liang, Han, Henske, Elizabeth P., Godwin, Andrew K., Park, Peter J., Kucherlapati, Raju, Scott, Kenneth L., Mills, Gordon B., Kwiatkowski, David J., and Creighton, Chad J.

Published
2017
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41. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Author

Anjum, Samreen, Arachchi, Harindra, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barnett, Gene, Baylin, Stephen, Bell, Sue, Benz, Christopher, Bir, Natalie, Black, Keith L., Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bristow, Christopher A., Butterfield, Yaron S.N., Chen, Qing-Rong, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Coetzee, Simon G., Cohen, Mark L., Colman, Howard, Couce, Marta, D’Angelo, Fulvio, Davidsen, Tanja, Davis, Amy, Demchok, John A., Devine, Karen, Ding, Li, Duell, Rebecca, Elder, J. Bradley, Eschbacher, Jennifer M., Fehrenbach, Ashley, Ferguson, Martin, Frazer, Scott, Fuller, Gregory, Fulop, Jordonna, Gabriel, Stacey B., Garofano, Luciano, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Giannini, Caterina, Gibson, William J., Hadjipanayis, Angela, Hayes, D. Neil, Heiman, David I., Hermes, Beth, Hilty, Joe, Hoadley, Katherine A., Hoyle, Alan P., Huang, Mei, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Ju, Zhenlin, Kastl, Alison, Kendler, Ady, Kim, Jaegil, Kucherlapati, Raju, Lai, Phillip H., Lawrence, Michael S., Lee, Semin, Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Yuexin, Liu, Jia, Ljubimova, Julia Y., Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Mahadeshwar, Harshad S., Marra, Marco A., McGraw, Mary, McPherson, Christopher, Meng, Shaowu, Mieczkowski, Piotr A., Miller, C. Ryan, Mills, Gordon B., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Naska, Theresa, Neder, Luciano, Noble, Michael S., Noss, Ardene, O’Neill, Brian Patrick, Ostrom, Quinn T., Palmer, Cheryl, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Perou, Charles M., Pierson, Christopher R., Pihl, Todd, Protopopov, Alexei, Radenbaugh, Amie, Ramirez, Nilsa C., Rathmell, W. Kimryn, Ren, Xiaojia, Roach, Jeffrey, Robertson, A. Gordon, Saksena, Gordon, Schein, Jacqueline E., Schumacher, Steven E., Seidman, Jonathan, Senecal, Kelly, Seth, Sahil, Shen, Hui, Shi, Yan, Shih, Juliann, Shimmel, Kristen, Sicotte, Hugues, Sifri, Suzanne, Silva, Tiago, Simons, Janae V., Singh, Rosy, Skelly, Tara, Sloan, Andrew E., Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Souza, Camila, Staugaitis, Susan M., Sun, Huandong, Sun, Charlie, Tan, Donghui, Tang, Jiabin, Tang, Yufang, Thorne, Leigh, Trevisan, Felipe Amstalden, Triche, Timothy, Van Den Berg, David J., Veluvolu, Umadevi, Voet, Doug, Wan, Yunhu, Wang, Zhining, Warnick, Ronald, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Williams, Felicia, Wise, Lisa, Wolinsky, Yingli, Wu, Junyuan, Xu, Andrew W., Yang, Lixing, Yang, Liming, Zack, Travis I., Zenklusen, Jean C., Zhang, Jianhua, Zhang, Wei, Zhang, Jiashan, Zmuda, Erik, Ceccarelli, Michele, Barthel, Floris P., Malta, Tathiane M., Sabedot, Thais S., Salama, Sofie R., Murray, Bradley A., Morozova, Olena, Newton, Yulia, Pagnotta, Stefano M., Wang, Jiguang, Manyam, Ganiraju, Zoppoli, Pietro, Ling, Shiyun, Rao, Arjun A., Grifford, Mia, Cherniack, Andrew D., Zhang, Hailei, Poisson, Laila, Carlotti, Carlos Gilberto, Jr., Tirapelli, Daniela Pretti da Cunha, Rao, Arvind, Mikkelsen, Tom, Lau, Ching C., Yung, W.K. Alfred, Rabadan, Raul, Huse, Jason, Brat, Daniel J., Lehman, Norman L., Barnholtz-Sloan, Jill S., Zheng, Siyuan, Hess, Kenneth, Rao, Ganesh, Meyerson, Matthew, Beroukhim, Rameen, Cooper, Lee, Akbani, Rehan, Wrensch, Margaret, Haussler, David, Aldape, Kenneth D., Laird, Peter W., Gutmann, David H., Noushmehr, Houtan, Iavarone, Antonio, and Verhaak, Roel G.W.

Published
2016
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44. Global impact of somatic structural variation on the DNA methylome of human cancers

Author

Zhang, Yiqun, Yang, Lixing, Kucherlapati, Melanie, Hadjipanayis, Angela, Pantazi, Angeliki, Bristow, Christopher A., Lee, Eunjung Alice, Mahadeshwar, Harshad S., Tang, Jiabin, Zhang, Jianhua, Seth, Sahil, Lee, Semin, Ren, Xiaojia, Song, Xingzhi, Sun, Huandong, Seidman, Jonathan, Luquette, Lovelace J., Xi, Ruibin, Chin, Lynda, Protopopov, Alexei, Park, Peter J., Kucherlapati, Raju, and Creighton, Chad J.

Published
2019
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48. Pancreatic Ductal Adenocarcinoma Patient-Derived Organoid Model for Application in Timely Clinical Treatment

Author

Kim, Hyemin, primary, Jang, Jinho, additional, Choi, Jin Ho, additional, Song, Joo Hye, additional, Lee, Sally, additional, Park, Jiho, additional, Ryoo, Si Kyong, additional, Lee, Eun Mi, additional, Jeong, Hyoung-oh, additional, Kim, Seunghoon, additional, Lee, Se-Hoon, additional, Lee, Kwang Hyuck, additional, Lee, Kyu Taek, additional, Kim, Kyoung Mee, additional, Jang, Kee-Taek, additional, Lee, Hyunsook, additional, Lee, Semin, additional, Lee, Jong Kyun, additional, and Park, Joo Kyung, additional

Published
2023
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49. The Molecular Taxonomy of Primary Prostate Cancer

Author

Abeshouse, Adam, Ahn, Jaeil, Akbani, Rehan, Ally, Adrian, Amin, Samirkumar, Andry, Christopher D., Annala, Matti, Aprikian, Armen, Armenia, Joshua, Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barbieri, Christopher E., Bauer, Thomas, Benz, Christopher C., Bergeron, Alain, Beroukhim, Rameen, Berrios, Mario, Bivol, Adrian, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Borges dos Reis, Rodolfo, Boutros, Paul C., Bowen, Jay, Bowlby, Reanne, Boyd, Jeffrey, Bradley, Robert K., Breggia, Anne, Brimo, Fadi, Bristow, Christopher A., Brooks, Denise, Broom, Bradley M., Bryce, Alan H., Bubley, Glenn, Burks, Eric, Butterfield, Yaron S.N., Button, Michael, Canes, David, Carlotti, Carlos G., Carlsen, Rebecca, Carmel, Michel, Carroll, Peter R., Carter, Scott L., Cartun, Richard, Carver, Brett S., Chan, June M., Chang, Matthew T., Chen, Yu, Cherniack, Andrew D., Chevalier, Simone, Chin, Lynda, Cho, Juok, Chu, Andy, Chuah, Eric, Chudamani, Sudha, Cibulskis, Kristian, Ciriello, Giovanni, Clarke, Amanda, Cooperberg, Matthew R., Corcoran, Niall M., Costello, Anthony J., Cowan, Janet, Crain, Daniel, Curley, Erin, David, Kerstin, Demchok, John A., Demichelis, Francesca, Dhalla, Noreen, Dhir, Rajiv, Doueik, Alexandre, Drake, Bettina, Dvinge, Heidi, Dyakova, Natalya, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Freedland, Stephen, Fu, Yao, Gabriel, Stacey B., Gao, Jianjiong, Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Gerstein, Mark B., Getz, Gad, Godwin, Andrew K., Gopalan, Anuradha, Graefen, Markus, Graim, Kiley, Gribbin, Thomas, Guin, Ranabir, Gupta, Manaswi, Hadjipanayis, Angela, Haider, Syed, Hamel, Lucie, Hayes, D. Neil, Heiman, David I., Hess, Julian, Hoadley, Katherine A., Holbrook, Andrea H., Holt, Robert A., Holway, Antonia, Hovens, Christopher M., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Ittmann, Michael, Iype, Lisa, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Juhl, Hartmut, Kahles, Andre, Kane, Christopher J., Kasaian, Katayoon, Kerger, Michael, Khurana, Ekta, Kim, Jaegil, Klein, Robert J., Kucherlapati, Raju, Lacombe, Louis, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Lander, Eric S., Latour, Mathieu, Lawrence, Michael S., Lau, Kevin, LeBien, Tucker, Lee, Darlene, Lee, Semin, Lehmann, Kjong-Van, Leraas, Kristen M., Leshchiner, Ignaty, Leung, Robert, Libertino, John A., Lichtenberg, Tara M., Lin, Pei, Linehan, W. Marston, Ling, Shiyun, Lippman, Scott M., Liu, Jia, Liu, Wenbin, Lochovsky, Lucas, Loda, Massimo, Logothetis, Christopher, Lolla, Laxmi, Longacre, Teri, Lu, Yiling, Luo, Jianhua, Ma, Yussanne, Mahadeshwar, Harshad S., Mallery, David, Mariamidze, Armaz, Marra, Marco A., Mayo, Michael, McCall, Shannon, McKercher, Ginette, Meng, Shaowu, Mes-Masson, Anne-Marie, Merino, Maria J., Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Shaw, Kenna R. Mills, Minner, Sarah, Moinzadeh, Alireza, Moore, Richard A., Morris, Scott, Morrison, Carl, Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Myers, Jerome B., Naresh, Rashi, Nelson, Joel, Nelson, Mark A., Nelson, Peter S., Newton, Yulia, Noble, Michael S., Noushmehr, Houtan, Nykter, Matti, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Piché, Alain, Pihl, Todd, Pinto, Peter A., Prandi, Davide, Protopopov, Alexei, Ramirez, Nilsa C., Rao, Arvind, Rathmell, W. Kimryn, Rätsch, Gunnar, Ren, Xiaojia, Reuter, Victor E., Reynolds, Sheila M., Rhie, Suhn K., Rieger-Christ, Kimberly, Roach, Jeffrey, Robertson, A. Gordon, Robinson, Brian, Rubin, Mark A., Saad, Fred, Sadeghi, Sara, Saksena, Gordon, Saller, Charles, Salner, Andrew, Sanchez-Vega, Francisco, Sander, Chris, Sandusky, George, Sauter, Guido, Sboner, Andrea, Scardino, Peter T., Scarlata, Eleonora, Schein, Jacqueline E., Schlomm, Thorsten, Schmidt, Laura S., Schultz, Nikolaus, Schumacher, Steven E., Seidman, Jonathan, Neder, Luciano, Seth, Sahil, Sharp, Alexis, Shelton, Candace, Shelton, Troy, Shen, Hui, Shen, Ronglai, Sherman, Mark, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simko, Jeffry, Simon, Ronald, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sorcini, Andrea, Sougnez, Carrie, Stepa, Serghei, Stewart, Chip, Stewart, John, Stuart, Joshua M., Sullivan, Travis B., Sun, Charlie, Sun, Huandong, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Tarvin, Katherine, Taylor, Barry S., Teebagy, Patrick, Tenggara, Imelda, Têtu, Bernard, Tewari, Ashutosh, Thiessen, Nina, Thompson, Timothy, Thorne, Leigh B., Tirapelli, Daniela P., Tomlins, Scott A., Trevisan, Felipe Amstalden, Troncoso, Patricia, True, Lawrence D., Tsourlakis, Maria Christina, Tyekucheva, Svitlana, Van Allen, Eliezer, Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel, Vocke, Cathy D., Voet, Doug, Wan, Yunhu, Wang, Qingguo, Wang, Wenyi, Wang, Zhining, Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Wise, Lisa, Witte, John, Wu, Chia-Chin, Wu, Junyuan, Wu, Ye, Xu, Andrew W., Yadav, Shalini S., Yang, Liming, Yang, Lixing, Yau, Christina, Ye, Huihui, Yena, Peggy, Zeng, Thomas, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jianhua, Zhang, Jiashan, Zhang, Wei, Zhong, Yi, Zhu, Kelsey, and Zmuda, Erik

Published
2015
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50. Genomic Classification of Cutaneous Melanoma

Author

Akbani, Rehan, Akdemir, Kadir C., Aksoy, B. Arman, Albert, Monique, Ally, Adrian, Amin, Samirkumar B., Arachchi, Harindra, Arora, Arshi, Auman, J. Todd, Ayala, Brenda, Baboud, Julien, Balasundaram, Miruna, Balu, Saianand, Barnabas, Nandita, Bartlett, John, Bartlett, Pam, Bastian, Boris C., Baylin, Stephen B., Behera, Madhusmita, Belyaev, Dmitry, Benz, Christopher, Bernard, Brady, Beroukhim, Rameen, Bir, Natalie, Black, Aaron D., Bodenheimer, Tom, Boice, Lori, Boland, Genevieve M., Bono, Riccardo, Bootwalla, Moiz S., Bosenberg, Marcus, Bowen, Jay, Bowlby, Reanne, Bristow, Christopher A., Brockway-Lunardi, Laura, Brooks, Denise, Brzezinski, Jakub, Bshara, Wiam, Buda, Elizabeth, Burns, William R., Butterfield, Yaron S.N., Button, Michael, Calderone, Tiffany, Cappellini, Giancarlo Antonini, Carter, Candace, Carter, Scott L., Cherney, Lynn, Cherniack, Andrew D., Chevalier, Aaron, Chin, Lynda, Cho, Juok, Cho, Raymond J., Choi, Yoon-La, Chu, Andy, Chudamani, Sudha, Cibulskis, Kristian, Ciriello, Giovanni, Clarke, Amanda, Coons, Stephen, Cope, Leslie, Crain, Daniel, Curley, Erin, Danilova, Ludmila, D’Atri, Stefania, Davidsen, Tanja, Davies, Michael A., Delman, Keith A., Demchok, John A., Deng, Qixia A., Deribe, Yonathan Lissanu, Dhalla, Noreen, Dhir, Rajiv, DiCara, Daniel, Dinikin, Michael, Dubina, Michael, Ebrom, J. Stephen, Egea, Sophie, Eley, Greg, Engel, Jay, Eschbacher, Jennifer M., Fedosenko, Konstantin V., Felau, Ina, Fennell, Timothy, Ferguson, Martin L., Fisher, Sheila, Flaherty, Keith T., Frazer, Scott, Frick, Jessica, Fulidou, Victoria, Gabriel, Stacey B., Gao, Jianjiong, Gardner, Johanna, Garraway, Levi A., Gastier-Foster, Julie M., Gaudioso, Carmelo, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Gershenwald, Jeffrey E., Getz, Gad, Gomez-Fernandez, Carmen, Gribbin, Thomas, Grimsby, Jonna, Gross, Benjamin, Guin, Ranabir, Gutschner, Tony, Hadjipanayis, Angela, Halaban, Ruth, Hanf, Benjamin, Haussler, David, Haydu, Lauren E., Hayes, D. Neil, Hayward, Nicholas K., Heiman, David I., Herbert, Lynn, Herman, James G., Hersey, Peter, Hoadley, Katherine A., Hodis, Eran, Holt, Robert A., Hoon, Dave SB., Hoppough, Susan, Hoyle, Alan P., Huang, Franklin W., Huang, Mei, Huang, Sharon, Hutter, Carolyn M., Ibbs, Matthew, Iype, Lisa, Jacobsen, Anders, Jakrot, Valerie, Janning, Alyssa, Jeck, William R., Jefferys, Stuart R., Jensen, Mark A., Jones, Corbin D., Jones, Steven J.M., Ju, Zhenlin, Kakavand, Hojabr, Kang, Hyojin, Kefford, Richard F., Khuri, Fadlo R., Kim, Jaegil, Kirkwood, John M., Klode, Joachim, Korkut, Anil, Korski, Konstanty, Krauthammer, Michael, Kucherlapati, Raju, Kwong, Lawrence N., Kycler, Witold, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lazar, Alexander J., Łaźniak, Radoslaw, Lee, Darlene, Lee, Jeffrey E., Lee, Junehawk, Lee, Kenneth, Lee, Semin, Lee, William, Leporowska, Ewa, Leraas, Kristen M., Li, Haiyan I., Lichtenberg, Tara M., Lichtenstein, Lee, Lin, Pei, Ling, Shiyun, Liu, Jia, Liu, Ouida, Liu, Wenbin, Long, Georgina V., Lu, Yiling, Ma, Singer, Ma, Yussanne, Mackiewicz, Andrzej, Mahadeshwar, Harshad S., Malke, Jared, Mallery, David, Manikhas, Georgy M., Mann, Graham J., Marra, Marco A., Matejka, Brenna, Mayo, Michael, Mehrabi, Sousan, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, John P., Miller, Martin L., Mills, Gordon B., Moiseenko, Fedor, Moore, Richard A., Morris, Scott, Morrison, Carl, Morton, Donald, Moschos, Stergios, Mose, Lisle E., Muller, Florian L., Mungall, Andrew J., Murawa, Dawid, Murawa, Pawel, Murray, Bradley A., Nezi, Luigi, Ng, Sam, Nicholson, Dana, Noble, Michael S., Osunkoya, Adeboye, Owonikoko, Taofeek K., Ozenberger, Bradley A., Pagani, Elena, Paklina, Oxana V., Pantazi, Angeliki, Parfenov, Michael, Parfitt, Jeremy, Park, Peter J., Park, Woong-Yang, Parker, Joel S., Passarelli, Francesca, Penny, Robert, Perou, Charles M., Pihl, Todd D., Potapova, Olga, Prieto, Victor G., Protopopov, Alexei, Quinn, Michael J., Radenbaugh, Amie, Rai, Kunal, Ramalingam, Suresh S., Raman, Ayush T., Ramirez, Nilsa C., Ramirez, Ricardo, Rao, Uma, Rathmell, W. Kimryn, Ren, Xiaojia, Reynolds, Sheila M., Roach, Jeffrey, Robertson, A. Gordon, Ross, Merrick I., Roszik, Jason, Russo, Giandomenico, Saksena, Gordon, Saller, Charles, Samuels, Yardena, Sander, Chris, Sander, Cindy, Sandusky, George, Santoso, Netty, Saul, Melissa, Saw, Robyn PM., Schadendorf, Dirk, Schein, Jacqueline E., Schultz, Nikolaus, Schumacher, Steven E., Schwallier, Charles, Scolyer, Richard A., Seidman, Jonathan, Sekhar, Pedamallu Chandra, Sekhon, Harmanjatinder S., Senbabaoglu, Yasin, Seth, Sahil, Shannon, Kerwin F., Sharpe, Samantha, Sharpless, Norman E., Shaw, Kenna R. Mills, Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shiau, Carolyn J., Shmulevich, Ilya, Sica, Gabriel L., Simons, Janae V., Sinha, Rileen, Sipahimalani, Payal, Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Spillane, Andrew J., Spychała, Arkadiusz, Stretch, Jonathan R., Stuart, Joshua, Suchorska, Wiktoria M., Sucker, Antje, Sumer, S. Onur, Sun, Yichao, Synott, Maria, Tabak, Barbara, Tabler, Teresa R., Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Tarvin, Katherine, Tatka, Honorata, Taylor, Barry S., Teresiak, Marek, Thiessen, Nina, Thompson, John F., Thorne, Leigh, Thorsson, Vesteinn, Trent, Jeffrey M., Triche, Timothy J., Jr., Tsai, Kenneth Y., Tsou, Peiling, Van Den Berg, David J., Van Allen, Eliezer M., Veluvolu, Umadevi, Verhaak, Roeland G., Voet, Douglas, Voronina, Olga, Walter, Vonn, Walton, Jessica S., Wan, Yunhu, Wang, Yuling, Wang, Zhining, Waring, Scot, Watson, Ian R., Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., White, Peter, Wilkerson, Matthew D., Wilmott, James S., Wise, Lisa, Wiznerowicz, Maciej, Woodman, Scott E., Wu, Chang-Jiun, Wu, Chia-Chin, Wu, Junyuan, Wu, Ye, Xi, Ruibin, Xu, Andrew Wei, Yang, Da, Yang, Liming, Yang, Lixing, Zack, Travis I., Zenklusen, Jean C., Zhang, Hailei, Zhang, Jianhua, Zhang, Wei, Zhao, Xiaobei, Zhu, Jingchun, Zhu, Kelsey, Zimmer, Lisa, Zmuda, Erik, and Zou, Lihua

Published
2015
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