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1. Cell-free DNA for the detection of emerging treatment failure in relapsed/ refractory multiple myeloma

Author

Waldschmidt, Johannes M., Yee, Andrew J., Vijaykumar, Tushara, Pinto, Ricardo A., Frede, Julia, Anand, Praveen, Bianchi, Giada, Guo, Guangwu, Potdar, Sayalee, Seifer, Charles, Nair, Monica S., Kokkalis, Antonis, Kloeber, Jake A., Shapiro, Samantha, Budano, Lillian, Mann, Mason, Friedman, Robb, Lipe, Brea, Campagnaro, Erica, O’Donnell, Elizabeth K., Zhang, Cheng-Zhong, Laubach, Jacob P., Munshi, Nikhil C., Richardson, Paul G., Anderson, Kenneth C., Raje, Noopur S., Knoechel, Birgit, and Lohr, Jens G.

Published
2022
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2. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

Author

Robertson, A Gordon, Kim, Jaegil, Al-Ahmadie, Hikmat, Bellmunt, Joaquim, Guo, Guangwu, Cherniack, Andrew D, Hinoue, Toshinori, Laird, Peter W, Hoadley, Katherine A, Akbani, Rehan, Castro, Mauro AA, Gibb, Ewan A, Kanchi, Rupa S, Gordenin, Dmitry A, Shukla, Sachet A, Sanchez-Vega, Francisco, Hansel, Donna E, Czerniak, Bogdan A, Reuter, Victor E, Su, Xiaoping, Carvalho, Benilton de Sa, Chagas, Vinicius S, Mungall, Karen L, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Lu, Yiling, Klimczak, Leszek J, Zhang, Jiexin, Choo, Caleb, Ojesina, Akinyemi I, Bullman, Susan, Leraas, Kristen M, Lichtenberg, Tara M, Wu, Catherine J, Schultz, Nicholaus, Getz, Gad, Meyerson, Matthew, Mills, Gordon B, McConkey, David J, Network, TCGA Research, Albert, Monique, Alexopoulou, Iakovina, Ally, Adrian, Antic, Tatjana, Aron, Manju, Balasundaram, Miruna, Bartlett, John, Baylin, Stephen B, Beaver, Allison, Birol, Inanc, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Broom, Bradley M, Bshara, Wiam, Burks, Eric, Cárcano, Flavio M, Carlsen, Rebecca, Carvalho, Benilton S, Carvalho, Andre L, Castle, Eric P, Castro, Patricia, Catto, James W, Chesla, David W, Chuah, Eric, Chudamani, Sudha, Cortessis, Victoria K, Cottingham, Sandra L, Crain, Daniel, Curley, Erin, Daneshmand, Siamak, Demchok, John A, Dhalla, Noreen, Djaladat, Hooman, Eckman, John, Egea, Sophie C, Engel, Jay, Felau, Ina, Ferguson, Martin L, Gardner, Johanna, Gastier-Foster, Julie M, Gerken, Mark, Gomez-Fernandez, Carmen R, and Harr, Jodi

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Genetics, Cancer Genomics, Urologic Diseases, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Aged, Cluster Analysis, DNA Methylation, Humans, MicroRNAs, Middle Aged, Muscle, Smooth, RNA, Long Noncoding, Survival Analysis, Urinary Bladder, Urinary Bladder Neoplasms, TCGA Research Network, APOBEC mutation, DNA methylation, basal mRNA subtype, lncRNA transcriptome, luminal mRNA subtype, microRNA, muscle-invasive bladder cancer, neoantigen, neuronal subtype, regulon, Biological Sciences, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.

Published
2017

3. Excess of rare variants in genes that are key epigenetic regulators of spermatogenesis in the patients with non-obstructive azoospermia.

Author

Li, Zesong, Huang, Yi, Li, Honggang, Hu, Jingchu, Liu, Xiao, Jiang, Tao, Sun, Guangqing, Tang, Aifa, Sun, Xiaojuan, Qian, Weiping, Zeng, Yong, Xie, Jun, Zhao, Wei, Xu, Yu, He, Tingting, Dong, Chengliang, Liu, Qunlong, Mou, Lisha, Lu, Jingxiao, Lin, Zheguang, Wu, Song, Gao, Shengjie, Guo, Guangwu, Feng, Qiang, Li, Yingrui, Zhang, Xiuqing, Wang, Jun, Yang, Huanming, Wang, Jian, Xiong, Chengliang, Cai, Zhiming, and Gui, Yaoting

Subjects
Humans, Genetic Markers, Gene Expression Profiling, Spermatogenesis, Epigenesis, Genetic, Gene Frequency, Alleles, Male, Azoospermia, Gene Regulatory Networks, Genetic Variation, Genetic Testing, Epigenomics, Epigenesis, Genetic
Abstract

Non-obstructive azoospermia (NOA), a severe form of male infertility, is often suspected to be linked to currently undefined genetic abnormalities. To explore the genetic basis of this condition, we successfully sequenced ~650 infertility-related genes in 757 NOA patients and 709 fertile males. We evaluated the contributions of rare variants to the etiology of NOA by identifying individual genes showing nominal associations and testing the genetic burden of a given biological process as a whole. We found a significant excess of rare, non-silent variants in genes that are key epigenetic regulators of spermatogenesis, such as BRWD1, DNMT1, DNMT3B, RNF17, UBR2, USP1 and USP26, in NOA patients (P = 5.5 × 10(-7)), corresponding to a carrier frequency of 22.5% of patients and 13.7% of controls (P = 1.4 × 10(-5)). An accumulation of low-frequency variants was also identified in additional epigenetic genes (BRDT and MTHFR). Our study suggested the potential associations of genetic defects in genes that are epigenetic regulators with spermatogenic failure in human.

Published
2015

4. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes.

Author

Udpa, Nitin, Ronen, Roy, Zhou, Dan, Liang, Junbin, Stobdan, Tsering, Appenzeller, Otto, Yin, Ye, Du, Yuanping, Guo, Lixia, Cao, Rui, Wang, Yu, Jin, Xin, Huang, Chen, Jia, Wenlong, Cao, Dandan, Guo, Guangwu, Claydon, Victoria E, Hainsworth, Roger, Gamboa, Jorge L, Zibenigus, Mehila, Zenebe, Guta, Xue, Jin, Liu, Siqi, Frazer, Kelly A, Li, Yingrui, Bafna, Vineet, and Haddad, Gabriel G

Subjects
Chromosomes, Human, Pair 19, Animals, Humans, Drosophila, Oxygen, Genetics, Population, Altitude, Acclimatization, Sequence Homology, Amino Acid, Polymorphism, Single Nucleotide, Genome, Human, Ethnic Groups, Ethiopia, Genetic Variation, High-Throughput Nucleotide Sequencing, Hypoxia, Chromosomes, Human, Pair 19, Genetics, Population, Sequence Homology, Amino Acid, Polymorphism, Single Nucleotide, Genome, Bioinformatics, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract

BackgroundAlthough it has long been proposed that genetic factors contribute to adaptation to high altitude, such factors remain largely unverified. Recent advances in high-throughput sequencing have made it feasible to analyze genome-wide patterns of genetic variation in human populations. Since traditionally such studies surveyed only a small fraction of the genome, interpretation of the results was limited.ResultsWe report here the results of the first whole genome resequencing-based analysis identifying genes that likely modulate high altitude adaptation in native Ethiopians residing at 3,500 m above sea level on Bale Plateau or Chennek field in Ethiopia. Using cross-population tests of selection, we identify regions with a significant loss of diversity, indicative of a selective sweep. We focus on a 208 kbp gene-rich region on chromosome 19, which is significant in both of the Ethiopian subpopulations sampled. This region contains eight protein-coding genes and spans 135 SNPs. To elucidate its potential role in hypoxia tolerance, we experimentally tested whether individual genes from the region affect hypoxia tolerance in Drosophila. Three genes significantly impact survival rates in low oxygen: cic, an ortholog of human CIC, Hsl, an ortholog of human LIPE, and Paf-AHα, an ortholog of human PAFAH1B3.ConclusionsOur study reveals evolutionarily conserved genes that modulate hypoxia tolerance. In addition, we show that many of our results would likely be unattainable using data from exome sequencing or microarray studies. This highlights the importance of whole genome sequencing for investigating adaptation by natural selection.

Published
2014

5. Whole-Genome Sequencing Uncovers the Genetic Basis of Chronic Mountain Sickness in Andean Highlanders

Author

Zhou, Dan, Udpa, Nitin, Ronen, Roy, Stobdan, Tsering, Liang, Junbin, Appenzeller, Otto, Zhao, Huiwen W, Yin, Yi, Du, Yuanping, Guo, Lixia, Cao, Rui, Wang, Yu, Jin, Xin, Huang, Chen, Jia, Wenlong, Cao, Dandan, Guo, Guangwu, Gamboa, Jorge L, Villafuerte, Francisco, Callacondo, David, Xue, Jin, Liu, Siqi, Frazer, Kelly A, Li, Yingrui, Bafna, Vineet, and Haddad, Gabriel G

Subjects
Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Adult, Altitude Sickness, Animals, Chronic Disease, Down-Regulation, Drosophila melanogaster, Female, Genetic Association Studies, Genetics, Population, Genome, Human, Genomics, Humans, Hypoxia, Male, Peru, Reproducibility of Results, Sequence Analysis, DNA, Survival Analysis, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

The hypoxic conditions at high altitudes present a challenge for survival, causing pressure for adaptation. Interestingly, many high-altitude denizens (particularly in the Andes) are maladapted, with a condition known as chronic mountain sickness (CMS) or Monge disease. To decode the genetic basis of this disease, we sequenced and compared the whole genomes of 20 Andean subjects (10 with CMS and 10 without). We discovered 11 regions genome-wide with significant differences in haplotype frequencies consistent with selective sweeps. In these regions, two genes (an erythropoiesis regulator, SENP1, and an oncogene, ANP32D) had a higher transcriptional response to hypoxia in individuals with CMS relative to those without. We further found that downregulating the orthologs of these genes in flies dramatically enhanced survival rates under hypoxia, demonstrating that suppression of SENP1 and ANP32D plays an essential role in hypoxia tolerance. Our study provides an unbiased framework to identify and validate the genetic basis of adaptation to high altitudes and identifies potentially targetable mechanisms for CMS treatment.

Published
2013

6. Genomic discovery and clonal tracking in multiple myeloma by cell-free DNA sequencing

Author

Guo, Guangwu, Raje, Noopur S., Seifer, Charles, Kloeber, Jake, Isenhart, Randi, Ha, Gavin, Yee, Andrew J., O’Donnell, Elizabeth K., Tai, Yu-Tzu, Richardson, Paul G., Bianchi, Giada, Laubach, Jacob P., Warren, Diane, Gemme, Erica, Voisine, Jordan, Frede, Julia, Kokkalis, Antonis, Yun, Huiyoung, Dimitrova, Valeriya, Vijaykumar, Tushara, Meyerson, Matthew, Munshi, Nikhil C., Anderson, Kenneth C., Knoechel, Birgit, and Lohr, Jens G.

Published
2018
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7. Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Author

Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary

Published
2023
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8. Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Author

Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary

Published
2023
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9. Supplementary Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Author

Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary

Published
2023
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10. Figure S3 from Single-Cell Profiling Reveals Metabolic Reprogramming as a Resistance Mechanism in BRAF-Mutated Multiple Myeloma

Author

Waldschmidt, Johannes M., primary, Kloeber, Jake A., primary, Anand, Praveen, primary, Frede, Julia, primary, Kokkalis, Antonis, primary, Dimitrova, Valeriya, primary, Potdar, Sayalee, primary, Nair, Monica S., primary, Vijaykumar, Tushara, primary, Im, Nam Gyu, primary, Guillaumet-Adkins, Amy, primary, Chopra, Nitish, primary, Stuart, Hannah, primary, Budano, Lillian, primary, Sotudeh, Noori, primary, Guo, Guangwu, primary, Grassberger, Clemens, primary, Yee, Andrew J., primary, Laubach, Jacob P., primary, Richardson, Paul G., primary, Anderson, Kenneth C., primary, Raje, Noopur S., primary, Knoechel, Birgit, primary, and Lohr, Jens G., primary

Published
2023
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11. Table S2 from Single-Cell Profiling Reveals Metabolic Reprogramming as a Resistance Mechanism in BRAF-Mutated Multiple Myeloma

Author

Waldschmidt, Johannes M., primary, Kloeber, Jake A., primary, Anand, Praveen, primary, Frede, Julia, primary, Kokkalis, Antonis, primary, Dimitrova, Valeriya, primary, Potdar, Sayalee, primary, Nair, Monica S., primary, Vijaykumar, Tushara, primary, Im, Nam Gyu, primary, Guillaumet-Adkins, Amy, primary, Chopra, Nitish, primary, Stuart, Hannah, primary, Budano, Lillian, primary, Sotudeh, Noori, primary, Guo, Guangwu, primary, Grassberger, Clemens, primary, Yee, Andrew J., primary, Laubach, Jacob P., primary, Richardson, Paul G., primary, Anderson, Kenneth C., primary, Raje, Noopur S., primary, Knoechel, Birgit, primary, and Lohr, Jens G., primary

Published
2023
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12. Supplementary Figure Legends from Single-Cell Profiling Reveals Metabolic Reprogramming as a Resistance Mechanism in BRAF-Mutated Multiple Myeloma

Author

Waldschmidt, Johannes M., primary, Kloeber, Jake A., primary, Anand, Praveen, primary, Frede, Julia, primary, Kokkalis, Antonis, primary, Dimitrova, Valeriya, primary, Potdar, Sayalee, primary, Nair, Monica S., primary, Vijaykumar, Tushara, primary, Im, Nam Gyu, primary, Guillaumet-Adkins, Amy, primary, Chopra, Nitish, primary, Stuart, Hannah, primary, Budano, Lillian, primary, Sotudeh, Noori, primary, Guo, Guangwu, primary, Grassberger, Clemens, primary, Yee, Andrew J., primary, Laubach, Jacob P., primary, Richardson, Paul G., primary, Anderson, Kenneth C., primary, Raje, Noopur S., primary, Knoechel, Birgit, primary, and Lohr, Jens G., primary

Published
2023
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13. Supplementary Figure S1 from Concurrent Alterations in TERT, KDM6A, and the BRCA Pathway in Bladder Cancer

Author

Nickerson, Michael L., primary, Dancik, Garrett M., primary, Im, Kate M., primary, Edwards, Michael G., primary, Turan, Sevilay, primary, Brown, Joseph, primary, Ruiz-Rodriguez, Christina, primary, Owens, Charles, primary, Costello, James C., primary, Guo, Guangwu, primary, Tsang, Shirley X., primary, Li, Yingrui, primary, Zhou, Quan, primary, Cai, Zhiming, primary, Moore, Lee E., primary, Lucia, M. Scott, primary, Dean, Michael, primary, and Theodorescu, Dan, primary

Published
2023
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14. Supplementary Methods, Tables 1 - 9 from Concurrent Alterations in TERT, KDM6A, and the BRCA Pathway in Bladder Cancer

Author

Nickerson, Michael L., primary, Dancik, Garrett M., primary, Im, Kate M., primary, Edwards, Michael G., primary, Turan, Sevilay, primary, Brown, Joseph, primary, Ruiz-Rodriguez, Christina, primary, Owens, Charles, primary, Costello, James C., primary, Guo, Guangwu, primary, Tsang, Shirley X., primary, Li, Yingrui, primary, Zhou, Quan, primary, Cai, Zhiming, primary, Moore, Lee E., primary, Lucia, M. Scott, primary, Dean, Michael, primary, and Theodorescu, Dan, primary

Published
2023
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18. Mesothelin-targeting T cells bearing a novel T cell receptor fusion construct (TRuC) exhibit potent antitumor efficacy against solid tumors

Author

Ding, Jian, primary, Guyette, Sarah, additional, Schrand, Brett, additional, Geirut, Jessica, additional, Horton, Holly, additional, Guo, Guangwu, additional, Delgoffe, Greg, additional, Menk, Ashley, additional, Baeuerle, Patrick A., additional, Hofmeister, Robert, additional, and Tighe, Robert, additional

Published
2023
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19. Single-Cell Profiling Reveals Metabolic Reprogramming as a Resistance Mechanism inBRAF-Mutated Multiple Myeloma

Author

Waldschmidt, Johannes M., primary, Kloeber, Jake A., additional, Anand, Praveen, additional, Frede, Julia, additional, Kokkalis, Antonis, additional, Dimitrova, Valeriya, additional, Potdar, Sayalee, additional, Nair, Monica S., additional, Vijaykumar, Tushara, additional, Im, Nam Gyu, additional, Guillaumet-Adkins, Amy, additional, Chopra, Nitish, additional, Stuart, Hannah, additional, Budano, Lillian, additional, Sotudeh, Noori, additional, Guo, Guangwu, additional, Grassberger, Clemens, additional, Yee, Andrew J., additional, Laubach, Jacob P., additional, Richardson, Paul G., additional, Anderson, Kenneth C., additional, Raje, Noopur S., additional, Knoechel, Birgit, additional, and Lohr, Jens G., additional

Published
2021
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20. Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL

Author

Anand, Praveen, primary, Guillaumet-Adkins, Amy, additional, Dimitrova, Valeriya, additional, Yun, Huiyoung, additional, Drier, Yotam, additional, Sotudeh, Noori, additional, Rogers, Anna, additional, Ouseph, Madhu M., additional, Nair, Monica, additional, Potdar, Sayalee, additional, Isenhart, Randi, additional, Kloeber, Jake A., additional, Vijaykumar, Tushara, additional, Niu, Leili, additional, Vincent, Tiffaney, additional, Guo, Guangwu, additional, Frede, Julia, additional, Harris, Marian H., additional, Place, Andrew E., additional, Silverman, Lewis B., additional, Teachey, David T., additional, Lane, Andrew A., additional, DeAngelo, Daniel J., additional, Aster, Jon C., additional, Bernstein, Bradley E., additional, Lohr, Jens G., additional, and Knoechel, Birgit, additional

Published
2021
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22. Multilayered molecular profiling supported the monoclonal origin of metastatic renal cell carcinoma

Author

Huang, Yi, Gao, Shengjie, Wu, Song, Song, Pengfei, Sun, Xiaojuan, Hu, Xueda, Zhang, Shiqiang, Yu, Yuan, Zhu, Jialou, Li, Cailing, Qin, Zike, Xie, Liangfu, Yao, Qiong, Tang, Aifa, Li, Zesong, Guo, Guangwu, Wan, Shengqing, Dong, Pei, Sun, Liang, Li, Weiping, Wang, Daping, Gui, Yaoting, Yang, Huanming, Zhou, Fangjian, Zhang, Xiuqing, and Cai, Zhiming

Published
2014
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23. Identification of genomic alterations in oesophageal squamous cell cancer

Author

Song, Yongmei, Li, Lin, Ou, Yunwei, Gao, Zhibo, Li, Enmin, Li, Xiangchun, Zhang, Weimin, Wang, Jiaqian, Xu, Liyan, Zhou, Yong, Ma, Xiaojuan, Liu, Lingyan, Zhao, Zitong, Huang, Xuanlin, Fan, Jing, Dong, Lijia, Chen, Gang, Ma, Liying, Yang, Jie, Chen, Longyun, He, Minghui, Li, Miao, Zhuang, Xuehan, Huang, Kai, Qiu, Kunlong, Yin, Guangliang, Guo, Guangwu, Feng, Qiang, Chen, Peishan, Wu, Zhiyong, Wu, Jianyi, Ma, Ling, Zhao, Jinyang, Luo, Longhai, Fu, Ming, Xu, Bainan, Chen, Bo, Li, Yingrui, Tong, Tong, Wang, Mingrong, Liu, Zhihua, Lin, Dongxin, Zhang, Xiuqing, Yang, Huanming, Wang, Jun, and Zhan, Qimin

Published
2014
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26. Single Cell RNA-Seq Reveals Deranged Developmental Hierarchy with Coexisting Oncogenic States and Immune Evasion Programs in ETP T-ALL

Author

Guillaumet-Adkins, Amy, primary, Anand, Praveen, additional, Yun, Huiyoung, additional, Drier, Yotam, additional, Rogers, Anna, additional, Ouseph, Madhu M., additional, Nair, Monica S., additional, Potdar, Sayalee, additional, Isenhart, Randi, additional, Kloeber, Jake A., additional, Vijaykumar, Tushara, additional, Guo, Guangwu, additional, Frede, Julia, additional, Harris, Marian H., additional, Silverman, Lewis B., additional, Lane, Andrew A., additional, DeAngelo, Daniel J., additional, Aster, Jon C., additional, Bernstein, Bradley E., additional, Lohr, Jens G., additional, and Knoechel, Birgit, additional

Published
2019
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27. Defining the Differentiation States of Multiple Myeloma at Single Cell Resolution Reveals Opportunities for Immunotherapy

Author

Frede, Julia, primary, Anand, Praveen, additional, Yee, Andrew J., additional, Vijaykumar, Tushara, additional, Nair, Monica S., additional, Waldschmidt, Johannes M., additional, Potdar, Sayalee V., additional, Kloeber, Jake A., additional, Kokkalis, Antonis, additional, Guo, Guangwu, additional, Shapiro, Samantha J., additional, Mann, Mason L., additional, Friedman, Robb S, additional, Lipe, Brea C., additional, Campagnaro, Erica L., additional, Cole, Craig E., additional, O'Donnell, Elizabeth K., additional, Guerrero, Thomas, additional, Nadeem, Omar, additional, Laubach, Jacob P., additional, Munshi, Nikhil C., additional, Richardson, Paul G., additional, Anderson, Kenneth C., additional, Raje, Noopur, additional, Knoechel, Birgit, additional, and Lohr, Jens G., additional

Published
2019
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28. Circulating Tumor DNA in the Peripheral Blood As Early Predictor of Clinical Outcome in Relapsed/ Refractory Multiple Myeloma

Author

Waldschmidt, Johannes M., primary, Yee, Andrew J., additional, Vijaykumar, Tushara, additional, Frede, Julia, additional, Anand, Praveen, additional, Potdar, Sayalee, additional, Nair, Monica S., additional, Kokkalis, Antonis, additional, Kloeber, Jake A., additional, Guo, Guangwu, additional, Shapiro, Samantha J., additional, Mann, Mason L., additional, Friedman, Robb S, additional, Lipe, Brea C., additional, Campagnaro, Erica L., additional, O'Donnell, Elizabeth K., additional, Guerrero, Thomas, additional, Laubach, Jacob P., additional, Munshi, Nikhil C., additional, Richardson, Paul G., additional, Anderson, Kenneth C., additional, Raje, Noopur S., additional, Knoechel, Birgit, additional, and Lohr, Jens G., additional

Published
2019
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29. International network of cancer genome projects

Author

Hudson, Thomas J., Anderson, Warwick, Aretz, Axel, Bell, Cindy, Bernabé, Rosa R., Bhan, M. K., Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S., Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M., Jennings, Jennifer L., Kerr, David, Klatt, Peter, Kolar, Patrik, Lane, David P., Laplace, Frank, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, T. S., Remacle, Jacques, Schafer, Alan J., Shibata, Tatsuhiro, Stratton, Michael R., Watanabe, Koichi, Yuen, Matthew M. F., Cambon-Thomsen, Anne, Dressler, Lynn G., Joly, Yann, Kennedy, Karen L., Parker, Michael J., Romeo-Casabona, Carlos M., Wallace, Susan, Wiesner, Georgia L., Zeps, Nikolajs, Biankin, Andrew V., Chabannon, Christian, de Alava, Enrique, Ferguson, Martin L., Geary, Peter, Hayes, Neil D., Johns, Amber L., Kasprzyk, Arek, Nakagawa, Hidewaki, Piris, Miguel A., van de Vijver, Marc, Aburatani, Hiroyuki, Bayés, Mónica, Bowtell, David D.L., Campbell, Peter J., Hirst, Martin, López-Otín, Carlos, Marra, Marco, Ning, Zemin, Puente, Xose S., Ruan, Yijun, Stunnenberg, Hendrik G., Swerdlow, Harold, Velculescu, Victor E., Xue, Hong H., Yang, Liu, Spellman, Paul T., Bader, Gary D., Boutros, Paul C., Flicek, Paul, Getz, Gad, Guigó, Roderic, Guo, Guangwu, Haussler, David, Hubbard, Tim J., Jiang, Tao, Jones, Steven M., Li, Qibin, López-Bigas, Nuria, Luo, Ruibang, Muthuswamy, Lakshmi, Ouellette, Francis B. F., Pearson, John V., Quesada, Victor, Raphael, Benjamin J., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Teague, Jon W., Totoki, Yasushi, Tsunoda, Tatsuhiko, Valencia, Alfonso, Wheeler, David A., Wu, Honglong, Zhao, Shancen, Zhou, Guangyu, Lathrop, Mark, Axton, Myles, Dyke, Stephanie O. M., Gunter, Chris, McPherson, John D., Miller, Linda J., Zhang, Junjun, Haider, Syed A., Wang, Jianxin, Yung, Christina K., Cross, Anthony, Liang, Yong, Gnaneshan, Saravanamuttu, Guberman, Jonathan, Hsu, Jack, Bobrow, Martin, Chalmers, Don R. C., Hasel, Karl W., Kaan, Terry S. H., Knoppers, Bartha M., Lowrance, William W., Masui, Tohru, Nicolás, Pilar, Rial-Sebbag, Emmanuelle, Rodriguez, Laura Lyman, Vergely, Catherine, Grimmond, Sean M., Bowtell, David D. L., Cloonan, Nicole, deFazio, Anna, Eshleman, James R., Etemadmoghadam, Dariush, Gardiner, Brooke A., Kench, James G., Scarpa, Aldo, Sutherland, Robert L., Tempero, Margaret A., Waddell, Nicola J., Wilson, Peter J., Gallinger, Steve, Tsao, Ming-Sound, Shaw, Patricia A., Petersen, Gloria M., Mukhopadhyay, Debabrata, Chin, Lynda, DePinho, Ronald A., Thayer, Sarah, Shazand, Kamran, Beck, Timothy, Sam, Michelle, Timms, Lee, Ballin, Vanessa, Ji, Jiafu, Zhang, Xiuqing, Chen, Feng, Hu, Xueda, Yang, Qi, Tian, Geng, Zhang, Lianhai, Xing, Xiaofang, Li, Xianghong, Zhu, Zhenggang, Yu, Yingyan, Yu, Jun, Yang, Huanming, Tost, Jörg, Brennan, Paul, Holcatova, Ivana, Zaridze, David, Brazma, Alvis, Egevad, Lars, Prokhortchouk, Egor, Banks, Rosamonde Elizabeth, Uhlén, Mathias, Viksna, Juris, Ponten, Fredrik, Skryabin, Konstantin, Futreal, Andrew P., Birney, Ewan, Caldas, Carlos, Reis-Filho, Jorge S., Richardson, Andrea L., Sotiriou, Christos, Birnbaum, Daniel, Blanche, Hélène, Boucher, Pascal, Boyault, Sandrine, Masson-Jacquemier, Jocelyne D., Pauporté, Iris, Pivot, Xavier, Vincent-Salomon, Anne, Tabone, Eric, Theillet, Charles, Treilleux, Isabelle, Bioulac-Sage, Paulette, Clément, Bruno, Decaens, Thomas, Degos, Françoise, Franco, Dominique, Gut, Ivo, Gut, Marta, Heath, Simon, Samuel, Didier, Thomas, Gilles, Zucman-Rossi, Jessica, Eils, Roland, Brors, Benedikt, Korbel, Jan O., Korshunov, Andrey, Landgraf, Pablo, Lehrach, Hans, Pfister, Stefan, Radlwimmer, Bernhard, Reifenberger, Guido, Taylor, Michael D., von Kalle, Christof, Majumder, Partha P., Sarin, Rajiv, Pederzoli, Paolo, Lawlor, Rita T., Delledonne, Massimo, Bardelli, Alberto, Gress, Thomas, Klimstra, David, Zamboni, Giuseppe, Nakamura, Yusuke, Kusuda, Jun, Miyano, Satoru, Kato, Kazuto, Fujimoto, Akihiro, Yoshida, Teruhiko, Campo, Elias, Estivill, Xavier, de Sanjosé, Silvia, Montserrat, Emili, González-Díaz, Marcos, Jares, Pedro, Himmelbaue, Heinz, Bea, Silvia, Aparicio, Samuel, Borg, Ake, Børresen-Dale, Anne-Lise, Foekens, John A., vanʼt Veer, Laura, Easton, Douglas F., Martin, Sancha, Compton, Carolyn C., Lander, Eric S., Penny, Robert, Shaw, Kenna M., Speed, Terence P., Vockley, Joseph G., Lichter, Peter, Barker, Anna D., Burke, Wylie, Collins, Francis S., Green, Anthony R., Hamilton, Stanley R., Kallioniemi, Olli P., Ley, Timothy J., Liu, Edison T., Lu, Youyong, Majumder, Partha, Wainwright, Brandon J., and Wilson, Richard K.

Published
2010
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30. The diploid genome sequence of an Asian individual

Author

Wang, Jun, Wang, Wei, Li, Ruiqiang, Li, Yingrui, Tian, Geng, Goodman, Laurie, Fan, Wei, Zhang, Junqing, Li, Jun, Zhang, Juanbin, Guo, Yiran, Feng, Binxiao, Li, Heng, Lu, Yao, Fang, Xiaodong, Liang, Huiqing, Du, Zhenglin, Li, Dong, Zhao, Yiqing, Hu, Yujie, Yang, Zhenzhen, Zheng, Hancheng, Hellmann, Ines, Inouye, Michael, Pool, John, Yi, Xin, Zhao, Jing, Duan, Jinjie, Zhou, Yan, Qin, Junjie, Ma, Lijia, Li, Guoqing, Yang, Zhentao, Zhang, Guojie, Yang, Bin, Yu, Chang, Liang, Fang, Li, Wenjie, Li, Shaochuan, Li, Dawei, Ni, Peixiang, Ruan, Jue, Li, Qibin, Zhu, Hongmei, Liu, Dongyuan, Lu, Zhike, Li, Ning, Guo, Guangwu, Zhang, Jianguo, Ye, Jia, Fang, Lin, Hao, Qin, Chen, Quan, Liang, Yu, Su, Yeyang, san, A., Ping, Cuo, Yang, Shuang, Chen, Fang, Li, Li, Zhou, Ke, Zheng, Hongkun, Ren, Yuanyuan, Yang, Ling, Gao, Yang, Yang, Guohua, Li, Zhuo, Feng, Xiaoli, Kristiansen, Karsten, Wong, Gane Ka-Shu, Nielsen, Rasmus, Durbin, Richard, Bolund, Lars, Zhang, Xiuqing, Li, Songgang, Yang, Huanming, and Wang, Jian

Published
2008
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31. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

Author

Li Yingrui, Xu Xun, Song Luting, Hou Yong, Li Zesong, Tsang Shirley, Li Fuqiang, Im Kate, Wu Kui, Wu Hanjie, Ye Xiaofei, Li Guibo, Wang Linlin, Zhang Bo, Liang Jie, Xie Wei, Wu Renhua, Jiang Hui, Liu Xiao, Yu Chang, Zheng Hancheng, Jian Min, Nie Liping, Wan Lei, Shi Min, Sun Xiaojuan, Tang Aifa, Guo Guangwu, Gui Yaoting, Cai Zhiming, Li Jingxiang, Wang Wen, Lu Zuhong, Zhang Xiuqing, Bolund Lars, Kristiansen Karsten, Wang Jian, Yang Huanming, Dean Michael, and Wang Jun

Subjects
Single-cell exome sequencing, Bladder cancer, Tumor evolution, Population genetics, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background Cancers arise through an evolutionary process in which cell populations are subjected to selection; however, to date, the process of bladder cancer, which is one of the most common cancers in the world, remains unknown at a single-cell level. Results We carried out single-cell exome sequencing of 66 individual tumor cells from a muscle-invasive bladder transitional cell carcinoma (TCC). Analyses of the somatic mutant allele frequency spectrum and clonal structure revealed that the tumor cells were derived from a single ancestral cell, but that subsequent evolution occurred, leading to two distinct tumor cell subpopulations. By analyzing recurrently mutant genes in an additional cohort of 99 TCC tumors, we identified genes that might play roles in the maintenance of the ancestral clone and in the muscle-invasive capability of subclones of this bladder cancer, respectively. Conclusions This work provides a new approach of investigating the genetic details of bladder tumoral changes at the single-cell level and a new method for assessing bladder cancer evolution at a cell-population level.

Published
2012
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33. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

Author

Robertson, A. Gordon, primary, Kim, Jaegil, additional, Al-Ahmadie, Hikmat, additional, Bellmunt, Joaquim, additional, Guo, Guangwu, additional, Cherniack, Andrew D., additional, Hinoue, Toshinori, additional, Laird, Peter W., additional, Hoadley, Katherine A., additional, Akbani, Rehan, additional, Castro, Mauro A.A., additional, Gibb, Ewan A., additional, Kanchi, Rupa S., additional, Gordenin, Dmitry A., additional, Shukla, Sachet A., additional, Sanchez-Vega, Francisco, additional, Hansel, Donna E., additional, Czerniak, Bogdan A., additional, Reuter, Victor E., additional, Su, Xiaoping, additional, de Sa Carvalho, Benilton, additional, Chagas, Vinicius S., additional, Mungall, Karen L., additional, Sadeghi, Sara, additional, Pedamallu, Chandra Sekhar, additional, Lu, Yiling, additional, Klimczak, Leszek J., additional, Zhang, Jiexin, additional, Choo, Caleb, additional, Ojesina, Akinyemi I., additional, Bullman, Susan, additional, Leraas, Kristen M., additional, Lichtenberg, Tara M., additional, Wu, Catherine J., additional, Schultz, Nicholaus, additional, Getz, Gad, additional, Meyerson, Matthew, additional, Mills, Gordon B., additional, McConkey, David J., additional, Weinstein, John N., additional, Kwiatkowski, David J., additional, and Lerner, Seth P., additional

Published
2018
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34. Circulating tumor DNA in the peripheral blood as early predictor of clinical outcome in relapsed/ refractory multiple myeloma

Author

Waldschmidt, Johannes M., Yee, Andrew, Raje, Noopur, Vijaykumar, Tushara, Frede, Julia, Anand, Praveen, Potdar, Sayalee, Nair, Monica S., Kokkalis, Antonis, Kloeber, Jake, Guo, Guangwu, Mann, Mason, Shapiro, Samantha, Friedman, Robb, Campagnero, Erica, Lipe, Brea, O´Donnell, Elizabeth K., Garcia, Thomas Guerrero, Laubach, Jacob, Munshi, Nikhil, Richardson, Paul G., Anderson, Kenneth C., Knoechel, Birgit, and Lohr, Jens

Published
2019
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36. Comprehensive Genetic Interrogation of Circulating Multiple Myeloma Cells at Single Cell Resolution

Author

Lohr, Jens G, primary, Kim, Sora, additional, Gould, Joshua, additional, Knoechel, Birgit, additional, Drier, Yotam, additional, Gray, Daniel, additional, Birrer, Nicole, additional, Wong, Bang, additional, Ha, Gavin, additional, Zhang, Cheng-Zhong, additional, Guo, Guangwu, additional, Meyerson, Matthew, additional, Yee, Andrew, additional, Boehm, Jesse, additional, Raje, Noopur, additional, and Golub, Todd R., additional

Published
2016
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37. Peptidomimetic Blockade of MYB in Acute Myeloid Leukemia

Author

Ramaswamy, Kavitha, primary, Forbes, Lauren, additional, Brown, Fiona C, additional, Koche, Richard, additional, Gindin, Tatyana, additional, Minuesa, Gerard, additional, Kharas, Michael G., additional, Krivtsov, Andrei, additional, Armstrong, Scott A., additional, Still, Eric, additional, de Stanchina, Elisa, additional, Isenhart, Randi, additional, Guo, Guangwu, additional, Knoechel, Birgit, additional, and Kentsis, Alex, additional

Published
2016
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38. Genetic interrogation of circulating multiple myeloma cells at single-cell resolution

Author

Lohr, Jens G., primary, Kim, Sora, additional, Gould, Joshua, additional, Knoechel, Birgit, additional, Drier, Yotam, additional, Cotton, Matthew J., additional, Gray, Daniel, additional, Birrer, Nicole, additional, Wong, Bang, additional, Ha, Gavin, additional, Zhang, Cheng-Zhong, additional, Guo, Guangwu, additional, Meyerson, Matthew, additional, Yee, Andrew J., additional, Boehm, Jesse S., additional, Raje, Noopur, additional, and Golub, Todd R., additional

Published
2016
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39. AB088. Genomic study on the cancers in urological system

Author

Gui, Yaoting, Huang, Yi, Guo, Guangwu, Tang, Aifa, Li, Zesong, Wu, Song, Li, Xianxin, and Cai, Zhiming

Subjects
Bladder cancer, renal cancer, genomics, Podium Lecture, sequencing
Abstract

Objective Bladder cancer and renal cancer are common malignancies in the urological system. The aims of the present study are to detect the genomic changes in the cancer tissues by massively parallel DNA sequence technology. Methods The cancer tissues with matched morphologically normal tissues and peripheral blood samples were collected from the patients with urothelial bladder carcinoma (UBC) and clear cell renal cell carcinoma (ccRCC). Whole genome, exome or transcriptome of the samples were sequenced by massively parallel DNA sequencing technology. The somatic mutations, copy number variations and mRNA variations were identified by different bioinformatic methods and validated by Sanger DNA sequencing. Results We sequenced the exomes of nine individuals with UBC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with UBC with different tumor stages and grades, and identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with UBC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. We sequenced whole exomes of 10 ccRCC samples and performed a screen of 1,100 genes in 88 additional ccRCCs, from which we discovered 12 previously unidentified genes mutated at elevated frequencies in ccRCC. Notably, we detected frequent mutations in the ubiquitin-mediated proteolysis pathway (UMPP), and alterations in the UMPP were significantly associated with overexpression of HIF1α and HIF2α in the tumors. Conclusions Our results provide an overview of the genetic basis of UBC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer. Our findings highlight the potential contribution of UMPP to ccRCC tumorigenesis through the activation of the hypoxia regulatory network.

Published
2015

40. CD4+ TSCMs in the Bone Marrow Assist in Maturation of Antibodies against Influenza in Mice.

Author

Wu, Kang, Wang, Fei, Guo, Guangwu, Li, Yuqing, Qiu, Li-Jun, and Li, Xuefeng

Subjects
B cells, BONE marrow, INFLUENZA, MEMORY, T cells
Abstract

The bone marrow (BM) is not only a reservoir of hematopoietic stem cells but a repository of immunological memory cells. Further characterizing BM-resident memory T cells would be helpful to reveal the complicated relationship between the BM and immunological memory. In this study, we identified CD122high stem cell antigen-1 (Sca-1) high B cell lymphoma 2 (Bcl-2) high CD4+ stem cell-like memory T cells (TSCMs) as a distinct memory T cell subset, which preferentially reside in the BM, where they respond vigorously to blood-borne antigens. Interestingly, the natural CD4+ TSCMs homing to the BM colocalized with VCAM-1+ IL-15+ IL-7+ CXCL-12+ stromal cells. Furthermore, compared to spleen-resident CD4+ TSCMs, BM-resident TSCMs induced the production of high-affinity antibodies against influenza by B lymphocytes more efficiently. Taken together, these observations indicate that the BM provides an appropriate microenvironment for the survival of CD4+ TSCMs, which broadens our knowledge regarding the memory maintenance of antigen-specific CD4+ T lymphocytes. [ABSTRACT FROM AUTHOR]

Published
2019
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41. Abstract 128: Comprehensive molecular characterization of 412 muscle-invasive urothelial bladder carcinomas: final analysis of The Cancer Genome Atlas (TCGA) project

Author

Weinstein, John N., primary, Lerner, Seth P., additional, Kwiatkowski, David J., additional, Getz, Gad, additional, Kim, Jaegil, additional, Al-ahmadie, Hikmat A., additional, Cherniack, Andrew D., additional, Guo, Guangwu, additional, Akbani, Rehan, additional, Hoadley, Katherine A., additional, Kim, William Y., additional, Robertson, Gordon, additional, Mungall, Andrew J., additional, Hinoue, Toshinori, additional, Laird, Peter W., additional, Rosenberg, Jonathan E., additional, Bellmunt, Joaquim, additional, Bajorin, Dean F., additional, Morgan, Margaret B., additional, Creighton, Chad J., additional, Gordenin, Dmitry, additional, Stuart, Joshua M., additional, Su, Xiaoping, additional, Ryan, Michael C., additional, Damrauer, Jeffrey S., additional, Zhang, Wei, additional, Liu, Yuexin, additional, Lu, Yiling, additional, Schultz, Nikolaus, additional, Kucherlapati, Raju, additional, Mills, Gordon B., additional, Hansel, Donna E., additional, Robinson, Brian D., additional, Czerniak, Bodgen A., additional, and Reuter, Victor E., additional

Published
2016
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45. Genomic landscape of high-grade T1 micropapillary bladder tumors.

Author

Bellmunt, Joaquim, primary, Guo, Guangwu, additional, Mullane, Stephanie A., additional, Orsola, Anna, additional, Werner, Lillian, additional, Van Hummelen, Paul, additional, Thorner, Aaron, additional, Loda, Massimo, additional, Choueiri, Toni K., additional, Barletta, Justine A., additional, Kwiatkowski, David J., additional, Meyerson, Matthew, additional, and Van Allen, Eliezer Mendel, additional

Published
2015
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47. Concurrent Alterations in TERT, KDM6A, and the BRCA Pathway in Bladder Cancer

Author

Nickerson, Michael L., primary, Dancik, Garrett M., additional, Im, Kate M., additional, Edwards, Michael G., additional, Turan, Sevilay, additional, Brown, Joseph, additional, Ruiz-Rodriguez, Christina, additional, Owens, Charles, additional, Costello, James C., additional, Guo, Guangwu, additional, Tsang, Shirley X., additional, Li, Yingrui, additional, Zhou, Quan, additional, Cai, Zhiming, additional, Moore, Lee E., additional, Lucia, M. Scott, additional, Dean, Michael, additional, and Theodorescu, Dan, additional

Published
2014
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48. Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431

Author

Yang, Yanfang, primary, Zhao, Hainan, additional, Barrero, Roberto A, additional, Zhang, Baohong, additional, Sun, Guiling, additional, Wilson, Iain W, additional, Xie, Fuliang, additional, Walker, Kevin D, additional, Parks, Joshua W, additional, Bruce, Robert, additional, Guo, Guangwu, additional, Chen, Li, additional, Zhang, Yong, additional, Huang, Xin, additional, Tang, Qi, additional, Liu, Hongwei, additional, Bellgard, Matthew I, additional, Qiu, Deyou, additional, Lai, Jinsheng, additional, and Hoffman, Angela, additional

Published
2014
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49. Multilayered molecular profiling supported the monoclonal origin of metastatic renal cell carcinoma

Author

Huang, Yi, primary, Gao, Shengjie, additional, Wu, Song, additional, Song, Pengfei, additional, Sun, Xiaojuan, additional, Hu, Xueda, additional, Zhang, Shiqiang, additional, Yu, Yuan, additional, Zhu, Jialou, additional, Li, Cailing, additional, Qin, Zike, additional, Xie, Liangfu, additional, Yao, Qiong, additional, Tang, Aifa, additional, Li, Zesong, additional, Guo, Guangwu, additional, Wan, Shengqing, additional, Dong, Pei, additional, Sun, Liang, additional, Li, Weiping, additional, Wang, Daping, additional, Gui, Yaoting, additional, Yang, Huanming, additional, Zhou, Fangjian, additional, Zhang, Xiuqing, additional, and Cai, Zhiming, additional

Published
2013
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50. Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation

Author

Guo, Guangwu, primary, Sun, Xiaojuan, additional, Chen, Chao, additional, Wu, Song, additional, Huang, Peide, additional, Li, Zesong, additional, Dean, Michael, additional, Huang, Yi, additional, Jia, Wenlong, additional, Zhou, Quan, additional, Tang, Aifa, additional, Yang, Zuoquan, additional, Li, Xianxin, additional, Song, Pengfei, additional, Zhao, Xiaokun, additional, Ye, Rui, additional, Zhang, Shiqiang, additional, Lin, Zhao, additional, Qi, Mingfu, additional, Wan, Shengqing, additional, Xie, Liangfu, additional, Fan, Fan, additional, Nickerson, Michael L, additional, Zou, Xiangjun, additional, Hu, Xueda, additional, Xing, Li, additional, Lv, Zhaojie, additional, Mei, Hongbin, additional, Gao, Shengjie, additional, Liang, Chaozhao, additional, Gao, Zhibo, additional, Lu, Jingxiao, additional, Yu, Yuan, additional, Liu, Chunxiao, additional, Li, Lin, additional, Fang, Xiaodong, additional, Jiang, Zhimao, additional, Yang, Jie, additional, Li, Cailing, additional, Zhao, Xin, additional, Chen, Jing, additional, Zhang, Fang, additional, Lai, Yongqi, additional, Lin, Zheguang, additional, Zhou, Fangjian, additional, Chen, Hao, additional, Chan, Hsiao Chang, additional, Tsang, Shirley, additional, Theodorescu, Dan, additional, Li, Yingrui, additional, Zhang, Xiuqing, additional, Wang, Jian, additional, Yang, Huanming, additional, Gui, Yaoting, additional, Wang, Jun, additional, and Cai, Zhiming, additional

Published
2013
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