25 results on '"Morgan, Margaret B."'
Search Results
2. Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer
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Lee, Sanghoon, Zhao, Li, Rojas, Christine, Bateman, Nicholas W., Yao, Hui, Lara, Olivia D., Celestino, Joseph, Morgan, Margaret B., Nguyen, Tri V., Conrads, Kelly A., Rangel, Kelly M., Dood, Robert L., Hajek, Richard A., Fawcett, Gloria L., Chu, Randy A., Wilson, Katlin, Loffredo, Jeremy L., Viollet, Coralie, Jazaeri, Amir A., Dalgard, Clifton L., Mao, Xizeng, Song, Xingzhi, Zhou, Ming, Hood, Brian L., Banskota, Nirad, Wilkerson, Matthew D., Te, Jerez, Soltis, Anthony R., Roman, Kristin, Dunn, Andrew, Cordover, David, Eterovic, Agda Karina, Liu, Jinsong, Burks, Jared K., Baggerly, Keith A., Fleming, Nicole D., Lu, Karen H., Westin, Shannon N., Coleman, Robert L., Mills, Gordon B., Casablanca, Yovanni, Zhang, Jianhua, Conrads, Thomas P., Maxwell, George L., Futreal, P. Andrew, and Sood, Anil K.
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- 2020
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3. Phase II Trial of Pembrolizumab in Combination with Chemotherapy for Frontline Treatment of Advanced Epithelial Ovarian Cancer
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How, Jeffrey Andrew, primary, Dang, Minghao, additional, Lee, Sanghoon, additional, Fellman, Bryan, additional, Westin, Shannon N., additional, Sood, Anil, additional, Fleming, Nicole D., additional, Shafer, Aaron, additional, Yuan, Ying, additional, Liu, Jinsong, additional, Zhao, Li, additional, Celestino, Joseph, additional, Hajek, Richard, additional, Morgan, Margaret B., additional, Parra, Edwin Roger, additional, Fernandez, Caddie D. Laberiano, additional, Arrechedera, Claudio A., additional, Solis, Luisa, additional, Schmeler, Kathleen, additional, Nick, Alpa, additional, Lu, Karen H., additional, Coleman, Robert, additional, Wang, Linghua, additional, and Jazaeri, Amir A., additional
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- 2024
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4. Next-generation sequencing identifies rare variants associated with Noonan syndrome
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Chen, Peng-Chieh, Yin, Jiani, Yu, Hui-Wen, Yuan, Tao, Fernandez, Minerva, Yung, Christina K, Trinh, Quang M, Peltekova, Vanya D, Reid, Jeffrey G, Tworog-Dube, Erica, Morgan, Margaret B, Muzny, Donna M, Stein, Lincoln, McPherson, John D, Roberts, Amy E, Gibbs, Richard A, Neel, Benjamin G, and Kucherlapati, Raju
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Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Genetics ,Congenital Structural Anomalies ,Rare Diseases ,Pediatric ,Neurosciences ,Brain Disorders ,Clinical Research ,2.1 Biological and endogenous factors ,Detection ,screening and diagnosis ,Aetiology ,4.1 Discovery and preclinical testing of markers and technologies ,Alleles ,Genetic Association Studies ,High-Throughput Nucleotide Sequencing ,Humans ,MAP Kinase Kinase 1 ,MAP Kinase Signaling System ,Mutation ,Neurofibromin 1 ,Noonan Syndrome ,ras Proteins ,human genetics ,developmental diseases ,whole exome sequencing ,PTPN11 ,RAS - Abstract
Noonan syndrome (NS) is a relatively common genetic disorder, characterized by typical facies, short stature, developmental delay, and cardiac abnormalities. Known causative genes account for 70-80% of clinically diagnosed NS patients, but the genetic basis for the remaining 20-30% of cases is unknown. We performed next-generation sequencing on germ-line DNA from 27 NS patients lacking a mutation in the known NS genes. We identified gain-of-function alleles in Ras-like without CAAX 1 (RIT1) and mitogen-activated protein kinase kinase 1 (MAP2K1) and previously unseen loss-of-function variants in RAS p21 protein activator 2 (RASA2) that are likely to cause NS in these patients. Expression of the mutant RASA2, MAP2K1, or RIT1 alleles in heterologous cells increased RAS-ERK pathway activation, supporting a causative role in NS pathogenesis. Two patients had more than one disease-associated variant. Moreover, the diagnosis of an individual initially thought to have NS was revised to neurofibromatosis type 1 based on an NF1 nonsense mutation detected in this patient. Another patient harbored a missense mutation in NF1 that resulted in decreased protein stability and impaired ability to suppress RAS-ERK activation; however, this patient continues to exhibit a NS-like phenotype. In addition, a nonsense mutation in RPS6KA3 was found in one patient initially diagnosed with NS whose diagnosis was later revised to Coffin-Lowry syndrome. Finally, we identified other potential candidates for new NS genes, as well as potential carrier alleles for unrelated syndromes. Taken together, our data suggest that next-generation sequencing can provide a useful adjunct to RASopathy diagnosis and emphasize that the standard clinical categories for RASopathies might not be adequate to describe all patients.
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- 2014
5. Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution
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Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, Thornton, Kevin, Todd, Melissa J., Chen, Rui, Meisel, Richard P., Couronne, Olivier, Hua, Sujun, Smith, Mark A., Bussemaker, Harmen J., van Batenburg, Marinus F., Howells, Sally L., Scherer, Steven E., Sodergren, Erica, Matthews, Beverly B., Crosby, Madeline A., Schroeder, Andrew J., Ortiz-Barrientos, Daniel, Rives, Catherine M., Metzker, Michael L., Muzny, Donna M., Scott, Graham, Steffen, David, Wheeler, David A., Worley, Kim C., Havlak, Paul, Durbin, K. James, Egan, Amy, Gill, Rachel, Hume, Jennifer, Morgan, Margaret B., Miner, George, Hamilton, Cerissa, Huang, Yanmei, Waldron, Lenee, Verduzco, Daniel, Blankenburg, Kerstin P., Dubchak, Inna, Noor, Mohamed A.F., Anderson, Wyatt, White, Kevin P., Clark, Andrew G., Schaeffer, Stephen W., Gelbart, William, Weinstock, George M., and Gibbs, Richard A.
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Applied life sciences - Abstract
The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.
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- 2004
6. Abstract 5738: Transcriptomic profiles of response to neoadjuvant chemotherapy in patients with high-grade serous ovarian cancer
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Lee, Sanghoon, primary, Zhao, Li, additional, Fleming, Nicole D., additional, Celestino, Joseph, additional, Hajek, Richard A., additional, Morgan, Margaret B., additional, Liu, Yan, additional, Westin, Shannon N., additional, Jazaeri, Amir A., additional, Liu, Jinsong, additional, Zhang, Jianhua, additional, Futreal, P Andrew, additional, and Sood, Anil K., additional
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- 2022
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7. Abstract 2200: NF1 copy number alterations in clinically-defined subsets of high-grade serous ovarian cancers
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Lee, Sanghoon, primary, Zhao, Li, additional, Celestino, Joseph, additional, Hajek, Richard A., additional, Morgan, Margaret B., additional, Kim, Mark S., additional, Westin, Shannon N., additional, Jazaeri, Amir A., additional, Fleming, Nicole D., additional, Liu, Jinsong, additional, Zhang, Jianhua, additional, Futreal, P Andrew, additional, and Sood, Anil K., additional
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- 2021
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8. Somatic mutations affect key pathways in lung adenocarcinoma
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Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, Sougnez, Carrie, Greulich, Heidi, Muzny, Donna M., Morgan, Margaret B., Fulton, Lucinda, Fulton, Robert S., Zhang, Qunyuan, Wendl, Michael C., Lawrence, Michael S., Larson, David E., Chen, Ken, Dooling, David J., Sabo, Aniko, Hawes, Alicia C., Shen, Hua, Jhangiani, Shalini N., Lewis, Lora R., Hall, Otis, Zhu, Yiming, Mathew, Tittu, Ren, Yanru, Yao, Jiqiang, Scherer, Steven E., Clerc, Kerstin, Metcalf, Ginger A., Ng, Brian, Milosavljevic, Aleksandar, Gonzalez-Garay, Manuel L., Osborne, John R., Meyer, Rick, Shi, Xiaoqi, Tang, Yuzhu, Koboldt, Daniel C., Lin, Ling, Abbott, Rachel, Miner, Tracie L., Pohl, Craig, Fewell, Ginger, Haipek, Carrie, Schmidt, Heather, Dunford-Shore, Brian H., Kraja, Aldi, Crosby, Seth D., Sawyer, Christopher S., Vickery, Tammi, Sander, Sacha, Robinson, Jody, Winckler, Wendy, Baldwin, Jennifer, Chirieac, Lucian R., Dutt, Amit, Fennell, Tim, Hanna, Megan, Johnson, Bruce E., Onofrio, Robert C., Thomas, Roman K., Tonon, Giovanni, Weir, Barbara A., Zhao, Xiaojun, Ziaugra, Liuda, Zody, Michael C., Giordano, Thomas, Orringer, Mark B., Roth, Jack A., Spitz, Margaret R., Wistuba, Ignacio I., Ozenberger, Bradley, Good, Peter J., Chang, Andrew C., Beer, David G., Watson, Mark A., Ladanyi, Marc, Broderick, Stephen, Yoshizawa, Akihiko, Travis, William D., Pao, William, Province, Michael A., Weinstock, George M., Varmus, Harold E., Gabriel, Stacey B., Lander, Eric S., Gibbs, Richard A., Meyerson, Matthew, and Wilson, Richard K.
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Gene mutations -- Research -- Physiological aspects -- Genetic aspects ,Nucleotide sequencing -- Research -- Physiological aspects -- Genetic aspects ,Adenocarcinoma -- Genetic aspects -- Research -- Care and treatment -- Prognosis -- Diagnosis ,DNA sequencing -- Research -- Physiological aspects -- Genetic aspects ,Lung cancer -- Genetic aspects -- Research -- Care and treatment -- Diagnosis -- Prognosis ,Environmental issues ,Science and technology ,Zoology and wildlife conservation ,Diagnosis ,Care and treatment ,Physiological aspects ,Genetic aspects ,Research ,Prognosis - Abstract
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations [...]
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- 2008
9. The finished DNA sequence of human chromosome 12
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Scherer, Steven E., Muzny, Donna M., Buhay, Christian J., Chen, Rui, Cree, Andrew, Ding, Yan, Dugan-Rocha, Shannon, Gill, Rachel, Gunaratne, Preethi, Harris, R. Alan, Hawes, Alicia C., Hernandez, Judith, Hodgson, Anne V., Hume, Jennifer, Jackson, Andrew, Khan, Ziad Mohid, Kovar-Smith, Christie, Lewis, Lora R., Lozado, Ryan J., Metzker, Michael L., Milosavljevic, Aleksandar, Miner, George R., Montgomery, Kate T., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Lovering, Ruth C., Wheeler, David A., Worley, Kim C., Yuan, Yi, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clerc-Blankenburg, Kerstin P., Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Draper, Heather, Gonzalez-Garay, Manuel L., Havlak, Paul, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Li, Li, Li, Zhangwan, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Pasternak, Shiran, Perez, Lesette M., Plopper, Farah J. H., Santibanez, Jireh, Shen, Hua, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Qiaoyan, Williams, Gabrielle A., Zhang, JingKun, Zhou, Jianling, Nelson, David, Kucherlapati, Raju, Weinstock, George, and Gibbs, Richard A.
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- 2006
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10. The DNA sequence, annotation and analysis of human chromosome 3
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Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, Sudbrak, Ralf, Buhay, Christian J., Chen, Rui, Cree, Andrew, Ding, Yan, Dugan-Rocha, Shannon, Gill, Rachel, Gunaratne, Preethi, Harris, R. Alan, Hawes, Alicia C., Hernandez, Judith, Hodgson, Anne V., Hume, Jennifer, Jackson, Andrew, Khan, Ziad Mohid, Kovar-Smith, Christie, Lewis, Lora R., Lozado, Ryan J., Metzker, Michael L., Milosavljevic, Aleksandar, Miner, George R., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Wei, Sharon, Wheeler, David A., Wright, Mathew W., Worley, Kim C., Yuan, Ye, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clendenning, James, Clerc-Blankenburg, Kerstin P., Chen, Runsheng, Chen, Zhu, Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Dong, Wei, Draper, Heather, Ernst, Stephen, Fu, Gang, Gonzalez-Garay, Manuel L., Garcia, Dawn K., Gillett, Will, Gu, Jun, Hao, Bailin, Haugen, Eric, Havlak, Paul, He, Xin, Hennig, Steffen, Hu, Songnian, Huang, Wei, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Kube, Michael, Levy, Ruth, Li, Zhangwan, Liu, Bin, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Palmeiri, Anthony, Pasternak, Shiran, Perez, Lesette M., Phelps, Karen A., Plopper, Farah J. H., Qiang, Boqin, Raymond, Christopher, Rodriguez, Ruben, Saenphimmachak, Channakhone, Santibanez, Jireh, Shen, Hua, Shen, Yan, Subramanian, Sandhya, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Jian, Wang, Jun, Wang, Qiaoyan, Williams, Gabrielle A., Wong, Gane K.-S., Yao, Zhijian, Zhang, JingKun, Zhang, Xiuqing, Zhao, Guoping, Zhou, Jianling, Zhou, Yang, contributors, further, Nelson, David, Lehrach, Hans, Reinhardt, Richard, Naylor, Susan L., Yang, Huanming, Olson, Maynard, Weinstock, George, and Gibbs, Richard A.
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Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Donna M. Muzny [1]; Steven E. Scherer (corresponding author) [1]; Rajinder Kaul [2]; Jing Wang [3]; Jun Yu [3]; Ralf Sudbrak [4, 5]; Christian J. Buhay [1]; Rui Chen [...]
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- 2006
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11. Comprehensive molecular characterization of human colon and rectal cancer
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Muzny, Donna M., Bainbridge, Matthew N., Chang, Kyle, Dinh, Huyen H., Drummond, Jennifer A., Fowler, Gerald, Kovar, Christie L., Lewis, Lora R., Morgan, Margaret B., Newsham, Irene F., Reid, Jeffrey G., Santibanez, Jireh, Shinbrot, Eve, Trevino, Lisa R., Wu, Yuan-Qing, Wang, Min, Gunaratne, Preethi, Donehower, Lawrence A., Creighton, Chad J., Wheeler, David A., Gibbs, Richard A., Lawrence, Michael S., Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S., Gabriel, Stacey, Getz, Gad, Ding, Li, Fulton, Robert S., Koboldt, Daniel C., Wylie, Todd, Walker, Jason, Dooling, David J., Fulton, Lucinda, Delehaunty, Kim D., Fronick, Catrina C., Demeter, Ryan, Mardis, Elaine R., Wilson, Richard K., Chu, Andy, Chun, Hye-Jung E., Mungall, Andrew J., Pleasance, Erin, Robertson, Gordon A., Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron S. N., Chuah, Eric, Coope, Robin J. N., Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Hirst, Martin, Holt, Robert A., Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Schein, Jacqueline E., Slobodan, Jared R., Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven J. M., Marra, Marco A., Bass, Adam J., Ramos, Alex H., Saksena, Gordon, Cherniack, Andrew D., Schumacher, Stephen E., Tabak, Barbara, Carter, Scott L., Pho, Nam H., Nguyen, Huy, Onofrio, Robert C., Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Meyerson, Matthew, Protopopov, Alexei, Zhang, Juinhua, Hadjipanayis, Angela, Lee, Eunjung, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Sathiamoorthy, Narayanan, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Xiao, Yonghong, Lee, Semin, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Auman, Todd J., Hoadley, Katherine A., Du, Ying, Wilkerson, Matthew D., Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J., Topal, Michael D., Tan, Donghui, Waring, Scot, Buda, Elizabeth, Walsh, Jesse, Jones, Corbin D., Mieczkowski, Piotr A., Singh, Darshan, Wu, Junyuan, Gulabani, Anisha, Dolina, Peter, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Matthew, Mose, Lisle E., Jefferys, Stuart R., Balu, Saianand, O’Connor, Brian D., Prins, Jan F., Chiang, Derek Y., Hayes, Neil D., Perou, Charles M., Hinoue, Toshinori, Weisenberger, Daniel J., Maglinte, Dennis T., Pan, Fei, Berman, Benjamin P., Van Den Berg, David J., Shen, Hui, Triche, Timothy, Jr, Baylin, Stephen B., Laird, Peter W., Noble, Michael, Voet, Doug, Gehlenborg, Nils, DiCara, Daniel, Wu, Chang-Jiun, Yingchun Liu, Spring, Zhou, Lihua, Lin, Pei, Park, Richard W., Nazaire, Marc-Danie, Robinson, Jim, Thorvaldsdottir, Helga, Mesirov, Jill, Thorsson, Vesteinn, Reynolds, Sheila M., Bernard, Brady, Kreisberg, Richard, Lin, Jake, Iype, Lisa, Bressler, Ryan, Erkkilä, Timo, Gundapuneni, Madhumati, Liu, Yuexin, Norberg, Adam, Robinson, Tom, Yang, Da, Zhang, Wei, Shmulevich, Ilya, de Ronde, Jorma J., Schultz, Nikolaus, Cerami, Ethan, Ciriello, Giovanni, Goldberg, Arthur P., Gross, Benjamin, Jacobsen, Anders, Gao, Jianjiong, Kaczkowski, Bogumil, Sinha, Rileen, Aksoy, Arman B., Antipin, Yevgeniy, Reva, Boris, Shen, Ronglai, Taylor, Barry S., Chan, Timothy A., Ladanyi, Marc, Sander, Chris, Akbani, Rehan, Zhang, Nianxiang, Broom, Bradley M., Casasent, Tod, Unruh, Anna, Wakefield, Chris, Hamilton, Stanley R., Cason, Craig R., Baggerly, Keith A., Weinstein, John N., Haussler, David, Benz, Christopher C., Stuart, Joshua M., Benz, Stephen C., Sanborn, Zachary J., Vaske, Charles J., Zhu, Jingchun, Szeto, Christopher, Scott, Gary K., Yau, Christina, Ng, Sam, Goldstein, Ted, Ellrott, Kyle, Collisson, Eric, Cozen, Aaron E., Zerbino, Daniel, Wilks, Christopher, Craft, Brian, Spellman, Paul, Penny, Robert, Shelton, Troy, Hatfield, Martha, Morris, Scott, Yena, Peggy, Shelton, Candace, Sherman, Mark, Paulauskis, Joseph, Gastier-Foster, Julie M., Bowen, Jay, Ramirez, Nilsa C., Black, Aaron, Pyatt, Robert, Wise, Lisa, White, Peter, Bertagnolli, Monica, Brown, Jen, Chu, Gerald C., Czerwinski, Christine, Denstman, Fred, Dhir, Rajiv, Dörner, Arnulf, Fuchs, Charles S., Guillem, Jose G., Iacocca, Mary, Juhl, Hartmut, Kaufman, Andrew, Kohl, Bernard, III, Van Le, Xuan, Mariano, Maria C., Medina, Elizabeth N., Meyers, Michael, Nash, Garrett M., Paty, Phillip B., Petrelli, Nicholas, Rabeno, Brenda, Richards, William G., Solit, David, Swanson, Pat, Temple, Larissa, Tepper, Joel E., Thorp, Richard, Vakiani, Efsevia, Weiser, Martin R., Willis, Joseph E., Witkin, Gary, Zeng, Zhaoshi, Zinner, Michael J., Zornig, Carsten, Jensen, Mark A., Sfeir, Robert, Kahn, Ari B., Chu, Anna L., Kothiyal, Prachi, Wang, Zhining, Snyder, Eric E., Pontius, Joan, Pihl, Todd D., Ayala, Brenda, Backus, Mark, Walton, Jessica, Whitmore, Jon, Baboud, Julien, Berton, Dominique L., Nicholls, Matthew C., Srinivasan, Deepak, Raman, Rohini, Girshik, Stanley, Kigonya, Peter A., Alonso, Shelley, Sanbhadti, Rashmi N., Barletta, Sean P., Greene, John M., Pot, David A., Mills Shaw, Kenna R., Dillon, Laura A. L., Buetow, Ken, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin, Fielding, Peter, Schaefer, Carl, Sheth, Margi, Yang, Liming, Guyer, Mark S., Ozenberger, Bradley A., Palchik, Jacqueline D., Peterson, Jane, Sofia, Heidi J., and Thomson, Elizabeth
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- 2012
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12. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
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Elsik, Christine G., Tellam, Ross L., Worley, Kim C., Gibbs, Richard A., Elsik, Christine G., Tellam, Ross L, Gibbs, Richard A., Muzny, Donna M., Weinstock, George M., Adelson, David L, Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Guigó, Roderic, Hamernik, Debora L., Kappes, Steve M., Lewin, Harris A, Lynn, David J., Nicholas, Frank W., Reymond, Alexandre, Rijnkels, Monique, Skow, Loren C., Tellam, Ross L, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Kappes, Steve M., Schook, Lawrence, Skow, Loren C., Weinstock, George M., Womack, James, Alioto, Tyler, Antonarakis, Stylianos E., Astashyn, Alex, Chapple, Charles E., Chen, Hsiu-Chuan, Chrast, Jacqueline, Câmara, Francisco, Elsik, Christine G., Ermolaeva, Olga, Guigó, Roderic, Henrichsen, Charlotte N., Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Landrum, Melissa, Maglott, Donna, Pruitt, Kim, Reymond, Alexandre, Sapojnikov, Victor, Searle, Stephen M., Solovyev, Victor, Souvorov, Alexandre, Ucla, Catherine, Weinstock, George M., Wyss, Carine, Alioto, Tyler, Antonarakis, Stylianos E., Chapple, Charles E., Chrast, Jacqueline, Câmara, Francisco, Guigó, Roderic, Henrichsen, Charlotte N., Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Anzola, Juan M., Gerlach, Daniel, Zdobnov, Evgeny M., Elhaik, Eran, Elsik, Christine G., Graur, Dan, Reese, Justin T., Adelson, David L., Edgar, Robert C., McEwan, John C., Payne, Gemma M., Raison, Joy M., Junier, Thomas, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Chrast, Jacqueline, Eyras, Eduardo, Henrichsen, Charlotte N., Plass, Mireya, Reymond, Alexandre, Donthu, Ravikiran, Larkin, Denis M., Lewin, Harris A., Nicholas, Frank W., Elnitski, Laura, Larkin, Denis M., Lewin, Harris A., Reecy, James, Yang, Mary Q., Adelson, David L, Chen, Lin, Cheng, Ze, Chitko-McKown, Carol G., Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Liu, George E., Matukumalli, Lakshmi K., Song, Jiuzhou, Zhu, Bin, Elsik, Christine G., Lynn, David J., Reese, Justin T., Bradley, Daniel G., Brinkman, Fiona S.L, Lau, Lilian P.L., Lynn, David J., Whiteside, Matthew D., Tellam, Ross L, Walker, Angela, Wheeler, Thomas T., Casey, Theresa, German, Bruce J., Lemay, Danielle G., Lynn, David J., Maqbool, Nauman J., Molenaar, Adrian J., Rijnkels, Monique, Lewin, Harris A., Seo, Seongwon, Stothard, Paul, Baldwin, Cynthia L., Baxter, Rebecca, Brinkmeyer-Langford, Candice L., Brown, Wendy C., Childers, Christopher P., Connelley, Timothy, Ellis, Shirley A., Fritz, Krista, Glass, Elizabeth J., Herzig, Carolyn T.A., livanainen, Antti, Lahmers, Kevin K., Skow, Loren C., Bennett, Anna K., Childers, Christopher P., Dickens, Michael C., Elsik, Christine G., Gilbert, James G.R., Hagen, Darren E., Reese, Justin T., Salih, Hanni, Aerts, Jan, Caetano, Alexandre R., Dalrymple, Brian, Elsik, Christine G., Fernando Garcia, Jose, Gibbs, Richard A., Gill, Clare A., Hamernik, Debora L, Hiendleder, Stefan G., Memili, Erdogan, Nicholas, Frank W., Reecy, James, Rijnkels, Monique, Skow, Loren C., Spurlock, Diane, Stothard, Paul, Tellam, Ross L, Weinstock, George M., Williams, John L, Worley, Kim C., Alexander, Lee, Brownstein, Michael J., Guan, Leluo, Holt, Robert A., Jones, Steven J.M., Marra, Marco A., Moore, Richard, Moore, Stephen S., Roberts, Andy, Taniguchi, Masaaki, Waterman, Richard C., Chacko, Joseph, Chandrabose, Mimi M., Cree, Andy, Diep Dao, Marvin, Dinh, Huyen H., Ayiesha Gabisi, Ramatu, Hines, Sandra, Hume, Jennifer, Jhangiani, Shalini N., Joshi, Vandita, Kovar, Christie L., Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Muzny, Donna M., Bich Nguyen, Ngoc, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Buhay, Christian, Ding, Yan, Dugan-Rocha, Shannon, Herdandez, Judith, Holder, Michael, Sabo, Aniko, Egan, Amy, Goodell, Jason, Wilczek-Boney, Katarzyna, Fowler, Gerald R., Edward Hitchens, Matthew, Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Chiu, Readman, Jones, Steven J.M., Marra, Marco A., Schein, Jacqueline E., James Durbin, K., Havlak, Paul, Jiang, Huaiyang, Liu, Yue, Qin, Xiang, Ren, Yanru, Shen, Yufeng, Song, Henry, Weinstock, George M., Worley, Kim C., Nicole Bell, Stephanie, Davis, Clay, Jolivet Johnson, Angela, Lee, Sandra, Nazareth, Lynne V., Patel, Bella Mayurkumar, Pu, Ling-Ling, Vattathil, Selina, Williams, Rex Lee, Jr., Curry, Stacey, Hamilton, Cerissa, Sodergren, Erica, Nazareth, Lynne V., Wheeler, David A., Adelson, David L, Aerts, Jan, Barris, Wes, Bennett, Gary L, Dalrymple, Brian, Eggen, André, Gill, Clare A., Green, Ronnie D., Harhay, Gregory P., Hobbs, Matthew, Jann, Oliver, Kappes, Steve M., Keele, John W., Kent, Matthew P., Larkin, Denis M., Lewin, Harris A., Lien, Sigbjørn, McEwan, John C., McKay, Stephanie D., McWilliam, Sean, Moore, Stephen S., Nicholas, Frank W., Payne, Gemma M., Ratnakumar, Abhirami, Salih, Hanni, Schnabel, Robert D., Smith, Timothy, Snelling, Warren M., Sonstegard, Tad S., Stone, Roger T., Sugimoto, Yoshikazu, Takasuga, Akiko, Taylor, Jeremy F., Tellam, Ross L., Van Tassell, Curtis P., Williams, John L, MacNeil, Michael D., Abatepaulo, Antonio R.R., Abbey, Colette A., Aerts, Jan, Ahola, Virpi, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Bahadue, Suria M., Baldwin, Cynthia L., Baxter, Rebecca, Bennett, Anna K., Biase, Fernando H., Boldt, Clayton R., Brinkmeyer-Langford, Candice L, Brown, Wendy C., Caetano, Alexandre R., Carroll, Jeffery A., Carvalho, Wanessa A, Casey, Theresa, Cervelatti, Eliane P., Chacko, Elsa, Chapin, Jennifer E., Cheng, Ye, Childers, Christopher P., Choi, Jungwoo, Colley, Adam J., Connelley, Timothy, de Campos, Tatiana A., De Donato, Marcos, de Miranda Santos, Isabel K.F., de Oliveira, Carlo J.F., Deobald, Heather, Devinoy, Eve, Dickens, Michael C., Donohue, Kaitlin E., Dovc, Peter, Eberlein, Annett, Ellis, Shirley A., Fitzsimmons, Carolyn J., Franzin, Alessandra M., Fritz, Krista, Garcia, Gustavo R., Fernando Garcia, Jose, Genini, Sem, German, Bruce J., Gilbert, James G.R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Grant, Jason R., Greaser, Marion L., Green, Jonathan A., Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Harrow, Jennifer L, Hart, Elizabeth A., Hastings, Nicola, Hernandez, Marta, Herzig, Carolyn T.A., Hiendleder, Stefan G., Hobbs, Matthew, Hu, Zhi-Liang, livanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Kapetis, Dimos, Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kolbehdari, Davood, Kumar, Charu G., Kumar, Dinesh, Leach, Richard, Lee, Justin C-M, Lemay, Danielle G., Li, Changxi, Liu, George E., Logan, Krystin M., Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Mazza, Raffaele, McLean, Kim L, Medrano, Juan F., Memili, Erdogan, Molenaar, Adrian J., Moreno, Barbara T., Moré, Daniela D., Muntean, Carl T., Nandakumar, Hari P., Nogueira, Marcelo F.G., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C.P., Poli, Mario A., Poslusny, Nathan, Rachagani, Satyanarayana, Ranganathan, Shoba, Razpet, Andrej, Reecy, James, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Sando, Lillian, Schmutz, Sheila M., Seo, Seongwon, Shen, Libing, Sherman, Laura, Skow, Loren C., Southey, Bruce R., Spurlock, Diane, Strandberg Lutzow, Ylva, Sweedler, Jonathan V., Tammen, Imke, Taniguchi, Masaaki, Tellam, Ross L, Telugu, Bhanu Prakash V.L, Urbanski, Jennifer M., Utsunomiya, Yuri T., Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Weikard, Rosemarie, Welsh, Thomas H., Jr., Wheeler, Thomas T., White, Stephen N., Williams, John L, Wilming, Laurens G., Wunderlich, Kris R., Yang, Jianqi, and Zhao, Feng-Qi
- Published
- 2009
13. Characterizing the cancer genome in lung adenocarcinoma
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Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, Lin, William M., Province, Michael A., Kraja, Aldi, Johnson, Laura A., Shah, Kinjal, Sato, Mitsuo, Thomas, Roman K., Barletta, Justine A., Borecki, Ingrid B., Broderick, Stephen, Chang, Andrew C., Chiang, Derek Y., Chirieac, Lucian R., Cho, Jeonghee, Fujii, Yoshitaka, Gazdar, Adi F., Giordano, Thomas, Greulich, Heidi, Hanna, Megan, Johnson, Bruce E., Kris, Mark G., Lash, Alex, Lin, Ling, Lindeman, Neal, Mardis, Elaine R., McPherson, John D., Minna, John D., Morgan, Margaret B., Nadel, Mark, Orringer, Mark B., Osborne, John R., Ozenberger, Brad, Ramos, Alex H., Robinson, James, Roth, Jack A., Rusch, Valerie, Sasaki, Hidefumi, Shepherd, Frances, Sougnez, Carrie, Spitz, Margaret R., Tsao, Ming-Sound, Twomey, David, Verhaak, Roel G. W., Weinstock, George M., Wheeler, David A., Winckler, Wendy, Yoshizawa, Akihiko, Yu, Soyoung, Zakowski, Maureen F., Zhang, Qunyuan, Beer, David G., Wistuba, Ignacio I., Watson, Mark A., Garraway, Levi A., Ladanyi, Marc, Travis, William D., Pao, William, Rubin, Mark A., Gabriel, Stacey B., Gibbs, Richard A., Varmus, Harold E., Wilson, Richard K., Lander, Eric S., and Meyerson, Matthew
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- 2007
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14. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
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Richards, Stephen, Metzker, Michael L., Bettencourt, Brian R., Yue Liu, Muzny, Donna M., Hradecky, Pavel, Scott, Graham, Letovsky, Stan, Nielsen, Rasmus, Meisel, Richard P., Thornton, Kevin, Steffen, David, Hubisz, Melissa J., Wheeler, David A., Rui Chen, Worley, Kim C., Couronne, Olivier, Durbin, K. James, Sujun Hua, Egan, Amy, Smith, Mark A., Gill, Rachel, Peili Zhang, Hume, Jennifer, Jing Liu, Havlak, Paul, Bussemaker, Harmen J., Sodergren, Erica, Batenburg, Marinus F. van, Morgan, Margaret B., Howells, Sally L., Miner, George, Scherer, Steven E., Matthews, Beverly B., Hamilton, Cerissa, Schroeder, Andrew J., Crosby, Madeline A., Yanmei Huang, Ortiz-Barrientos, Daniel, Waldron, Lenee, Rives, Catharine M., and Verduzco, Daniel
- Subjects
Nucleotide sequence -- Research ,Drosophila -- Genetic aspects ,Genetic research ,Health - Abstract
The genome of a second Drosophila species, Drosophila pseudoobscura, is sequenced and is compared to the genome sequence of Drosophila melanogaster, a primary model organism. A repetitive sequence is found in the Drosophila pseudoobscura genome at many junctions between adjacent syntentic blocks.
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- 2005
15. Abstract 128: Comprehensive molecular characterization of 412 muscle-invasive urothelial bladder carcinomas: final analysis of The Cancer Genome Atlas (TCGA) project
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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
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- 2016
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16. Comparison of DNA and RNA analyte extraction and melanin removal methods from formalin-fixed, paraffin-embedded (FFPE) melanoma.
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Haydu, Lauren Elaine, primary, Calderone, Tiffany L, additional, Miller, John, additional, Bassett, Roland L., additional, Joon, Aron, additional, Zhang, Jianhua, additional, Morgan, Margaret B., additional, Shaw, Kenna Rael, additional, Cooper, Zachary A, additional, Burton, Elizabeth M, additional, Siroy, Alan, additional, Wani, Khalida M, additional, Stingo, Franceso, additional, Baladandayuthapani, Veera, additional, Tetzlaff, Michael T., additional, Wargo, Jennifer Ann, additional, Lazar, Alexander J. F., additional, Davies, Michael A., additional, and Gershenwald, Jeffrey E., additional
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- 2015
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17. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
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Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, Levchenko, Tanya, Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, and Levchenko, Tanya
- Abstract
BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
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- 2011
18. Genome Sequence of the Pea Aphid Acyrthosiphon pisum
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Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne
- Abstract
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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- 2010
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19. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.
- Author
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Werren, John H, Richards, Stephen, Desjardins, Christopher A, Niehuis, Oliver, Gadau, Jürgen, Colbourne, John K, Beukeboom, Leo W, Desplan, Claude, Elsik, Christine G, Grimmelikhuijzen, Cornelis J P, Kitts, Paul, Lynch, Jeremy A, Murphy, Terence, Oliveira, Deodoro C S G, Smith, Christopher D, van de Zande, Louis, Worley, Kim C, Zdobnov, Evgeny M, Aerts, Maarten, Albert, Stefan, Anaya, Victor H, Anzola, Juan M, Barchuk, Angel R, Behura, Susanta K, Bera, Agata N, Berenbaum, May R, Bertossa, Rinaldo C, Bitondi, Márcia M G, Bordenstein, Seth R, Bork, Peer, Bornberg-Bauer, Erich, Brunain, Marleen, Cazzamali, Giuseppe, Chaboub, Lesley, Chacko, Joseph, Chavez, Dean, Childers, Christopher P, Choi, Jeong-Hyeon, Clark, Michael E, Claudianos, Charles, Clinton, Rochelle A, Cree, Andrew G, Cristino, Alexandre S, Dang, Phat M, Darby, Alistair C, de Graaf, Dirk C, Devreese, Bart, Dinh, Huyen H, Edwards, Rachel, Elango, Navin, Elhaik, Eran, Ermolaeva, Olga, Evans, Jay D, Foret, Sylvain, Fowler, Gerald R, Gerlach, Daniel, Gibson, Joshua D, Gilbert, Donald G, Graur, Dan, Gründer, Stefan, Hagen, Darren E, Han, Yi, Hauser, Frank, Hultmark, Dan, Hunter, Henry C, Hurst, Gregory D D, Jhangian, Shalini N, Jiang, Huaiyang, Johnson, Reed M, Jones, Andrew K, Junier, Thomas, Kadowaki, Tatsuhiko, Kamping, Albert, Kapustin, Yuri, Kechavarzi, Bobak, Kim, Jaebum, Kim, Jay, Kiryutin, Boris, Koevoets, Tosca, Kovar, Christie L, Kriventseva, Evgenia V, Kucharski, Robert, Lee, Heewook, Lee, Sandra L, Lees, Kristin, Lewis, Lora R, Loehlin, David W, Logsdon, John M, Lopez, Jacqueline A, Lozado, Ryan J, Maglott, Donna, Maleszka, Ryszard, Mayampurath, Anoop, Mazur, Danielle J, McClure, Marcella A, Moore, Andrew D, Morgan, Margaret B, Muller, Jean, Munoz-Torres, Monica C, Muzny, Donna M, Nazareth, Lynne V, Neupert, Susanne, Nguyen, Ngoc B, Nunes, Francis M F, Oakeshott, John G, Okwuonu, Geoffrey O, Pannebakker, Bart A, Pejaver, Vikas R, Peng, Zuogang, Pratt, Stephen C, Predel, Reinhard, Pu, Ling-Ling, Ranson, Hilary, Raychoudhury, Rhitoban, Rechtsteiner, Andreas, Reese, Justin T, Reid, Jeffrey G, Riddle, Megan, Robertson, Hugh M, Romero-Severson, Jeanne, Rosenberg, Miriam, Sackton, Timothy B, Sattelle, David B, Schlüns, Helge, Schmitt, Thomas, Schneider, Martina, Schüler, Andreas, Schurko, Andrew M, Shuker, David M, Simões, Zilá L P, Sinha, Saurabh, Smith, Zachary, Solovyev, Victor, Souvorov, Alexandre, Springauf, Andreas, Stafflinger, Elisabeth, Stage, Deborah E, Stanke, Mario, Tanaka, Yoshiaki, Telschow, Arndt, Trent, Carol, Vattathil, Selina, Verhulst, Eveline C, Viljakainen, Lumi, Wanner, Kevin W, Waterhouse, Robert M, Whitfield, James B, Wilkes, Timothy E, Williamson, Michael, Willis, Judith H, Wolschin, Florian, Wyder, Stefan, Yamada, Takuji, Yi, Soojin V, Zecher, Courtney N, Zhang, Lan, Gibbs, Richard A, Werren, John H, Richards, Stephen, Desjardins, Christopher A, Niehuis, Oliver, Gadau, Jürgen, Colbourne, John K, Beukeboom, Leo W, Desplan, Claude, Elsik, Christine G, Grimmelikhuijzen, Cornelis J P, Kitts, Paul, Lynch, Jeremy A, Murphy, Terence, Oliveira, Deodoro C S G, Smith, Christopher D, van de Zande, Louis, Worley, Kim C, Zdobnov, Evgeny M, Aerts, Maarten, Albert, Stefan, Anaya, Victor H, Anzola, Juan M, Barchuk, Angel R, Behura, Susanta K, Bera, Agata N, Berenbaum, May R, Bertossa, Rinaldo C, Bitondi, Márcia M G, Bordenstein, Seth R, Bork, Peer, Bornberg-Bauer, Erich, Brunain, Marleen, Cazzamali, Giuseppe, Chaboub, Lesley, Chacko, Joseph, Chavez, Dean, Childers, Christopher P, Choi, Jeong-Hyeon, Clark, Michael E, Claudianos, Charles, Clinton, Rochelle A, Cree, Andrew G, Cristino, Alexandre S, Dang, Phat M, Darby, Alistair C, de Graaf, Dirk C, Devreese, Bart, Dinh, Huyen H, Edwards, Rachel, Elango, Navin, Elhaik, Eran, Ermolaeva, Olga, Evans, Jay D, Foret, Sylvain, Fowler, Gerald R, Gerlach, Daniel, Gibson, Joshua D, Gilbert, Donald G, Graur, Dan, Gründer, Stefan, Hagen, Darren E, Han, Yi, Hauser, Frank, Hultmark, Dan, Hunter, Henry C, Hurst, Gregory D D, Jhangian, Shalini N, Jiang, Huaiyang, Johnson, Reed M, Jones, Andrew K, Junier, Thomas, Kadowaki, Tatsuhiko, Kamping, Albert, Kapustin, Yuri, Kechavarzi, Bobak, Kim, Jaebum, Kim, Jay, Kiryutin, Boris, Koevoets, Tosca, Kovar, Christie L, Kriventseva, Evgenia V, Kucharski, Robert, Lee, Heewook, Lee, Sandra L, Lees, Kristin, Lewis, Lora R, Loehlin, David W, Logsdon, John M, Lopez, Jacqueline A, Lozado, Ryan J, Maglott, Donna, Maleszka, Ryszard, Mayampurath, Anoop, Mazur, Danielle J, McClure, Marcella A, Moore, Andrew D, Morgan, Margaret B, Muller, Jean, Munoz-Torres, Monica C, Muzny, Donna M, Nazareth, Lynne V, Neupert, Susanne, Nguyen, Ngoc B, Nunes, Francis M F, Oakeshott, John G, Okwuonu, Geoffrey O, Pannebakker, Bart A, Pejaver, Vikas R, Peng, Zuogang, Pratt, Stephen C, Predel, Reinhard, Pu, Ling-Ling, Ranson, Hilary, Raychoudhury, Rhitoban, Rechtsteiner, Andreas, Reese, Justin T, Reid, Jeffrey G, Riddle, Megan, Robertson, Hugh M, Romero-Severson, Jeanne, Rosenberg, Miriam, Sackton, Timothy B, Sattelle, David B, Schlüns, Helge, Schmitt, Thomas, Schneider, Martina, Schüler, Andreas, Schurko, Andrew M, Shuker, David M, Simões, Zilá L P, Sinha, Saurabh, Smith, Zachary, Solovyev, Victor, Souvorov, Alexandre, Springauf, Andreas, Stafflinger, Elisabeth, Stage, Deborah E, Stanke, Mario, Tanaka, Yoshiaki, Telschow, Arndt, Trent, Carol, Vattathil, Selina, Verhulst, Eveline C, Viljakainen, Lumi, Wanner, Kevin W, Waterhouse, Robert M, Whitfield, James B, Wilkes, Timothy E, Williamson, Michael, Willis, Judith H, Wolschin, Florian, Wyder, Stefan, Yamada, Takuji, Yi, Soojin V, Zecher, Courtney N, Zhang, Lan, and Gibbs, Richard A
- Abstract
We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
- Published
- 2010
- Full Text
- View/download PDF
20. Whole-Genome Sequencing for Optimized Patient Management
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Bainbridge, Matthew N., primary, Wiszniewski, Wojciech, additional, Murdock, David R., additional, Friedman, Jennifer, additional, Gonzaga-Jauregui, Claudia, additional, Newsham, Irene, additional, Reid, Jeffrey G., additional, Fink, John K., additional, Morgan, Margaret B., additional, Gingras, Marie-Claude, additional, Muzny, Donna M., additional, Hoang, Linh D., additional, Yousaf, Shahed, additional, Lupski, James R., additional, and Gibbs, Richard A., additional
- Published
- 2011
- Full Text
- View/download PDF
21. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
- Author
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Renfree, Marilyn B, primary, Papenfuss, Anthony T, additional, Deakin, Janine E, additional, Lindsay, James, additional, Heider, Thomas, additional, Belov, Katherine, additional, Rens, Willem, additional, Waters, Paul D, additional, Pharo, Elizabeth A, additional, Shaw, Geoff, additional, Wong, Emily SW, additional, Lefèvre, Christophe M, additional, Nicholas, Kevin R, additional, Kuroki, Yoko, additional, Wakefield, Matthew J, additional, Zenger, Kyall R, additional, Wang, Chenwei, additional, Ferguson-Smith, Malcolm, additional, Nicholas, Frank W, additional, Hickford, Danielle, additional, Yu, Hongshi, additional, Short, Kirsty R, additional, Siddle, Hannah V, additional, Frankenberg, Stephen R, additional, Chew, Keng Y, additional, Menzies, Brandon R, additional, Stringer, Jessica M, additional, Suzuki, Shunsuke, additional, Hore, Timothy A, additional, Delbridge, Margaret L, additional, Patel, Hardip, additional, Mohammadi, Amir, additional, Schneider, Nanette Y, additional, Hu, Yanqiu, additional, O'Hara, William, additional, Al Nadaf, Shafagh, additional, Wu, Chen, additional, Feng, Zhi-Ping, additional, Cocks, Benjamin G, additional, Wang, Jianghui, additional, Flicek, Paul, additional, Searle, Stephen MJ, additional, Fairley, Susan, additional, Beal, Kathryn, additional, Herrero, Javier, additional, Carone, Dawn M, additional, Suzuki, Yutaka, additional, Sugano, Sumio, additional, Toyoda, Atsushi, additional, Sakaki, Yoshiyuki, additional, Kondo, Shinji, additional, Nishida, Yuichiro, additional, Tatsumoto, Shoji, additional, Mandiou, Ion, additional, Hsu, Arthur, additional, McColl, Kaighin A, additional, Lansdell, Benjamin, additional, Weinstock, George, additional, Kuczek, Elizabeth, additional, McGrath, Annette, additional, Wilson, Peter, additional, Men, Artem, additional, Hazar-Rethinam, Mehlika, additional, Hall, Allison, additional, Davis, John, additional, Wood, David, additional, Williams, Sarah, additional, Sundaravadanam, Yogi, additional, Muzny, Donna M, additional, Jhangiani, Shalini N, additional, Lewis, Lora R, additional, Morgan, Margaret B, additional, Okwuonu, Geoffrey O, additional, Ruiz, San J, additional, Santibanez, Jireh, additional, Nazareth, Lynne, additional, Cree, Andrew, additional, Fowler, Gerald, additional, Kovar, Christie L, additional, Dinh, Huyen H, additional, Joshi, Vandita, additional, Jing, Chyn, additional, Lara, Fremiet, additional, Thornton, Rebecca, additional, Chen, Lei, additional, Deng, Jixin, additional, Liu, Yue, additional, Shen, Joshua Y, additional, Song, Xing-Zhi, additional, Edson, Janette, additional, Troon, Carmen, additional, Thomas, Daniel, additional, Stephens, Amber, additional, Yapa, Lankesha, additional, Levchenko, Tanya, additional, Gibbs, Richard A, additional, Cooper, Desmond W, additional, Speed, Terence P, additional, Fujiyama, Asao, additional, M Graves, Jennifer A, additional, O'Neill, Rachel J, additional, Pask, Andrew J, additional, Forrest, Susan M, additional, and Worley, Kim C, additional
- Published
- 2011
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- View/download PDF
22. Next-generation sequencing identifies rare variants associated with Noonan syndrome.
- Author
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Peng-Chieh Chen, Jiani Yin, Hui-Wen Yu, Tao Yuan, Fernandez, Minerva, Yung, Christina K., Trinh, Quang M., Peltekova, Vanya D., Reid, Jeffrey G., Tworog-Dube, Erica, Morgan, Margaret B., Muzny, Donna M., Stein, Lincoln, McPherson, John D., Roberts, Amy E., Gibbs, Richard A., Neel, Benjamin G., and Kucherlapati, Raju
- Subjects
NOONAN syndrome ,GENETIC disorders ,HEART diseases ,COFFIN-Lowry syndrome ,MITOGENS - Abstract
Noonan syndrome (NS) is a relatively common genetic disorder, characterized by typical facies, short stature, developmental delay, and cardiac abnormalities. Known causative genes account for 70-80% of clinically diagnosed NS patients, but the genetic basis for the remaining 20-30% of cases is unknown. We performed next-generation sequencing on germ-line DNA from 27 NS patients lacking a mutation in the known NS genes. We identified gain-of-function alleles in Ras-like without CAAX 1 (RIT1) and mitogen-activated protein kinase kinase 1 (MAP2K1) and previously unseen loss-of-function variants in RAS p21 protein activator 2 (RASA2) that are likely to cause NS in these patients. Expression of the mutant RASA2, MAP2K1, or RIT1 alleles in heterologous cells increased RAS-ERK pathway activation, supporting a causative role in NS pathogenesis. Two patients had more than one disease-associated variant. Moreover, the diagnosis of an individual initially thought to have NS was revised to neurofibromatosis type 1 based on an NF1 nonsense mutation detected in this patient. Another patient harbored a missense mutation in NF1 that resulted in decreased protein stability and impaired ability to suppress RAS-ERK activation; however, this patient continues to exhibit a NS-like phe-notype. In addition, a nonsense mutation in RPS6KA3 was found in one patient initially diagnosed with NS whose diagnosis was later revised to Coffin-Lowry syndrome. Finally, we identified other potential candidates for new NS genes, as well as potential carrier alleles for unrelated syndromes. Taken together, our data suggest that next-generation sequencing can provide a useful adjunct to RASopathy diagnosis and emphasize that the standard clinical categories for RASopathies might not be adequate to describe all patients. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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- View/download PDF
23. Somatic mutations affect key pathways in lung adenocarcinoma.
- Author
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Li Ding, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, Sougnez, Carrie, Greulich, Heidi, Muzny, Donna M., Morgan, Margaret B., Fulton, Lucinda, Fulton, Robert S., Qunyuan Zhang, Wendl, Michael C., Lawrence, Michael S., Larson, David E., Chen, Ken, Dooling, David J., Sabo, Aniko, and Hawes, Alicia C.
- Subjects
ADENOCARCINOMA ,CANCER ,HISTOPATHOLOGY ,TUMORS ,GENETIC mutation ,DNA - Abstract
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers—including NF1, APC, RB1 and ATM—and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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24. Pembrolizumab plus chemotherapy in frontline treatment of advanced ovarian cancer: Clinical and translational results from a phase 2 trial.
- Author
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How JA, Dang M, Lee S, Fellman B, Westin SN, Sood AK, Fleming ND, Shafer A, Yuan Y, Liu J, Zhao L, Celestino J, Hajek R, Morgan MB, Parra ER, Laberiano Fernandez CD, Arrechedera CA, Solis Soto LM, Schmeler KM, Nick A, Lu KH, Coleman R, Wang L, and Jazaeri AA
- Abstract
Background: The efficacy and feasibility of pembrolizumab combined with chemotherapy in frontline management of advanced high-grade epithelial ovarian cancer (EOC) is unknown. Additionally, modification of the tumor microenvironment following neoadjuvant therapy is not well understood., Methods: In this single-arm phase 2 trial (this study was registered at ClinicalTrials.gov: NCT02520154), eligible patients received up to 4 cycles of neoadjuvant chemotherapy followed by interval cytoreduction, 3 cycles of adjuvant intravenous carboplatin/weekly paclitaxel/pembrolizumab, and finally maintenance pembrolizumab until progression or toxicity (maximum 20 cycles). The primary endpoint was progression-free survival (PFS). Secondary endpoints included feasibility, toxicity, and overall survival (OS). PD-L1 staining, multiplex immunofluorescence staining, RNA sequencing, reverse-phase protein array analyses were performed on pre- and post-chemotherapy samples., Findings: Thirty-one eligible patients were enrolled. Median PFS and OS was 14.88 (95% CI 12.39-23.00) and 57.43 months (95% CI 30.88-not reached), respectively. Among those with PD-L1 combined positive score (CPS) ≥10, the median PFS and OS were not reached compared to those with CPS <10 (10.50 and 30.90 months, respectively). Feasibility was met, with all patients completing their planned adjuvant cycles. Treatment discontinuation due to immune-related toxicity occurred in 6 patients (20%). Chemotherapy resulted in an infiltration of anti-tumor immune cells in the tumor microenvironment. Samples of patients with the best PFS demonstrated increased expression of NF-κB, TGF-β, and β-catenin signaling., Conclusions: Pembrolizumab with chemotherapy was feasible and resulted in PFS within the historical range for this EOC population. Patients with CPS ≥10 may benefit more from this regimen, and future studies should investigate this potential biomarker., Funding: This investigator-initiated trial was funded by Merck., Competing Interests: Declaration of interests S.N.W. reports grants from NIH, GOG Foundation, Cotinga Pharmaceuticals, Bayer, and ArQule during the conduct of the study. She also reports grants and personal fees from AstraZeneca, Clovis Oncology, GlaxoSmithKline/Tesaro, Roche/Genentech, and Novartis. She reports personal fees from Merck, Pfizer, Eisai, CIrculogene, Zentalis, and Agenus outside the submitted work. N.D.F. reports personal fees from Tesaro, Pfizer, Bristol Myers Squibb, and GlaxoSmithKline outside the submitted work. A.K.S. discloses the following competing interests: consulting (Merck, GSK, ImmunoGen, Iylon, Kiyatec, Astra Zeneca, Onxeo) and shareholder (BioPath). R.C. reports the following competing interests: consulting (Clovis Oncology, Genentech/Roche, AstraZeneca/MedImmune, Genmab, OncoMed, Immunogen, AbbVie, Agenus, Novocure, Merck, OncXerna Therapeutics, Alkermes, Gradalis, GlaxoSmithKline, Alkermes, Eisai, GOG Foundation, Karyopharm Therapeutics), employment (Vanium Group, US Oncology Network), leadership (Onsexo), stock and other ownership interests (McKesson/US Oncology Network), and research funding (AstraZeneca/MedImmune, Clovis Oncology, Merck, Roche/Genentech, Immunogen, Mirati Therapeutics, Amgen, Pfizer, Lilly, Regeneron, Alkermes, Karyopharm Therapeutics). A.A.J. reports personal fees from Gerson Lehrman Group, Guidepoint, Iovance advisory board, NuProbe, Simcere, PACT Pharma, Genentech-Roche, Eisai, Agenus, and Macrogenics. He also reports grants from AstraZeneca, Bristol Myers Squibb, Iovance, Aravive, Pfizer, Immatics US, Eli Lilly, and Merck, and stock/stock options from AvengeBio outside the submitted work., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
25. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.
- Author
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Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, and Gibbs RA
- Subjects
- Animals, Arthropods parasitology, DNA Methylation, DNA Transposable Elements, Female, Gene Transfer, Horizontal, Genes, Insect, Genetic Speciation, Genetic Variation, Host-Parasite Interactions, Insect Proteins genetics, Insect Proteins metabolism, Insect Viruses genetics, Insecta genetics, Male, Molecular Sequence Data, Quantitative Trait Loci, Recombination, Genetic, Sequence Analysis, DNA, Wasp Venoms chemistry, Wasp Venoms toxicity, Wasps physiology, Wolbachia genetics, Biological Evolution, Genome, Insect, Wasps genetics
- Abstract
We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
- Published
- 2010
- Full Text
- View/download PDF
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