Search

Your search keyword '"Simpson, Jared T"' showing total 36 results
Start Over Author "Simpson, Jared T" Search Limiters Peer Reviewed
36 results on '"Simpson, Jared T"'

4. Nanopore native RNA sequencing of a human poly(A) transcriptome

Author

Workman, Rachael E., Tang, Alison D., Tang, Paul S., Jain, Miten, Tyson, John R., Razaghi, Roham, Zuzarte, Philip C., Gilpatrick, Timothy, Payne, Alexander, Quick, Joshua, Sadowski, Norah, Holmes, Nadine, de Jesus, Jaqueline Goes, Jones, Karen L., Soulette, Cameron M., Snutch, Terrance P., Loman, Nicholas, Paten, Benedict, Loose, Matthew, Simpson, Jared T., Olsen, Hugh E., Brooks, Angela N., Akeson, Mark, and Timp, Winston

Published
2019
Full Text
View/download PDF

7. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Author

Quick, Joshua, Grubaugh, Nathan D, Pullan, Steven T, Claro, Ingra M, Smith, Andrew D, Gangavarapu, Karthik, Oliveira, Glenn, Robles-Sikisaka, Refugio, Rogers, Thomas F, Beutler, Nathan A, Burton, Dennis R, Lewis-Ximenez, Lia Laura, de Jesus, Jaqueline Goes, Giovanetti, Marta, Hill, Sarah C, Black, Allison, Bedford, Trevor, Carroll, Miles W, Nunes, Marcio, Alcantara, Jr., Luiz Carlos, Sabino, Ester C, Baylis, Sally A, Faria, Nuno R, Loose, Matthew, Simpson, Jared T, Pybus, Oliver G, Andersen, Kristian G, and Loman, Nicholas J

Published
2017
Full Text
View/download PDF

8. Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

Author

Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu, Li, Yilong, Wilson, Gavin W., Connor, Ashton A., Denroche, Robert E., Liang, Sheng-Ben, Brown, Andrew M. K., Kim, Jaeseung C., Wang, Tao, Simpson, Jared T., Beck, Timothy, Borgida, Ayelet, Buchner, Nicholas, Chadwick, Dianne, Hafezi-Bakhtiari, Sara, Dick, John E., Heisler, Lawrence, Hollingsworth, Michael A., Ibrahimov, Emin, Jang, Gun Ho, Johns, Jeremy, Jorgensen, Lars G. T., Law, Calvin, Ludkovski, Olga, Lungu, Ilinca, Ng, Karen, Pasternack, Danielle, Petersen, Gloria M., Shlush, Liran I., Timms, Lee, Tsao, Ming-Sound, Wilson, Julie M., Yung, Christina K., Zogopoulos, George, Bartlett, John M. S., Alexandrov, Ludmil B., Real, Francisco X., Cleary, Sean P., Roehrl, Michael H., McPherson, John D., Stein, Lincoln D., Hudson, Thomas J., Campbell, Peter J., and Gallinger, Steven

Published
2017
Full Text
View/download PDF

9. Real-time, portable genome sequencing for Ebola surveillance

Author

Quick, Joshua, Loman, Nicholas J., Duraffour, Sophie, Simpson, Jared T., Severi, Ettore, Cowley, Lauren, Bore, Joseph Akoi, Koundouno, Raymond, Dudas, Gytis, Mikhail, Amy, Ouédraogo, Nobila, Afrough, Babak, Bah, Amadou, Baum, Jonathan H. J., Becker-Ziaja, Beate, Boettcher, Jan Peter, Cabeza-Cabrerizo, Mar, Camino-Sánchez, Álvaro, Carter, Lisa L., Doerrbecker, Juliane, Enkirch, Theresa, Dorival, Isabel García-, Hetzelt, Nicole, Hinzmann, Julia, Holm, Tobias, Kafetzopoulou, Liana Eleni, Koropogui, Michel, Kosgey, Abigael, Kuisma, Eeva, Logue, Christopher H., Mazzarelli, Antonio, Meisel, Sarah, Mertens, Marc, Michel, Janine, Ngabo, Didier, Nitzsche, Katja, Pallasch, Elisa, Patrono, Livia Victoria, Portmann, Jasmine, Repits, Johanna Gabriella, Rickett, Natasha Y., Sachse, Andreas, Singethan, Katrin, Vitoriano, Inês, Yemanaberhan, Rahel L., Zekeng, Elsa G., Racine, Trina, Bello, Alexander, Sall, Amadou Alpha, Faye, Ousmane, Faye, Oumar, Magassouba, NʼFaly, Williams, Cecelia V., Amburgey, Victoria, Winona, Linda, Davis, Emily, Gerlach, Jon, Washington, Frank, Monteil, Vanessa, Jourdain, Marine, Bererd, Marion, Camara, Alimou, Somlare, Hermann, Camara, Abdoulaye, Gerard, Marianne, Bado, Guillaume, Baillet, Bernard, Delaune, Déborah, Nebie, Koumpingnin Yacouba, Diarra, Abdoulaye, Savane, Yacouba, Pallawo, Raymond Bernard, Gutierrez, Giovanna Jaramillo, Milhano, Natacha, Roger, Isabelle, Williams, Christopher J., Yattara, Facinet, Lewandowski, Kuiama, Taylor, James, Rachwal, Phillip, Turner, Daniel J., Pollakis, Georgios, Hiscox, Julian A., Matthews, David A., Shea, Matthew K. Oʼ, Johnston, Andrew McD., Wilson, Duncan, Hutley, Emma, Smit, Erasmus, Di Caro, Antonino, Wölfel, Roman, Stoecker, Kilian, Fleischmann, Erna, Gabriel, Martin, Weller, Simon A., Koivogui, Lamine, Diallo, Boubacar, Keïta, Sakoba, Rambaut, Andrew, Formenty, Pierre, Günther, Stephan, and Carroll, Miles W.

Published
2016
Full Text
View/download PDF

10. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
Full Text
View/download PDF

13. Complex landscapes of somatic rearrangement in human breast cancer genomes

Author

Stephens, Philip J., McBride, David J., Lin, Meng-Lay, Varela, Ignacio, Pleasance, Erin D., Simpson, Jared T., Stebbings, Lucy A., Leroy, Catherine, Edkins, Sarah, Mudie, Laura J., Greenman, Chris D., Jia, Mingming, Latimer, Calli, Teague, Jon W., Lau, King Wai, Burton, John, Quail, Michael A., Swerdlow, Harold, Churcher, Carol, Natrajan, Rachael, Sieuwerts, Anieta M., Martens, John W.M., Silver, Daniel P., Langerod, Anita, Russnes, Hege E.G., Foekens, John A., Reis-Filho, Jorge S., van 't Veer, Laura, Richardson, Andrea L., Borresen-Dales, Anne-Lise, Campbell, Peter J., Futreal, P. Andrew, and Stratton, Michael R.

Subjects
DNA -- Genetic aspects, Cancer -- Genetic aspects, Somatic cells -- Research, Breast cancer -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Genetic aspects, Research
Abstract

Multiple somatic rearrangements are often found in cancer genomes; however, the underlying processes of rearrangement and their contribution to cancer development are poorly characterized. Here we use a paired-end sequencing strategy to identify somatic rearrangements in breast cancer genomes. There are more rearrangements in some breast cancers than previously appreciated. Rearrangements are more frequent over gene footprints and most are intrachromosomal. Multiple rearrangement architectures are present, but tandem duplications are particularly common in some cancers, perhaps reflecting a specific defect in DNA maintenance. Short overlapping sequences at most rearrangement junctions indicate that these have been mediated by non-homologous end-joining DNA repair, although varying sequence patterns indicate that multiple processes of this type are operative. Several expressed in-frame fusion genes were identified but none was recurrent. The study provides a new perspective on cancer genomes, highlighting the diversity of somatic rearrangements and their potential contribution to cancer development., Cytogenetic studies over several decades have shown that somatic rearrangements, in particular chromosomal translocations, occur in many human cancer genomes (1-3). The prevalence of rearrangements is, however, variable with some [...]

Published
2009
Full Text
View/download PDF

14. Insights into hominid evolution from the gorilla genome sequence

Author

Scally, Aylwyn, Dutheil, Julien Y., Hillier, LaDeana W., Jordan, Gregory E., Goodhead, Ian, Herrero, Javier, Hobolth, Asger, Lappalainen, Tuuli, Mailund, Thomas, Marques-Bonet, Tomas, McCarthy, Shane, Montgomery, Stephen H., Schwalie, Petra C., Tang, Amy Y., Ward, Michelle C., Xue, Yali, Yngvadottir, Bryndis, Alkan, Can, Andersen, Lars N., Ayub, Qasim, Ball, Edward V., Beal, Kathryn, Bradley, Brenda J., Chen, Yuan, Clee, Chris M., Fitzgerald, Stephen, Graves, Tina A., Gu, Yong, Heath, Paul, Heger, Andreas, Karakoc, Emre, Kolb-Kokocinski, Anja, Laird, Gavin K., Lunter, Gerton, Meader, Stephen, Mort, Matthew, Mullikin, James C., Munch, Kasper, O’Connor, Timothy D., Phillips, Andrew D., Prado-Martinez, Javier, Rogers, Anthony S., Sajjadian, Saba, Schmidt, Dominic, Shaw, Katy, Simpson, Jared T., Stenson, Peter D., Turner, Daniel J., Vigilant, Linda, Vilella, Albert J., Whitener, Weldon, Zhu, Baoli, Cooper, David N., de Jong, Pieter, Dermitzakis, Emmanouil T., Eichler, Evan E., Flicek, Paul, Goldman, Nick, Mundy, Nicholas I., Ning, Zemin, Odom, Duncan T., Ponting, Chris P., Quail, Michael A., Ryder, Oliver A., Searle, Stephen M., Warren, Wesley C., Wilson, Richard K., Schierup, Mikkel H., Rogers, Jane, Tyler-Smith, Chris, and Durbin, Richard

Published
2012
Full Text
View/download PDF

16. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

Author

Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu, Li, Yilong, Wilson, Gavin W., Connor, Ashton A., Denroche, Robert E., Liang, Sheng-Ben, Brown, Andrew M. K., Kim, Jaeseung C., Wang, Tao, Simpson, Jared T., Beck, Timothy, Borgida, Ayelet, Buchner, Nicholas, Chadwick, Dianne, Hafezi-Bakhtiari, Sara, Dick, John E., Heisler, Lawrence, Hollingsworth, Michael A., Ibrahimov, Emin, Jang, Gun Ho, Johns, Jeremy, Jorgensen, Lars G. T., Law, Calvin, Ludkovski, Olga, Lungu, Ilinca, Ng, Karen, Pasternack, Danielle, Petersen, Gloria M., Shlush, Liran I., Timms, Lee, Tsao, Ming-Sound, Wilson, Julie M., Yung, Christina K., Zogopoulos, George, Bartlett, John M. S., Alexandrov, Ludmil B., Real, Francisco X., Cleary, Sean P., Roehrl, Michael H., McPherson, John D., Stein, Lincoln D., Hudson, Thomas J., Campbell, Peter J., and Gallinger, Steven

Subjects
Cancer genetics -- Analysis, Pancreatic cancer -- Research -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Faiyaz Notta (corresponding author) [1]; Michelle Chan-Seng-Yue [1]; Mathieu Lemire [1]; Yilong Li [2]; Gavin W. Wilson [1]; Ashton A. Connor [1]; Robert E. Denroche [1]; Sheng-Ben Liang [3]; [...]

Published
2016
Full Text
View/download PDF

17. Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada.

Author

Sjaarda, Calvin P., Guthrie, Jennifer L., Mubareka, Samira, Simpson, Jared T., Hamelin, Bettina, Wong, Henry, Mortimer, Leanne, Slinger, Robert, McArthur, Andrew G., Desjardins, Marc, McGeer, Allison, Mazzulli, Tony, Douchant, Katya, Brabant-Kirwan, Danielle, Fattouh, Ramzi, Campigotto, Aaron, Patel, Samir N., Fittipaldi, Nahuel, Colautti, Robert I., and Shethi, Prameet M.

Published
2021
Full Text
View/download PDF

19. Detection of Structural Rearrangements in Embryos.

Author

Madjunkova, Svetlana, Simpson, Jared T., and Librach, Clifford

Subjects
*EMBRYOS, *SINGLE nucleotide polymorphisms
Abstract

The article offers information about the carriers of balanced chromosomal rearrangements (BCRs) are at risk for infertility, recurrent miscarriages, and abnormal offspring because of unbalanced rearrangements. It mentions the prevention of vertical transmission of the BCR to future generations and the detection of cryptic potential disease causing imbalances, complex rearrangements, or gene disruptions at breakpoint sites.

Published
2020
Full Text
View/download PDF

21. Shotgun metagenomics, from sampling to analysis.

Author

Quince, Christopher, Walker, Alan W, Simpson, Jared T, Loman, Nicholas J, and Segata, Nicola

Abstract

Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offers biotechnological promise in therapeutic discovery and innovative ways to synthesize products using microbial factories and can pinpoint the contributions of microorganisms to planetary, animal and human health. [ABSTRACT FROM AUTHOR]

Published
2017
Full Text
View/download PDF

22. Nanocall: an open source basecaller for Oxford Nanopore sequencing data.

Author

David, Matei, Dursi, L. J., Yao, Delia, Boutros, Paul C., and Simpson, Jared T.

Subjects
NUCLEOTIDE sequencing, CLOUD computing, ESCHERICHIA coli, GENOMES
Abstract

Motivation: The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls. Results: To allow offline and private analysis of MinION data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. Using R7.3 chemistry, on two E.coli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have ~68% identity, directly comparable to Metrichor '1D' data. Further, Nanocall is efficient, processing ~2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a MinION sequencing run in real time. Metrichor provides the ability to integrate the '1D' sequencing of template and complement strands of a single DNA molecule, and create a '2D' read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data. [ABSTRACT FROM AUTHOR]

Published
2017
Full Text
View/download PDF

23. The Theory and Practice of Genome Sequence Assembly.

Author

Simpson, Jared T. and Pop, Mihai

Subjects
*NUCLEOTIDE sequencing, *DNA analysis, *ALGORITHMS, *ALGEBRA, *BIOINFORMATICS
Abstract

The current genomic revolution was made possible by joint advances in genome sequencing technologies and computational approaches for analyzing sequence data. The close interaction between biologists and computational scientists is perhaps most apparent in the development of approaches for sequencing entire genomes, a feat that would not be possible without sophisticated computational tools called genome assemblers (short for genome sequence assemblers). Here, we survey the key developments in algorithms for assembling genome sequences since the development of the first DNA sequencing methods more than 35 years ago. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

26. Trait Variation in Yeast Is Defined by Population History.

Author

Warringer, Jonas, Zörgo, Enikö, Cubillos, Francisco A., Zia, Amin, Gjuvsland, Arne, Simpson, Jared T., Forsmark, Annabelle, Durbin, Richard, Omholt, Stig W., Louis, Edward J., Liti, Gianni, Moses, Alan, and Blomberg, Anders

Abstract

A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism. [ABSTRACT FROM AUTHOR]

Published
2011
Full Text
View/download PDF

27. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Author

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

Abstract

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

Published
2015
Full Text
View/download PDF

28. A complete bacterial genome assembled de novo using only nanopore sequencing data.

Author

Loman, Nicholas J, Quick, Joshua, and Simpson, Jared T

Subjects
BACTERIAL genomes, NUCLEOTIDE sequence, NANOPORES, NUCLEOTIDES, ESCHERICHIA coli
Abstract

We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data. Our method has three stages: (i) overlaps are detected between reads and then corrected by a multiple-alignment process; (ii) corrected reads are assembled using the Celera Assembler; and (iii) the assembly is polished using a probabilistic model of the signal-level data. The assembly reconstructs gene order and has 99.5% nucleotide identity. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

31. Efficient de novo assembly of large genomes using compressed data structures.

Author

Simpson, Jared T. and Durbin, Richard

Subjects
*GENOMES, *GENETICS, *GENOMICS, *ALGORITHMS, *HUMAN chromosomes
Abstract

De novo genome sequence assembly is important both to generate new sequence assemblies for previously uncharacterized genomes and to identify the genome sequence of individuals in a reference-unbiased way. We present memory efficient data structures and algorithms for assembly using the FM-index derived from the compressed Burrows-Wheeler transform, and a new assembler based on these called SGA (String Graph Assembler). We describe algorithms to error-correct, assemble, and scaffold large sets of sequence data. SGA uses the overlap-based string graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply parallelizable. We demonstrate the error correction and assembly performance of SGA on 1.2 billion sequence reads from a human genome, which we are able to assemble using 54 GB of memory. The resulting contigs are highly accurate and contiguous, while covering 95% of the reference genome (excluding contigs <200 bp in length). Because of the low memory requirements and parallelization without requiring inter-process communication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome on a low-end computing cluster. [ABSTRACT FROM AUTHOR]

Published
2012
Full Text
View/download PDF

32. Efficient construction of an assembly string graph using the FM-index.

Author

Simpson, Jared T. and Durbin, Richard

Subjects
*GENE mapping, *GRAPH algorithms, *COMPUTER software, *GENETIC techniques, *GRAPH theory, *ALGORITHMS
Abstract

Motivation: Sequence assembly is a difficult problem whose importance has grown again recently as the cost of sequencing has dramatically dropped. Most new sequence assembly software has started by building a de Bruijn graph, avoiding the overlap-based methods used previously because of the computational cost and complexity of these with very large numbers of short reads. Here, we show how to use suffix array-based methods that have formed the basis of recent very fast sequence mapping algorithms to find overlaps and generate assembly string graphs asymptotically faster than previously described algorithms. [ABSTRACT FROM PUBLISHER]

Published
2010
Full Text
View/download PDF

33. Assemblathon 1: A competitive assessment of de novo short read assembly methods.

Author

Earl, Dent, Bradnam, Keith, John, John St., Darling, Aaron, Dawei Lin, Fass, Joseph, Hung On Ken Yu, Buffalo, Vince, Zerbino, Daniel R., Diekhans, Mark, Ngan Nguyen, Ariyaratne, Pramila Nuwantha, Wing-Kin Sung, Zemin Ning, Haimel, Matthias, Simpson, Jared T., Fonseca, Nuno A., Birol, İnanç, Docking, T. Roderick, and Ho, Isaac Y.

Subjects
*GENOMICS, *MOLECULAR genetics, *GENOMES, *HAPLOTYPES, *GENETIC research
Abstract

Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/. [ABSTRACT FROM AUTHOR]

Published
2013

34. Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.

Author

Zhu, Helen, Uusküla-Reimand, Liis, Isaev, Keren, Wadi, Lina, Alizada, Azad, Shuai, Shimin, Huang, Vincent, Aduluso-Nwaobasi, Dike, Paczkowska, Marta, Abd-Rabbo, Diala, Ocsenas, Oliver, Liang, Minggao, Thompson, J. Drew, Li, Yao, Ruan, Luyao, Krassowski, Michal, Dzneladze, Irakli, Simpson, Jared T., Lupien, Mathieu, and Stein, Lincoln D.

Subjects
*SOMATIC mutation, *CANCER genes, *CHROMATIN, *GENETIC mutation, *GENE regulatory networks, *CELL proliferation, *GENOMES
Abstract

A comprehensive catalog of cancer driver mutations is essential for understanding tumorigenesis and developing therapies. Exome-sequencing studies have mapped many protein-coding drivers, yet few non-coding drivers are known because genome-wide discovery is challenging. We developed a driver discovery method, ActiveDriverWGS, and analyzed 120,788 cis -regulatory modules (CRMs) across 1,844 whole tumor genomes from the ICGC-TCGA PCAWG project. We found 30 CRMs with enriched SNVs and indels (FDR < 0.05). These frequently mutated regulatory elements (FMREs) were ubiquitously active in human tissues, showed long-range chromatin interactions and mRNA abundance associations with target genes, and were enriched in motif-rewiring mutations and structural variants. Genomic deletion of one FMRE in human cells caused proliferative deficiencies and transcriptional deregulation of cancer genes CCNB1IP1 , CDH1 , and CDKN2B , validating observations in FMRE-mutated tumors. Pathway analysis revealed further sub-significant FMREs at cancer genes and processes, indicating an unexplored landscape of infrequent driver mutations in the non-coding genome. • Pan-cancer driver analysis highlights frequently mutated regulatory elements (FMREs) • FMREs are active in many tissues and interact with genes via chromatin loops • FMRE deletion in human cells caused alterations in pathway activity and proliferation • Additional less-frequent regulatory mutations are enriched at cancer genes and pathways Cancer is driven by somatic mutations in critical genes, but few non-coding drivers are known. In a pan-cancer analysis, Zhu et al. identified frequently mutated, multi-tissue regulatory elements with chromatin loops to distal genes. Genomic deletion of one region caused deregulation of cancer genes, pathways, and proliferation in human cells. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

35. Assemblathon 1: A competitive assessment of de novo short read assembly methods.

Author

Earl, Dent, Bradnam, Keith, John, John St., Darling, Aaron, Lin, Dawei, Fass, Joseph, Yu, Hung On Ken, Buffalo, Vince, Zerbino, Daniel R., Diekhans, Mark, Nguyen, Ngan, Ariyaratne, Pramila Nuwantha, Sung, Wing-Kin, Ning, Zemin, Haime, Matthias, Simpson, Jared T., Fonseca, Nuno A., Docking, T. Roderick, Holl, Isaac Y., and Rokhsar, Daniel S.

Subjects
*GENOMICS, *MOLECULAR genetics, *DIPLOIDY, *GENETIC research, *NUCLEOTIDE sequence, *PLANT chromosomes
Abstract

Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated I llumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. [ABSTRACT FROM AUTHOR]

Published
2011
Full Text
View/download PDF

36. Revealing the genetic structure of a trait by sequencing a population under selection.

Author

Parts, Leopold, Cubillos, Francisco A., Warringer, Jonas, Jain, Kanika, Salinas, Francisco, Bumpstead, Suzannah J., Molin, Mikael, Zia, Amin, Simpson, Jared T., Quail, Michael A., Moses, Alan, Louis, Edward J., Durbin, Richard, and Liti, Gianni

Subjects
*HUMAN genetics, *DNA, *PHENOTYPES, *PARENTS, *GENOMICS, *GENES
Abstract

One approach to understanding the genetic basis of traits is to study their pattern of inheritance among offspring of phenotypically different parents. Previously, such analysis has been limited by low mapping resolution, high labor costs, and large sample size requirements for detecting modest effects. Here, we present a novel approach to map trait loci using artificial selection. First, we generated populations of 10-100 million haploid and diploid segregants by crossing two budding yeast strains of different heat tolerance for up to 12 generations. We then subjected these large segregant pools to heat stress for up to 12 d, enriching for beneficial alleles. Finally, we sequenced total DNA from the pools before and during selection to measure the changes in parental allele frequency. We mapped 21 intervals with significant changes in genetic background in response to selection, which is several times more than found with traditional linkage methods. Nine of these regions contained two or fewer genes, yielding much higher resolution than previous genomic linkage studies. Multiple members of the RAS/cAMP signaling pathway were implicated, along with genes previously not annotated with heat stress response function. Surprisingly, at most selected loci, allele frequencies stopped changing before the end of the selection experiment, but alleles did not become fixed. Furthermore, we were able to detect the same set of trait loci in a population of diploid individuals with similar power and resolution, and observed primarily additive effects, similar to what is seen for complex trait genetics in other diploid organisms such as humans. [ABSTRACT FROM AUTHOR]

Published
2011
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results