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3. Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic “functional” symptomatology including pain, fatigue and gastrointestinal dysmotility

Author

Boles, Richard G., Hornung, Holly A., Moody, Alastair E., Ortiz, Thomas B., Wong, Stacey A., Eggington, Julie M., Stanley, Christine M., Gao, Mu, Zhou, Hongyi, McLaughlin, Stephen, Zare, Amir S., Sheldon, Katherine M., Skolnick, Jeffrey, and McKernan, Kevin J.

Published
2015
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5. Mutation in The Nuclear-Encoded Mitochondrial Isoleucyl–tRNA Synthetase IARS2 in Patients with Cataracts, Growth Hormone Deficiency with Short Stature, Partial Sensorineural Deafness, and Peripheral Neuropathy or with Leigh Syndrome

Author

Schwartzentruber, Jeremy, Buhas, Daniela, Majewski, Jacek, Sasarman, Florin, Papillon-Cavanagh, Simon, Thiffaut, Isabelle, Sheldon, Katherine M., Massicotte, Christine, Patry, Lysanne, Simon, Mariella, Zare, Amir S., McKernan, Kevin J., Consortium, FORGE Canada, Michaud, Jacques, Boles, Richard G., Deal, Cheri L., Desilets, Valerie, Shoubridge, Eric A., and Samuels, Mark E.

Published
2014
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6. Evolution of genes and genomes on the Drosophila phylogeny

Author

Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain

Abstract

Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]

Published
2007
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7. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Author

Jaillon, Olivier, Aury, Jean-Marc, Brunet, Frederic, Petit, Jean-Louis, Stange-Thomann, Nicole, Mauceli, Evan, Bouneau, Laurence, Fischer, Cecile, Ozouf-Costaz, Catherine, Bernot, Alain, Nicaud, Sophie, Jaffe, David, Fisher, Sheila, Lutfalla, Georges, Dossat, Carole, Segurens, Beatrice, Dasilva, Corinne, Salanoubat, Marcel, Levy, Michael, Boudet, Nathalie, Castellano, Sergi, Anthouard, Veronique, Jubin, Claire, Castelli, Vanina, Katinka, Michael, Vacherie, Benoit, Biemont, Christian, Skalli, Zineb, Cattolico, Laurence, Poulain, Julie, de Berardinis, Veronique, Cruaud, Corinne, Duprat, Simone, Brottier, Philippe, Coutanceau, Jean-Pierre, Gouzy, Jerome, Parra, Genis, Lardier, Guillaume, Chapple, Charles, McKernan, Kevin J., McEwan, Paul, Bosak, Stephanie, Kellis, Manolis, Volff, Jean-Nicolas, Guigo, Roderic, Zody, Michael C., Mesirov, Jill, Lindblad-Toh, Kerstin, Birren, Bruce, Nusbaum, Chad, Kahn, Daniel, Robinson-Rechavi, Marc, Laudet, Vincent, Schachter, Vincent, Quetier, Francis, Saurin, William, Scarpelli, Claude, Wincker, Patrick, Lander, Eric S., Weissenbach, Jean, and Roest Crollius, Hugues

Abstract

Author(s): Olivier Jaillon [1]; Jean-Marc Aury [1]; Frédéric Brunet [2]; Jean-Louis Petit [1]; Nicole Stange-Thomann [3]; Evan Mauceli [3]; Laurence Bouneau [1]; Cécile Fischer [1]; Catherine Ozouf-Costaz [4]; Alain Bernot [...]

Published
2004
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8. Initial sequencing and analysis of the human genome

Author

Lander, Eric S., Linton, Lauren M., Birren, Bruce, Nusbaum, Chad, Zody, Michael C., Baldwin, Jennifer, Devon, Keri, Dewar, Ken, Doyle, Michael, FitzHugh, William, Funke, Roel, Gage, Diane, Harris, Katrina, Heaford, Andrew, Howland, John, Kann, Lisa, Lehoczky, Jessica, LeVine, Rosie, McEwan, Paul, McKernan, Kevin, Meldrim, James, Mesirov, Jill P., Miranda, Cher, Morris, William, Naylor, Jerome, Raymond, Christina, Rosetti, Mark, Santos, Ralph, Sheridan, Andrew, Sougnez, Carrie, Stange-Thomann, Nicole, Stojanovic, Nikola, Subramanian, Aravind, Wyman, Dudley, Rogers, Jane, Sulston, John, Ainscough, Rachael, Beck, Stephan, Bentley, David, Burton, John, Clee, Christopher, Carter, Nigel, Coulson, Alan, Deadman, Rebecca, Deloukas, Panos, Dunham, Andrew, Dunham, Ian, Durbin, Richard, French, Lisa, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Humphray, Sean, Hunt, Adrienne, Jones, Matthew, Lloyd, Christine, McMurray, Amanda, Matthews, Lucy, Mercer, Simon, Milne, Sarah, Mullikin, James C., Mungall, Andrew, Plumb, Robert, Ross, Mark, Shownkeen, Ratna, Sims, Sarah, Waterston, Robert H., Wilson, Richard K., Hillier, LaDeana W., McPherson, John D., Marra, Marco A., Mardis, Elaine R., Fulton, Lucinda A., Chinwalla, Asif T., Pepin, Kymberlie H., Gish, Warren R., Chissoe, Stephanie L., Wendl, Michael C., Delehaunty, Kim D., Miner, Tracie L., Delehaunty, Andrew, Kramer, Jason B., Cook, Lisa L., Fulton, Robert S., Johnson, Douglas L., Minx, Patrick J., Clifton, Sandra W., Hawkins, Trevor, Branscomb, Elbert, Predki, Paul, Richardson, Paul, Wenning, Sarah, Slezak, Tom, Doggett, Norman, Cheng, Jan-Fang, Olsen, Anne, Lucas, Susan, Elkin, Christopher, Uberbacher, Edward, Frazier, Marvin, Gibbs, Richard A., Muzny, Donna M., Scherer, Steven E., Bouck, John B., Sodergren, Erica J., Worley, Kim C., Rives, Catherine M., Gorrell, James H., Metzker, Michael L., Naylor, Susan L., Kucherlapati, Raju S., Nelson, David L., Weinstock, George M., Sakaki, Yoshiyuki, Fujiyama, Asao, Hattori, Masahira, Yada, Tetsushi, Toyoda, Atsushi, Itoh, Takehiko, Kawagoe, Chiharu, Watanabe, Hidemi, Totoki, Yasushi, Taylor, Todd, Weissenbach, Jean, Heilig, Roland, Saurin, William, Artiguenave, Francois, Brottier, Philippe, Bruls, Thomas, Pelletier, Eric, Robert, Catherine, Wincker, Patrick, Rosenthal, Andre, Platzer, Matthias, Nyakatura, Gerald, Taudien, Stefan, Rump, Andreas, Smith, Douglas R., Doucette-Stamm, Lynn, Rubenfield, Marc, Weinstock, Keith, Lee, Hong Mei, Dubois, JoAnn, Yang, Huanming, Yu, Jun, Wang, Jian, Huang, Guyang, Gu, Jun, Hood, Leroy, Rowen, Lee, Madan, Anup, Qin, Shizen, Davis, Ronald W., Federspiel, Nancy A., Abola, A. Pia, Proctor, Michael J., Roe, Bruce A., Chen, Feng, Pan, Huaqin, Ramser, Juliane, Lehrach, Hans, Reinhardt, Richard, McCombie, W. Richard, de la Bastide, Melissa, Dedhia, Neilay, Blocker, Helmut, Hornischer, Klaus, Nordsiek, Gabriele, Agarwala, Richa, Aravind, L., Bailey, Jeffrey A., Bateman, Alex, Batzoglou, Serafim, Birney, Ewan, Bork, Peer, Brown, Daniel G., Burge, Christopher B., Cerutti, Lorenzo, Chen, Hsiu-Chuan, Church, Deanna, Clamp, Michele, Copley, Richard R., Doerks, Tobias, Eddy, Sean R., Eichler, Evan E., Furey, Terrence S., Galagan, James, Gilbert, James G. R., Harmon, Cyrus, Hayashizaki, Yoshihide, Haussler, David, Hermjakob, Henning, Hokamp, Karsten, Jang, Wonhee, Johnson, L. Steven, Jones, Thomas A., Kasif, Simon, Kaspryzk, Arek, Kennedy, Scot, Kent, W. James, Kitts, Paul, Koonin, Eugene V., Korf, Ian, Kulp, David, Lancet, Doron, Lowe, Todd M., McLysaght, Aoife, Mikkelsen, Tarjei, Moran, John V., Mulder, Nicola, Pollara, Victor J., Ponting, Chris P., Schuler, Greg, Schultz, Jorg, Slater, Guy, Smit, Arian F. A., Stupka, Elia, Szustakowki, Joseph, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Wallis, John, Wheeler, Raymond, Williams, Alan, Wolf, Yuri I., Wolfe, Kenneth H., Yang, Shiaw-Pyng, Yeh, Ru-Fang, Collins, Francis, Guyer, Mark S., Peterson, Jane, Felsenfeld, Adam, Wetterstrand, Kris A., Myers, Richard M., Schmutz, Jeremy, Dickson, Mark, Grimwood, Jane, Cox, David R., Olson, Maynard V., Kaul, Rajinder, Raymond, Christopher, Shimizu, Nobuyoshi, Kawasaki, Kazuhiko, Minoshima, Shinsei, Evans, Glen A., Athanasiou, Maria, Schultz, Roger, Patrinos, Aristides, and Morgan, Michael J.

Abstract

Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]

Published
2001
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9. An integrated semiconductor device enabling non-optical genome sequencing

Author

Rothberg, Jonathan M., Hinz, Wolfgang, Rearick, Todd M., Schultz, Jonathan, Mileski, William, Davey, Mel, Leamon, John H., Johnson, Kim, Milgrew, Mark J., Edwards, Matthew, Hoon, Jeremy, Simons, Jan F., Marran, David, Myers, Jason W., Davidson, John F., Branting, Annika, Nobile, John R., Puc, Bernard P., Light, David, Clark, Travis A., Huber, Martin, Branciforte, Jeffrey T., Stoner, Isaac B., Cawley, Simon E., Lyons, Michael, Fu, Yutao, Homer, Nils, Sedova, Marina, Miao, Xin, Reed, Brian, Sabina, Jeffrey, Feierstein, Erika, Schorn, Michelle, Alanjary, Mohammad, Dimalanta, Eileen, Dressman, Devin, Kasinskas, Rachel, Sokolsky, Tanya, Fidanza, Jacqueline A., Namsaraev, Eugeni, McKernan, Kevin J., and Williams, Alan

Published
2011
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10. A map of human genome variation from population-scale sequencing

Author

Durbin, Richard M., Altshuler, David L., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Collins, Francis S., De La Vega, Francisco M., Donnelly, Peter, Egholm, Michael, Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Knoppers, Bartha M., Lander, Eric S., Lehrach, Hans, Mardis, Elaine R., McVean, Gil A., Nickerson, Debbie A., Peltonen, Leena, Schafer, Alan J., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Gibbs, Richard A., Deiros, David, Metzker, Mike, Muzny, Donna, Reid, Jeff, Wheeler, David, Wang, Jun, Li, Jingxiang, Jian, Min, Li, Guoqing, Li, Ruiqiang, Liang, Huiqing, Tian, Geng, Wang, Bo, Wang, Jian, Wang, Wei, Yang, Huanming, Zhang, Xiuqing, Zheng, Huisong, Lander, Eric S., Altshuler, David L., Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Gabriel, Stacey B., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., Bentley, David R., Gormley, Niall, Humphray, Sean, Kingsbury, Zoya, Koko-Gonzales, Paula, Stone, Jennifer, McKernan, Kevin J., Costa, Gina L., Ichikawa, Jeffry K., Lee, Clarence C., Sudbrak, Ralf, Lehrach, Hans, Borodina, Tatiana A., Dahl, Andreas, Davydov, Alexey N., Marquardt, Peter, Mertes, Florian, Nietfeld, Wilfiried, Rosenstiel, Philip, Schreiber, Stefan, Soldatov, Aleksey V., Timmermann, Bernd, Tolzmann, Marius, Egholm, Michael, Affourtit, Jason, Ashworth, Dana, Attiya, Said, Bachorski, Melissa, Buglione, Eli, Burke, Adam, Caprio, Amanda, Celone, Christopher, Clark, Shauna, Conners, David, Desany, Brian, Gu, Lisa, Guccione, Lorri, Kao, Kalvin, Kebbel, Andrew, Knowlton, Jennifer, Labrecque, Matthew, McDade, Louise, Mealmaker, Craig, Minderman, Melissa, Nawrocki, Anne, Niazi, Faheem, Pareja, Kristen, Ramenani, Ravi, Riches, David, Song, Wanmin, Turcotte, Cynthia, Wang, Shally, Mardis, Elaine R., Wilson, Richard K., Dooling, David, Fulton, Lucinda, Fulton, Robert, Weinstock, George, Durbin, Richard M., Burton, John, Carter, David M., Churcher, Carol, Coffey, Alison, Cox, Anthony, Palotie, Aarno, Quail, Michael, Skelly, Tom, Stalker, James, Swerdlow, Harold P., Turner, Daniel, De Witte, Anniek, Giles, Shane, Bainbridge, Matthew, Challis, Danny, Sabo, Aniko, Yu, Fuli, Yu, Jin, Fang, Xiaodong, Guo, Xiaosen, Li, Yingrui, Luo, Ruibang, Tai, Shuaishuai, Wu, Honglong, Zheng, Hancheng, Zheng, Xiaole, Zhou, Yan, Marth, Gabor T., Garrison, Erik P., Huang, Weichun, Indap, Amit, Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Quinlan, Aaron R., Stewart, Chip, Stromberg, Michael P., Ward, Alistair N., Wu, Jiantao, Lee, Charles, Mills, Ryan E., Shi, Xinghua, Daly, Mark J., DePristo, Mark A., Ball, Aaron D., Banks, Eric, Browning, Brian L., Garimella, Kiran V., Grossman, Sharon R., Handsaker, Robert E., Hanna, Matt, Hartl, Chris, Kernytsky, Andrew M., Korn, Joshua M., Li, Heng, Maguire, Jared R., McCarroll, Steven A., McKenna, Aaron, Nemesh, James C., Philippakis, Anthony A., Poplin, Ryan E., Price, Alkes, Rivas, Manuel A., Sabeti, Pardis C., Schaffner, Stephen F., Shlyakhter, Ilya A., Cooper, David N., Ball, Edward V., Mort, Matthew, Phillips, Andrew D., Stenson, Peter D., Sebat, Jonathan, Makarov, Vladimir, Ye, Kenny, Yoon, Seungtai C., Bustamante, Carlos D., Clark, Andrew G., Boyko, Adam, Degenhardt, Jeremiah, Gravel, Simon, Gutenkunst, Ryan N., Kaganovich, Mark, Keinan, Alon, Lacroute, Phil, Ma, Xin, Reynolds, Andy, Clarke, Laura, Flicek, Paul, Cunningham, Fiona, Herrero, Javier, Keenen, Stephen, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Smith, Richard E., Zalunin, Vadim, Zheng-Bradley, Xiangqun, Korbel, Jan O., Stütz, Adrian M., Humphray, Sean, Bauer, Markus, Cheetham, Keira R., Cox, Tony, Eberle, Michael, James, Terena, Kahn, Scott, Murray, Lisa, Ye, Kai, De La Vega, Francisco M., Fu, Yutao, Hyland, Fiona C. L., Manning, Jonathan M., McLaughlin, Stephen F., Peckham, Heather E., Sakarya, Onur, Sun, Yongming A., Tsung, Eric F., Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Herwig, Ralf, Parkhomchuk, Dimitri V., Sherry, Stephen T., Agarwala, Richa, Khouri, Hoda M., Morgulis, Aleksandr O., Paschall, Justin E., Phan, Lon D., Rotmistrovsky, Kirill E., Sanders, Robert D., Shumway, Martin F., Xiao, Chunlin, McVean, Gil A., Auton, Adam, Iqbal, Zamin, Lunter, Gerton, Marchini, Jonathan L., Moutsianas, Loukas, Myers, Simon, Tumian, Afidalina, Desany, Brian, Knight, James, Winer, Roger, Craig, David W., Beckstrom-Sternberg, Steve M., Christoforides, Alexis, Kurdoglu, Ahmet A., Pearson, John V., Sinari, Shripad A., Tembe, Waibhav D., Haussler, David, Hinrichs, Angie S., Katzman, Sol J., Kern, Andrew, Kuhn, Robert M., Przeworski, Molly, Hernandez, Ryan D., Howie, Bryan, Kelley, Joanna L., Cord Melton, S., Abecasis, Gonçalo R., Li, Yun, Anderson, Paul, Blackwell, Tom, Chen, Wei, Cookson, William O., Ding, Jun, Min Kang, Hyun, Lathrop, Mark, Liang, Liming, Moffatt, Miriam F., Scheet, Paul, Sidore, Carlo, Snyder, Matthew, Zhan, Xiaowei, Zöllner, Sebastian, Awadalla, Philip, Casals, Ferran, Idaghdour, Youssef, Keebler, John, Stone, Eric A., Zilversmit, Martine, Jorde, Lynn, Xing, Jinchuan, Eichler, Evan E., Aksay, Gozde, Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Sahinalp, Cenk S., Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Koboldt, Daniel C., McLellan, Mike D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Albers, Cornelis A., Ayub, Qasim, Balasubramaniam, Senduran, Barrett, Jeffrey C., Chen, Yuan, Conrad, Donald F., Danecek, Petr, Dermitzakis, Emmanouil T., Hu, Min, Huang, Ni, Hurles, Matt E., Jin, Hanjun, Jostins, Luke, Keane, Thomas M., Quang Le, Si, Lindsay, Sarah, Long, Quan, MacArthur, Daniel G., Montgomery, Stephen B., Parts, Leopold, Tyler-Smith, Chris, Walter, Klaudia, Zhang, Yujun, Gerstein, Mark B., Snyder, Michael, Abyzov, Alexej, Balasubramanian, Suganthi, Bjornson, Robert, Du, Jiang, Grubert, Fabian, Habegger, Lukas, Haraksingh, Rajini, Jee, Justin, Khurana, Ekta, Lam, Hugo Y. K., Leng, Jing, Jasmine Mu, Xinmeng, Urban, Alexander E., Zhang, Zhengdong, Lee, Charles, McCarroll, Steven A., DePristo, Mark A., Korbel, Jan O., De La Vega, Francisco M., Blackwell, Tom, Eichler, Evan E., Kidd, Jeffrey M., Hurles, Matt E., Gibbs, Richard A., Coafra, Cristian, Dinh, Huyen, Kovar, Christie, Lee, Sandy, Nazareth, Lynne, Marth, Gabor T., Wilkinson, Jane, Flicek, Paul, Sherry, Stephen T., Abecasis, Gonçalo R., Mardis, Elaine R., Coffey, Allison, Scott, Carol, Gerstein, Mark B., Chakravarti, Aravinda, Knoppers, Bartha M., Bustamante, Carlos D., Gharani, Neda, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Li, Taosha, McGuire, Amy L., Ossorio, Pilar N., Rotimi, Charles N., Su, Yeyang, Toji, Lorraine H., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Abdallah, Assya, Juenger, Christopher R., Clemm, Nicholas C., Duncanson, Audrey, Green, Eric D., Guyer, Mark S., and Peterson, Jane L.

Published
2010
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11. A small-cell lung cancer genome with complex signatures of tobacco exposure

Author

Pleasance, Erin D., Stephens, Philip J., OʼMeara, Sarah, McBride, David J., Meynert, Alison, Jones, David, Lin, Meng-Lay, Beare, David, Lau, King Wai, Greenman, Chris, Varela, Ignacio, Nik-Zainal, Serena, Davies, Helen R., Ordoñez, Gonzalo R., Mudie, Laura J., Latimer, Calli, Edkins, Sarah, Stebbings, Lucy, Chen, Lina, Jia, Mingming, Leroy, Catherine, Marshall, John, Menzies, Andrew, Butler, Adam, Teague, Jon W., Mangion, Jonathon, Sun, Yongming A., McLaughlin, Stephen F., Peckham, Heather E., Tsung, Eric F., Costa, Gina L., Lee, Clarence C., Minna, John D., Gazdar, Adi, Birney, Ewan, Rhodes, Michael D., McKernan, Kevin J., Stratton, Michael R., Futreal, Andrew P., and Campbell, Peter J.

Published
2010
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12. Mapping and sequencing of structural variation from eight human genomes

Author

Kidd, Jeffrey M., Cooper, Gregory M., Donahue, William F., Hayden, Hillary S., Sampas, Nick, Graves, Tina, Hansen, Nancy, Teague, Brian, Alkan, Can, Antonacci, Francesca, Haugen, Eric, Zerr, Troy, Yamada, N. Alice, Tsang, Peter, Newman, Tera L., Tüzün, Eray, Cheng, Ze, Ebling, Heather M., Tusneem, Nadeem, David, Robert, Gillett, Will, Phelps, Karen A., Weaver, Molly, Saranga, David, Brand, Adrianne, Tao, Wei, Gustafson, Erik, McKernan, Kevin, Chen, Lin, Malig, Maika, Smith, Joshua D., Korn, Joshua M., McCarroll, Steven A., Altshuler, David A., Peiffer, Daniel A., Dorschner, Michael, Stamatoyannopoulos, John, Schwartz, David, Nickerson, Deborah A., Mullikin, James C., Wilson, Richard K., Bruhn, Laurakay, Olson, Maynard V., Kaul, Rajinder, Smith, Douglas R., and Eichler, Evan E.

Published
2008
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14. A small cell lung cancer genome reports complex tobacco exposure signatures

Author

Pleasance, Erin D, Stephens, Philip J, O'Meara, Sarah, McBride, David J, Meynert, Alison, Jones, David, Lin, Meng-Lay, Beare, David, Lau, King Wai, Greenman, Chris, Varela, Ignacio, Nik-Zainal, Serena, Davies, Helen R, Ordoñez, Gonzalo R, Mudie, Laura J, Latimer, Calli, Edkins, Sarah, Stebbings, Lucy, Chen, Lina, Jia, Mingming, Leroy, Catherine, Marshall, John, Menzies, Andrew, Butler, Adam, Teague, Jon W, Mangion, Jonathon, Sun, Yongming A, McLaughlin, Stephen F, Peckham, Heather E, Tsung, Eric F, Costa, Gina L, Lee, Clarence C, Minna, John D, Gazdar, Adi, Birney, Ewan, Rhodes, Michael D, McKernan, Kevin J, Stratton, Michael R, Futreal, P Andrew, and Campbell, Peter J

Subjects
Lung Neoplasms, DNA Copy Number Variations, DNA Repair, Genome, Human, DNA Mutational Analysis, Smoking, DNA Helicases, Exons, Small Cell Lung Carcinoma, Article, DNA-Binding Proteins, Gene Expression Regulation, Neoplastic, Mutagenesis, Insertional, Cell Line, Tumor, Mutation, Tobacco, Carcinogens, Humans, Promoter Regions, Genetic, DNA Damage, Sequence Deletion
Abstract

Cancer is driven by mutation. Worldwide, tobacco smoking is the principal lifestyle exposure that causes cancer, exerting carcinogenicity through60 chemicals that bind and mutate DNA. Using massively parallel sequencing technology, we sequenced a small-cell lung cancer cell line, NCI-H209, to explore the mutational burden associated with tobacco smoking. A total of 22,910 somatic substitutions were identified, including 134 in coding exons. Multiple mutation signatures testify to the cocktail of carcinogens in tobacco smoke and their proclivities for particular bases and surrounding sequence context. Effects of transcription-coupled repair and a second, more general, expression-linked repair pathway were evident. We identified a tandem duplication that duplicates exons 3-8 of CHD7 in frame, and another two lines carrying PVT1-CHD7 fusion genes, indicating that CHD7 may be recurrently rearranged in this disease. These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer.

Published
2009

15. Genomic characterization of the complete terpene synthase gene family from Cannabis sativa.

Author

Allen, Keith D., McKernan, Kevin, Pauli, Christopher, Roe, Jim, Torres, Anthony, and Gaudino, Reggie

Subjects
*GENE families, *CANNABIS (Genus), *MONOTERPENES, *COMPUTATIONAL biology, *PLANT cells & tissues, *ORGANIC chemistry
Abstract

Terpenes are responsible for most or all of the odor and flavor properties of Cannabis sativa, and may also impact effects users experience either directly or indirectly. We report the diversity of terpene profiles across samples bound for the Washington dispensary market. The remarkable degree of variation in terpene profiles ultimately results from action of a family of terpene synthase genes, only some of which have been described. Using a recently available genome assembly we describe 55 terpene synthases with genomic context, and tissue specific expression. The family is quite diverse from a protein similarity perspective, and subsets of the family are expressed in all tissues in the plant, including a set of root specific monoterpene synthases that could well have agronomic importance. Ultimately understanding and breeding for specific terpene profiles will require a good understanding of the gene family that underlies it. We intend for this work to serve as a foundation for that. [ABSTRACT FROM AUTHOR]

Published
2019
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16. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

Author

McKernan, Kevin Judd, Peckham, Heather E, Costa, Gina L., McLaughlin, Stephen F., Yutao Fu, Tsung, Eric F., Clouser, Christopher R., Duncan, Cisyla, Ichikawa, Jeffrey K., Lee, Clarence C., Zheng Zhang, Ranade, Swati S., Dimalanta, Eileen T., Hyland, Fiona C., Sokolsky, Tanya D., Lei Zhang, Sheridan, Andrew, Haoning Fu, Hendrickson, Cynthia L., Bin Li, Kotler, Lev, Stuart, Jeremy R., Malek, Joel A., Manning, Jonathan M., Antipova, Alena A., Perez, Damon S., Moore, Michael P., Hayashibara, Kathleen C., Lyons, Michael R., Beaudoin, Robert E., Coleman, Brittany E., Laptewicz, Michael W., Sannicandro, Adam E, Rhodes, Michael D., Gottimukkala, Rajesh K., Shan Yang, Bafna, Vineet, Bashir, Ali, MacBride, Andrew, Alkan, Can, Kidd, Jeffrey M., Eichler, Evan E., Reese, Martin G., De La Vega, Francisco M., and Blanchard, Alan P.

Subjects
Nucleotide sequence -- Analysis, Haplotypes -- Analysis, Human genome -- Research, Single nucleotide polymorphisms -- Research, Health
Published
2009

17. Rapid whole-genome mutational profiling using next-generation sequencing technologies

Author

Smith, Douglas R., Quinlan, Aaron R., Peckham, Heather E., Marth, Gabor T., Jeffries, Thomas W., McKernan, Kevin J., Rokhsar, Daniel S., Makowsky, Kathryn, Wei Tao, Woolf, Betty, Lei Shen, Donahue, William F., Tusneem, Nadeem, Stromberg, Michael P., Stewart, Donald A., Lu Zhang, Feng Chen, Hillman, David, Chapman, Jarrod, Blanchard, Alan P., Ranade, Swati S., Warner, Jason B., Lee, Clarence C., Coleman, Brittney E., Zheng Zhang, McLaughlin, Stephen F., Malek, Joel A., and Sorenson, Jon M.

Subjects
Gene mutations -- Research, Nucleotide sequencing -- Usage, Genomes -- Research, Health
Abstract

The article demonstrates the application of various new, high-throughput, next-generation parallel sequencing technologies in conducting the rapid whole-genome mutational profiling of various organisms. The new technologies are shown to be extremely rapid and cost-effective in detecting mutations in various evolved and engineered organisms.

Published
2008

18. The genome of M. acetivorans reveals extensive metabolic and physiological diversity

Author

Galagan, James E., Naylor, Jerome; Stange-Thomann, Nicole; DeArellano, Kurt; Johnson, Robin; Linton, Lauren;, Barber, Robert D.; Cann, Isaac; Graham, David E.; Grahame, David A.; Guss, Adam M.; Hedderich, Reiner; Ingram-Smith, Cheryl; Kuettner, H. Craig; Krzycki, Joseph A.; Leigh, John A.; Weixi Li, Liu, Jinfeng; Mukhopadhyay, Biswarup; Reeve, John N.; Smith, Kerry; Springer, Timothy A.; Umayam, Lowell A.; White, Owen; White, Robert H.; Macario, Everly Conway de; Ferry, James G., Jarrell, Ken F.; Jing, Hua; Macario, Alberto J.L.; Paulsen, Ian; Pritchett, Matthew; Sowers, Kevin R.; Swanson, Ronald V.; Zinder, Steven H.; Lander, Eric; Metcalf, William W.; Birren, Bruce, Allen, Nicole, Brown, Adam, Atnoor, Deven, Smirnov, Serge, Engels, Reinhard, Calvo, Sarah, FitzHugh, Will, Macdonald, Pendexter, Endrizzi, Matthew G., Roy, Alice, Nusbaum, Chad, McEwan, Paul, Zimmer, Andrew, Ye, Wenjuan, Tirrell, Andrea, Talamas, Jessica, and McKernan, Kevin

Subjects
Methanobacteriaceae -- Research, Archaeabacteria -- Research, Nucleotide sequence -- Research, Genomes -- Research, Genetic research, Health
Abstract

The complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A is presented. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology.

Published
2002

19. Rare genetic variants in the endocannabinoid system genes CNR1 and DAGLA are associated with neurological phenotypes in humans.

Author

Smith, Douglas R., Stanley, Christine M., Foss, Theodore, Boles, Richard G., and McKernan, Kevin

Subjects
NEUROLOGICAL disorders, CANNABINOID receptors, SLEEP disorders, MEMORY disorders, DIGLYCERIDES, LIPASES, GENETICS, PATIENTS
Abstract

Rare genetic variants in the core endocannabinoid system genes CNR1, CNR2, DAGLA, MGLL and FAAH were identified in molecular testing data from 6,032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous rare coding variants in CNR1, which encodes the type 1 cannabinoid receptor (CB1), were found to be significantly associated with pain sensitivity (especially migraine), sleep and memory disorders—alone or in combination with anxiety—compared to a set of controls without such CNR1 variants. Similarly, heterozygous rare variants in DAGLA, which encodes diacylglycerol lipase alpha, were found to be significantly associated with seizures and neurodevelopmental disorders, including autism and abnormalities of brain morphology, compared to controls. Rare variants in MGLL, FAAH and CNR2 were not associated with any neurological phenotypes in the patients tested. Diacylglycerol lipase alpha synthesizes the endocannabinoid 2-AG in the brain, which interacts with CB1 receptors. The phenotypes associated with rare CNR1 variants are reminiscent of those implicated in the theory of clinical endocannabinoid deficiency syndrome. The severe phenotypes associated with rare DAGLA variants underscore the critical role of rapid 2-AG synthesis and the endocannabinoid system in regulating neurological function and development. Mapping of the variants to the 3D structure of the type 1 cannabinoid receptor, or primary structure of diacylglycerol lipase alpha, reveals clustering of variants in certain structural regions and is consistent with impacts to function. [ABSTRACT FROM AUTHOR]

Published
2017
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22. Mutation in The Nuclear-Encoded Mitochondrial Isoleucyl-t RNA Synthetase IARS2 in Patients with Cataracts, Growth Hormone Deficiency with Short Stature, Partial Sensorineural Deafness, and Peripheral Neuropathy or with Leigh Syndrome.

Author

Schwartzentruber, Jeremy, Buhas, Daniela, Majewski, Jacek, Sasarman, Florin, Papillon‐Cavanagh, Simon, Thiffaut, Isabelle, Sheldon, Katherine M., Massicotte, Christine, Patry, Lysanne, Simon, Mariella, Zare, Amir S., McKernan, Kevin J., Michaud, Jacques, Boles, Richard G., Deal, Cheri L., Desilets, Valerie, Shoubridge, Eric A., and Samuels, Mark E.

Abstract

ABSTRACT Mutations in the nuclear-encoded mitochondrial aminoacyl-t RNA synthetases are associated with a range of clinical phenotypes. Here, we report a novel disorder in three adult patients with a phenotype including cataracts, short-stature secondary to growth hormone deficiency, sensorineural hearing deficit, peripheral sensory neuropathy, and skeletal dysplasia. Using SNP genotyping and whole-exome sequencing, we identified a single likely causal variant, a missense mutation in a conserved residue of the nuclear gene IARS2, encoding mitochondrial isoleucyl-t RNA synthetase. The mutation is homozygous in the affected patients, heterozygous in carriers, and absent in control chromosomes. IARS2 protein level was reduced in skin cells cultured from one of the patients, consistent with a pathogenic effect of the mutation. Compound heterozygous mutations in IARS2 were independently identified in a previously unreported patient with a more severe mitochondrial phenotype diagnosed as Leigh syndrome. This is the first report of clinical findings associated with IARS2 mutations. [ABSTRACT FROM AUTHOR]

Published
2014
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23. Expanded Genetic Codes in Next Generation Sequencing Enable Decontamination and Mitochondrial Enrichment.

Author

McKernan, Kevin J., Spangler, Jessica, Zhang, Lei, Tadigotla, Vasisht, McLaughlin, Stephen, Warner, Jason, Zare, Amir, and Boles, Richard G.

Subjects
*GENETIC code, *NUCLEOTIDE sequence, *BIOLOGICAL decontamination, *MITOCHONDRIAL membranes, *POLYMERASE chain reaction, *NUCLEOTIDE analysis
Abstract

We have developed a PCR method, coined Déjà vu PCR, that utilizes six nucleotides in PCR with two methyl specific restriction enzymes that respectively digest these additional nucleotides. Use of this enzyme-and-nucleotide combination enables what we term a “DNA diode”, where DNA can advance in a laboratory in only one direction and cannot feedback into upstream assays. Here we describe aspects of this method that enable consecutive amplification with the introduction of a 5th and 6th base while simultaneously providing methylation dependent mitochondrial DNA enrichment. These additional nucleotides enable a novel DNA decontamination technique that generates ephemeral and easy to decontaminate DNA. [ABSTRACT FROM AUTHOR]

Published
2014
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24. DREAMing of a patent-free human genome for clinical sequencing.

Author

McKernan, Kevin J, Spangler, Jessica, Helbert, Yvonne, Zhang, Lei, and Tadigotla, Vasisht

Subjects
*HUMAN genome, *SEQUENCE alignment, *POLYMERASE chain reaction, *GENE patents
Abstract

In this article, authors discuss a study related to the dreaming of patent free human genome for clinical sequencing. They state that a Myriad Genetics Inc. Myriad cDNA-based patent is not the only gene patent to make short sequences. In this study a simple PCR (Polymerase chain reaction) method has been demonstrated that utilizes additional methylated nucleotides. The study shows an alternative economic perspective on profit motivation and its impact on the ethics of gene patents.

Published
2013
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27. Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding.

Author

Chung, Christina A. Bormann, Boyd, Victoria L., McKernan, Kevin J., Yutao Fu, Monighetti, Cinna, Peckham, Heather E., and Barker, Melissa

Subjects
METHYLATION, ALKYLATION, THYMINE, URACIL, DNA, DEOXYRIBOSE, NUCLEIC acids, GENE expression, GENOMES, GENOMICS
Abstract

Methylation, the addition of methyl groups to cytosine (C), plays an important role in the regulation of gene expression in both normal and dysfunctional cells. During bisulfite conversion and subsequent PCR amplification, unmethylated Cs are converted into thymine (T), while methylated Cs will not be converted. Sequencing of this bisulfite-treated DNA permits the detection of methylation at specific sites. Through the introduction of next-generation sequencing technologies (NGS) simultaneous analysis of methylation motifs in multiple regions provides the opportunity for hypothesis-free study of the entire methylome. Here we present a whole methylome sequencing study that compares two different bisulfite conversion methods (in solution versus in gel), utilizing the high throughput of the SOLiD™ System. Advantages and disadvantages of the two different bisulfite conversion methods for constructing sequencing libraries are discussed. Furthermore, the application of the SOLiD™ bisulfite sequencing to larger and more complex genomes is shown with preliminary in silico created bisulfite converted reads. [ABSTRACT FROM AUTHOR]

Published
2010
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28. Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Author

Cloonan, Nicole, Forrest, Alistair R. R., Kolle, Gabriel, Gardiner, Brooke B. A., Faulkner, Geoffrey J., Brown, Mellissa K., Taylor, Darrin F., Steptoe, Anita L., Wani, Shivangi, Bethel, Graeme, Robertson, Alan J., Perkins, Andrew C., Bruce, Stephen J., Lee, Clarence C., Ranade, Swati S., Peckham, Heather E., Manning, Jonathan M., McKernan, Kevin J., and Grimmond, Sean M.

Subjects
NUCLEOTIDE sequence, EMBRYONIC stem cells, GENETIC polymorphisms, CELL differentiation, RNA splicing
Abstract

We developed a massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, to survey the complexity, dynamics and sequence content of transcriptomes in a near-complete fashion. This method generates directional, random-primed, linear cDNA libraries that are optimized for next-generation short-tag sequencing. We surveyed the poly(A)+ transcriptomes of undifferentiated mouse embryonic stem cells (ESCs) and embryoid bodies (EBs) at an unprecedented depth (10 Gb), using the Applied Biosystems SOLiD technology. These libraries capture the genomic landscape of expression, state-specific expression, single-nucleotide polymorphisms (SNPs), the transcriptional activity of repeat elements, and both known and new alternative splicing events. We investigated the impact of transcriptional complexity on current models of key signaling pathways controlling ESC pluripotency and differentiation, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that our understanding of transcriptional complexity is far from complete. [ABSTRACT FROM AUTHOR]

Published
2008
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30. ALLPATHS 2: Small Genomes Assembled Accurately and with High Continuity from Short Paired Reads

Author

MacCallum, Iain, Przybylski, Dariusz, Gnerre, Sante, Burton, Joshua, Gnirke, Andreas, Malek, Joel, McKernan, Kevin, Ranade, Swati, Shea, Terrance P, Williams, Louise, Nusbaum, Chad, Jaffe, David B, Shlyakhter, Ilya, and Young, Sarah

Abstract

We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR)., Organismic and Evolutionary Biology, Version of Record

Published
2009
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31. LETTERS.

Author

Orecchio, Mark, G. M., Laurenceau, Sidney, File, Jerry, M. J. P., and McKernan, Kevin

Subjects
LETTERS to the editor, LIQUID crystal display television sets, PLASMA television sets, DVD players, DIGITAL projectors, ELECTRONIC commerce
Abstract

Several letters to the editor in response to articles in previous issues including a comparison between liquid crystal displays and plasma television, the principles behind a digital light processing (DLP) system, a review on the Arcam AVR300 A/V receiver and DV 79 DVD player by Steve Guttenberg in the December 2004 issue and the list of risks of getting a DLP TV from an Internet dealer.

Published
2005

32. The chloroplast genome hidden in plain sight, open access publishing and anti-fragile distributed data sources.

Author

McKernan, Kevin Judd

Subjects
*CANNABIS (Genus), *CHLOROPLAST DNA, *MITOCHONDRIAL DNA, *OPEN access publishing, *DATA analysis, *PLANTS
Abstract

We sequenced several cannabis genomes in 2011 of June and the first and the longest contigs to emerge were the chloroplast and mitochondrial genomes. Having been a contributor to the Human Genome Project and an eye-witness to the real benefits of immediate data release, I have first hand experience with the potential mal-investment of millions of dollars of tax payer money narrowly averted due to the adopted global rapid data release policy. The policy was vital in reducing duplication of effort and economic waste. As a result, we felt obligated to publish the Cannabis genome data in a similar spirit and placed them immediately on a cloud based Amazon server in August of 2011. While these rapid data release practices were heralded by many in the media, we still find some authors fail to find or reference said work and hope to compel the readership that this omission has more pervasive repercussions than bruised egos and is a regression for our community. [ABSTRACT FROM AUTHOR]

Published
2016
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33. Mutation in The Nuclear-Encoded Mitochondrial Isoleucyl-tRNA Synthetase IARS2 in Patients with Cataracts, Growth Hormone Deficiency with Short Stature, Partial Sensorineural Deafness, and Peripheral Neuropathy or with Leigh Syndrome.

Author

Schwartzentruber, Jeremy, Buhas, Daniela, Majewski, Jacek, Sasarman, Florin, Papillon‐Cavanagh, Simon, Thiffault, Isabelle, Sheldon, Katherine M., Massicotte, Christine, Patry, Lysanne, Simon, Mariella, Zare, Amir S., McKernan, Kevin J., Consortium, FORGE Canada, Michaud, Jacques, Boles, Richard G., Deal, Cheri L., Desilets, Valerie, Shoubridge, Eric A., and Samuels, Mark E.

Published
2015
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34. A Proteogenomics Approach.

Author

McKernan, Kevin

Subjects
*GENOMICS, *DRUG target, *GENETIC polymorphisms
Abstract

Editorial. Focuses on the application of proteogenomics approach in Human Genome Project. Determination of proteome expression levels and drug targets; Integration of pharmacogenomics with protein interactions; Analysis of genomic polymorphisms in genes.

Published
2002

35. Genotyping System Provides a Solution For SNP-Based Studies.

Author

McEwan, Paul and McKernan, Kevin

Subjects
*NUCLEOTIDES, *GENOMES
Abstract

Focuses on the discovery of single nucleotide polymorphism markers across the genome. Development of Whole Genome Shotgun sequencing; Offers of pharmaceutical development by the Agencourt Bioscience Corp; Synthesis of oligonucleotide primers.

Published
2002

36. Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells.

Author

Kolle, Gabriel, Shepherd, Jill L., Gardiner, Brooke, Kassahn, Karin S., Cloonan, Nicole, Wood, David L. A., Nourbakhsh, Ehsan, Wani, Shivangi, Chy, Hun S., Zhou, Qi, McKernan, Kevin, Kuersten, Scott, Laslett, Andrew L., Grimmond, Sean M., and Taylor, Darrin F.

Subjects
*NUCLEOTIDE sequence, *NUCLEIC acid analysis, *EMBRYONIC stem cells, *PROTEOMICS, *PLURIPOTENT stem cells
Abstract

Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem cells (hESCs). We have shown that human embryonic stem (ES) cells display a high degree of transcriptional diversity, with more than half of active genes generating RNAs that differ from conventional gene models. We found evidence that more than 1000 genes express long 5' and/or extended 3'UTRs, which was confirmed by "virtual Northern" analysis. Exhaustive sequencing of the membrane-polysome and cytosolic/untranslated fractions of hESCs was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. The impact of this newly defined complexity on known gene-centric network models such as the Plurinet and the cell surface signaling machinery in human ES cells revealed a significant expansion of known transcript isoforms at play, many predicting possible alternative functions based on sequence alterations within key functional domains. [ABSTRACT FROM AUTHOR]

Published
2011
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37. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Author

Valouev, Anton, Ichikawa, Jeffrey, Tonthat, Thaisan, Stuart, Jeremy, Ranade, Swati, Peckham, Heather, Zeng, Kathy, Malek, Joel A., Costa, Gina, McKernan, Kevin, Sidow, Arend, Fire, Andrew, and Johnson, Steven M.

Subjects
*GENE mapping, *CAENORHABDITIS elegans, *CHROMATIN, *OLIGONUCLEOTIDES, *GENOMES
Abstract

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome. [ABSTRACT FROM AUTHOR]

Published
2008
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38. Whole genome sequencing of colonies derived from cannabis flowers and the impact of media selection on benchmarking total yeast and mold detection tools.

Author

McKernan K, Helbert Y, Kane L, Houde N, Zhang L, and McLaughlin S

Subjects
Benchmarking, Colony Count, Microbial, Flowers, Food Microbiology, Fungi genetics, Humans, Saccharomyces cerevisiae, Whole Genome Sequencing, Cannabis
Abstract

Background: Cannabis products are subjected to microbial testing for human pathogenic fungi and bacteria. These testing requirements often rely on non-specific colony forming unit (CFU/g) specifications without clarity on which medium, selection or growth times are required. We performed whole genome sequencing to assess the specificity of colony forming units (CFU) derived from three different plating media: Potato Dextrose Agar (PDA), PDA with chloramphenicol and Dichloran Rose Bengal with chloramphenicol (DRBC)., Methods: Colonies were isolated from each medium type and their whole genomes sequenced to identify the diversity of microbes present on each medium selection. Fungal Internal Transcribed Spacer (ITS3) and Bacterial 16S RNA(16S) quantitative polymerase chain reactions (qPCR) were performed, to correlate these CFUs with fungi- and bacterial- specific qPCR., Results: Each plating medium displayed a ten-fold difference in CFU counts. PDA with chloramphenicol showed the highest diversity and the highest concordance with whole genome sequencing. According to ITS3 and 16S qPCR confirmed with whole genome sequencing, DRBC under counted yeast and mold while PDA without chloramphenicol over counted CFUs due to bacterial growth without selection., Conclusions: Colony Forming Unit regulations lack specificity. Each medium produces significant differences in CFU counts. These are further dependent on subjective interpretation, failure to culture most microbes, and poor selection between bacteria and fungi. Given the most human pathogenic microbes found on cannabis are endophytes which culture fails to detect, molecular methods offer a solution to this long-standing quantification problem in the cannabis testing field., Competing Interests: Competing interests: The authors are employees of Medicinal Genomics which manufacture qPCR reagents for Cannabis testing., (Copyright: © 2021 McKernan K et al.)

Published
2021
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39. Bayes Lines Tool (BLT): a SQL-script for analyzing diagnostic test results with an application to SARS-CoV-2-testing.

Author

Aukema W, Malhotra BR, Goddek S, Kämmerer U, Borger P, McKernan K, and Klement RJ

Subjects
Bayes Theorem, Diagnostic Tests, Routine, Humans, Sensitivity and Specificity, COVID-19 diagnosis, COVID-19 epidemiology, SARS-CoV-2
Abstract

The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place within the context of the world-wide SARS-CoV-2 crisis. Here, for the first time in history, laboratory test results have a dramatic impact on political decisions. Therefore, transparent, comprehensible, and reliable data is mandatory. It is in the nature of wet lab tests that their quality and outcome are influenced by multiple factors reducing their performance by handling procedures, underlying test protocols, and analytical reagents. These limitations in sensitivity and specificity have to be taken into account when calculating the real test results. As a resolution method, we have developed a Bayesian calculator, the Bayes Lines Tool (BLT), for analyzing disease prevalence, test sensitivity, test specificity, and, therefore, true positive, false positive, true negative, and false negative numbers from official test outcome reports. The calculator performs a simple SQL (Structured Query Language) query and can easily be implemented on any system supporting SQL. We provide an example of influenza test results from California, USA, as well as two examples of SARS-CoV-2 test results from official government reports from The Netherlands and Germany-Bavaria, to illustrate the possible parameter space of prevalence, sensitivity, and specificity consistent with the observed data. Finally, we discuss this tool's multiple applications, including its putative importance for informing policy decisions., Competing Interests: No competing interests were disclosed., (Copyright: © 2022 Aukema W et al.)

Published
2021
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40. A draft reference assembly of the Psilocybe cubensis genome.

Author

McKernan K, Kane LT, Crawford S, Chin CS, Trippe A, and McLaughlin S

Subjects
Psilocybin, Agaricales genetics, Psilocybe
Abstract

We describe the use of high-fidelity single molecule sequencing to assemble the genome of the psychoactive Psilocybe cubensis mushroom. The genome is 46.6Mb, 46% GC, and in 32 contigs with an N50 of 3.3Mb. The BUSCO completeness scores are 97.6% with 1.2% duplicates. The Psilocybin synthesis cluster exists in a single 3.2Mb contig. The dataset is available from NCBI BioProject with accessions PRJNA687911 and PRJNA700437., Competing Interests: Competing interests: No current conflicts but potential future conflicts should be disclosed. Medicinal Genomics offers DNA and RNA sequencing services in the Cannabis space and are likely to offer similar services in the P.cubensis space if market demand matures., (Copyright: © 2021 McKernan K et al.)

Published
2021
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41. A draft sequence reference of the Psilocybe cubensis genome.

Author

McKernan K, Kane LT, Crawford S, Chin CS, Trippe A, and McLaughlin S

Subjects
Psilocybin, Agaricales genetics, Psilocybe
Abstract

We describe the use of high-fidelity single molecule sequencing to assemble the genome of the psychoactive Psilocybe cubensis mushroom. The genome is 46.6Mb, 46% GC, and in 32 contigs with an N50 of 3.3Mb. The BUSCO completeness scores are 97.6% with 1.2% duplicates. The Psilocybin synthesis cluster exists in a single 3.2Mb contig. The dataset is available from NCBI BioProject with accessions PRJNA687911 and PRJNA700437., Competing Interests: Competing interests: No current conflicts but potential future conflicts should be disclosed. Medicinal Genomics offers DNA and RNA sequencing services in the Cannabis space and are likely to offer similar services in the P.cubensis space if market demand matures., (Copyright: © 2021 McKernan K et al.)

Published
2021
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42. Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests.

Author

McKernan K, Spangler J, Helbert Y, Lynch RC, Devitt-Lee A, Zhang L, Orphe W, Warner J, Foss T, Hudalla CJ, Silva M, and Smith DR

Abstract

Background : The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods : A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results : Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions : These findings have important implications for the Cannabis and food safety testing industries., Competing Interests: KM, JS, YH, RCL, AD-L, LZ, WO, JW, TF and DRS are employees of Courtagen Life Sciences, the parent company of Medicinal Genomics, which manufactures the commercial qPCR test used in this study.

Published
2016
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43. Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers.

Author

McKernan K, Spangler J, Zhang L, Tadigotla V, Helbert Y, Foss T, and Smith D

Abstract

The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medical Cannabis and is of particular concern with inhaled, vaporized and even concentrated Cannabis products . As a result, third party microbial testing has become a regulatory requirement in the medical and recreational Cannabis markets, yet knowledge of the Cannabis microbiome is limited. Here we describe the first next generation sequencing survey of the fungal communities found in dispensary based Cannabis flowers by ITS2 sequencing, and demonstrate the sensitive detection of several toxigenic Penicillium and Aspergillus species, including P. citrinum and P. paxilli, that were not detected by one or more culture-based methods currently in use for safety testing.

Published
2015
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44. MicroRNAs and their isomiRs function cooperatively to target common biological pathways.

Author

Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbakhsh E, Krishnan K, Gardiner B, Wang X, Nones K, Steen JA, Matigian NA, Wood DL, Kassahn KS, Waddell N, Shepherd J, Lee C, Ichikawa J, McKernan K, Bramlett K, Kuersten S, and Grimmond SM

Subjects
Base Sequence, Biotinylation, DEAD-box RNA Helicases genetics, Gene Expression Profiling, HEK293 Cells, HeLa Cells, High-Throughput Nucleotide Sequencing, Humans, MicroRNAs classification, MicroRNAs isolation & purification, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Ribonuclease III genetics, Sequence Alignment, Transcriptome, Transfection, Argonaute Proteins genetics, Gene Regulatory Networks genetics, MicroRNAs genetics, RNA, Messenger genetics
Abstract

Background: Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for these molecules., Results: To assess the biological relevance of isomiRs, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline called miRNA-MATE to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. A large proportion of isomiRs potentially derive from AGO2 cleavage independent of Dicer. We isolated polyribosome-associated mRNA, captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies allow us to experimentally determine genome-wide mRNA targets, and these experiments showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs., Conclusions: Together, these results find isomiRs to be biologically relevant and functionally cooperative partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur when the specificity of miRNA targeting is mediated by only 6 to 11 nucleotides.

Published
2011
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45. Whole methylome analysis by ultra-deep sequencing using two-base encoding.

Author

Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, Peckham HE, and Barker M

Subjects
Base Sequence, Binding Sites genetics, DNA chemistry, DNA genetics, Electrophoresis, Polyacrylamide Gel methods, Genomic Library, Humans, Molecular Sequence Data, Polymerase Chain Reaction, Sequence Homology, Nucleic Acid, Sulfites chemistry, DNA Methylation, Genome, Human genetics, Sequence Analysis, DNA methods
Abstract

Methylation, the addition of methyl groups to cytosine (C), plays an important role in the regulation of gene expression in both normal and dysfunctional cells. During bisulfite conversion and subsequent PCR amplification, unmethylated Cs are converted into thymine (T), while methylated Cs will not be converted. Sequencing of this bisulfite-treated DNA permits the detection of methylation at specific sites. Through the introduction of next-generation sequencing technologies (NGS) simultaneous analysis of methylation motifs in multiple regions provides the opportunity for hypothesis-free study of the entire methylome. Here we present a whole methylome sequencing study that compares two different bisulfite conversion methods (in solution versus in gel), utilizing the high throughput of the SOLiD System. Advantages and disadvantages of the two different bisulfite conversion methods for constructing sequencing libraries are discussed. Furthermore, the application of the SOLiD bisulfite sequencing to larger and more complex genomes is shown with preliminary in silico created bisulfite converted reads.

Published
2010
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46. Polymorphism discovery in high-throughput resequenced microarray-enriched human genomic loci.

Author

Antipova AA, Sokolsky TD, Clouser CR, Dimalanta ET, Hendrickson CL, Kosnopo C, Lee CC, Ranade SS, Zhang L, Blanchard AP, and McKernan KJ

Subjects
Base Sequence, Biomedical Technology methods, Exons, Genetic Variation, Genome, Human, Heterozygote, Homozygote, Humans, Molecular Sequence Data, Mutation, Oligonucleotide Array Sequence Analysis, Polymorphism, Genetic, Sequence Analysis, DNA methods
Abstract

Identifying genetic variants and mutations that underlie human diseases requires development of robust, cost-effective tools for routine resequencing of regions of interest in the human genome. Here, we demonstrate that coupling Applied Biosystems SOLiD system-sequencing platform with microarray capture of targeted regions provides an efficient and robust method for high-coverage resequencing and polymorphism discovery in human protein-coding exons.

Published
2009

47. Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.

Author

Motallebipour M, Ameur A, Reddy Bysani MS, Patra K, Wallerman O, Mangion J, Barker MA, McKernan KJ, Komorowski J, and Wadelius C

Subjects
Alleles, Cell Lineage, Chromatin Immunoprecipitation, Gene Expression Profiling, Gene Library, Genome, Hep G2 Cells, Hepatocyte Nuclear Factor 3-alpha metabolism, Hepatocyte Nuclear Factor 3-beta genetics, Hepatocyte Nuclear Factor 3-beta metabolism, Hepatocyte Nuclear Factor 3-gamma metabolism, Humans, Liver cytology, Liver metabolism, Models, Genetic, Promoter Regions, Genetic, Hepatocyte Nuclear Factor 3-alpha genetics, Hepatocyte Nuclear Factor 3-gamma genetics, Histones chemistry
Abstract

Background: The forkhead box/winged helix family members FOXA1, FOXA2, and FOXA3 are of high importance in development and specification of the hepatic linage and the continued expression of liver-specific genes., Results: Here, we present a genome-wide location analysis of FOXA1 and FOXA3 binding sites in HepG2 cells through chromatin immunoprecipitation with detection by sequencing (ChIP-seq) studies and compare these with our previous results on FOXA2. We found that these factors often bind close to each other in different combinations and consecutive immunoprecipitation of chromatin for one and then a second factor (ChIP-reChIP) shows that this occurs in the same cell and on the same DNA molecule, suggestive of molecular interactions. Using co-immunoprecipitation, we further show that FOXA2 interacts with both FOXA1 and FOXA3 in vivo, while FOXA1 and FOXA3 do not appear to interact. Additionally, we detected diverse patterns of trimethylation of lysine 4 on histone H3 (H3K4me3) at transcriptional start sites and directionality of this modification at FOXA binding sites. Using the sequence reads at polymorphic positions, we were able to predict allele specific binding for FOXA1, FOXA3, and H3K4me3. Finally, several SNPs associated with diseases and quantitative traits were located in the enriched regions., Conclusions: We find that ChIP-seq can be used not only to create gene regulatory maps but also to predict molecular interactions and to inform on the mechanisms for common quantitative variation.

Published
2009
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48. Sample preparation.

Author

McKernan KJ

Subjects
Automation, DNA isolation & purification, Humans, Polymerase Chain Reaction, Genetics, Medical, Specimen Handling
Abstract

Today's human genetic studies are requiring an ever-increasing number of sample manipulations. Although a significant investment of time and money are required, automation can considerably reduce human error and improve sample tracking fidelity when applied to such repetitive projects. This unit presents issues involved in the automation of sample preparation for genomic DNA isolation and PCR.

Published
2004
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49. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

Author

Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, and Marra MA

Subjects
Algorithms, Animals, DNA, Complementary analysis, Gene Library, Humans, Mice, Open Reading Frames, DNA, Complementary chemistry, Sequence Analysis, DNA
Abstract

The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov).

Published
2002
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