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1. Supplementary Figure S7 from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

Author

Shern, Jack F., primary, Chen, Li, primary, Chmielecki, Juliann, primary, Wei, Jun S., primary, Patidar, Rajesh, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Wang, Jianjun, primary, Song, Young K., primary, Tolman, Catherine, primary, Hurd, Laura, primary, Liao, Hongling, primary, Zhang, Shile, primary, Bogen, Dominik, primary, Brohl, Andrew S., primary, Sindiri, Sivasish, primary, Catchpoole, Daniel, primary, Badgett, Thomas, primary, Getz, Gad, primary, Mora, Jaume, primary, Anderson, James R., primary, Skapek, Stephen X., primary, Barr, Frederic G., primary, Meyerson, Matthew, primary, Hawkins, Douglas S., primary, and Khan, Javed, primary

Published
2023
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2. Supplementary Table S7 from The Genomic Landscape of Pediatric Ewing Sarcoma

Author

Crompton, Brian D., primary, Stewart, Chip, primary, Taylor-Weiner, Amaro, primary, Alexe, Gabriela, primary, Kurek, Kyle C., primary, Calicchio, Monica L., primary, Kiezun, Adam, primary, Carter, Scott L., primary, Shukla, Sachet A., primary, Mehta, Swapnil S., primary, Thorner, Aaron R., primary, de Torres, Carmen, primary, Lavarino, Cinzia, primary, Suñol, Mariona, primary, McKenna, Aaron, primary, Sivachenko, Andrey, primary, Cibulskis, Kristian, primary, Lawrence, Michael S., primary, Stojanov, Petar, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Seepo, Sara, primary, Blumenstiel, Brendan, primary, DeFelice, Matthew, primary, Imaz-Rosshandler, Ivan, primary, Schwarz-Cruz y Celis, Angela, primary, Rivera, Miguel N., primary, Rodriguez-Galindo, Carlos, primary, Fleming, Mark D., primary, Golub, Todd R., primary, Getz, Gad, primary, Mora, Jaume, primary, and Stegmaier, Kimberly, primary

Published
2023
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3. Data from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

Author

Shern, Jack F., primary, Chen, Li, primary, Chmielecki, Juliann, primary, Wei, Jun S., primary, Patidar, Rajesh, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Wang, Jianjun, primary, Song, Young K., primary, Tolman, Catherine, primary, Hurd, Laura, primary, Liao, Hongling, primary, Zhang, Shile, primary, Bogen, Dominik, primary, Brohl, Andrew S., primary, Sindiri, Sivasish, primary, Catchpoole, Daniel, primary, Badgett, Thomas, primary, Getz, Gad, primary, Mora, Jaume, primary, Anderson, James R., primary, Skapek, Stephen X., primary, Barr, Frederic G., primary, Meyerson, Matthew, primary, Hawkins, Douglas S., primary, and Khan, Javed, primary

Published
2023
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4. Supplementary Tables S1-S10 from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

Author

Shern, Jack F., primary, Chen, Li, primary, Chmielecki, Juliann, primary, Wei, Jun S., primary, Patidar, Rajesh, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Wang, Jianjun, primary, Song, Young K., primary, Tolman, Catherine, primary, Hurd, Laura, primary, Liao, Hongling, primary, Zhang, Shile, primary, Bogen, Dominik, primary, Brohl, Andrew S., primary, Sindiri, Sivasish, primary, Catchpoole, Daniel, primary, Badgett, Thomas, primary, Getz, Gad, primary, Mora, Jaume, primary, Anderson, James R., primary, Skapek, Stephen X., primary, Barr, Frederic G., primary, Meyerson, Matthew, primary, Hawkins, Douglas S., primary, and Khan, Javed, primary

Published
2023
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5. Supplementary Legends from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

Author

Shern, Jack F., primary, Chen, Li, primary, Chmielecki, Juliann, primary, Wei, Jun S., primary, Patidar, Rajesh, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Wang, Jianjun, primary, Song, Young K., primary, Tolman, Catherine, primary, Hurd, Laura, primary, Liao, Hongling, primary, Zhang, Shile, primary, Bogen, Dominik, primary, Brohl, Andrew S., primary, Sindiri, Sivasish, primary, Catchpoole, Daniel, primary, Badgett, Thomas, primary, Getz, Gad, primary, Mora, Jaume, primary, Anderson, James R., primary, Skapek, Stephen X., primary, Barr, Frederic G., primary, Meyerson, Matthew, primary, Hawkins, Douglas S., primary, and Khan, Javed, primary

Published
2023
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6. Supplementary Methods, Figure Legends, Figures S1 - S6, Tables S1, S3 - S6, S8 - S15, S17 from The Genomic Landscape of Pediatric Ewing Sarcoma

Author

Crompton, Brian D., primary, Stewart, Chip, primary, Taylor-Weiner, Amaro, primary, Alexe, Gabriela, primary, Kurek, Kyle C., primary, Calicchio, Monica L., primary, Kiezun, Adam, primary, Carter, Scott L., primary, Shukla, Sachet A., primary, Mehta, Swapnil S., primary, Thorner, Aaron R., primary, de Torres, Carmen, primary, Lavarino, Cinzia, primary, Suñol, Mariona, primary, McKenna, Aaron, primary, Sivachenko, Andrey, primary, Cibulskis, Kristian, primary, Lawrence, Michael S., primary, Stojanov, Petar, primary, Rosenberg, Mara, primary, Ambrogio, Lauren, primary, Auclair, Daniel, primary, Seepo, Sara, primary, Blumenstiel, Brendan, primary, DeFelice, Matthew, primary, Imaz-Rosshandler, Ivan, primary, Schwarz-Cruz y Celis, Angela, primary, Rivera, Miguel N., primary, Rodriguez-Galindo, Carlos, primary, Fleming, Mark D., primary, Golub, Todd R., primary, Getz, Gad, primary, Mora, Jaume, primary, and Stegmaier, Kimberly, primary

Published
2023
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7. Complementary genomic approaches highlight the P13K/mTOR pathway as a common vulnerability in osteosarcoma

Author

Perry, Jennifer A., Kiezun, Adam, Tonzi, Peter, Van Allen, Eliezer M., Carter, Scott L., Baca, Sylvan C., Cowley, Glenn S., Bhatt, Ami S., Rheinbay, Esther, Pedamallu, Chandra Sekhar, Helman, Elena, Taylor-Weiner, Amaro, McKenna, Aaron, DeLuca, David S., Lawrence, Michael S., Ambrogio, Lauren, Sougnez, Carrie, Sivachenko, Andrey, Walensky, Loren D., Wagle, Nikhil, Mora, Jaume, de Torres, Carmen, Lavarino, Cinzia, Dos Santos Aguiar, Simone, Yunes, Jose Andres, Brandalise, Silvia Regina, Mercado-Celis, Gabriela Elisa, Melendez-Zajgla, Jorge, Cárdenas-Cardós, Rocío, Velasco-Hidalgo, Liliana, Roberts, Charles W. M., Garraway, Levi A., Rodriguez-Galindo, Carlos, Gabriel, Stacey B., Lander, Eric S., Golub, Todd R., Orkin, Stuart H., Getz, Gad, and Janeway, Katherine A.

Published
2014

8. Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2

Author

Greulich, Heidi, Kaplan, Bethany, Mertins, Philipp, Chen, Tzu-Hsiu, Tanaka, Kumiko E., Yun, Cai-Hong, Zhang, Xiaohong, Lee, Se-Hoon, Cho, Jeonghee, Ambrogio, Lauren, Liao, Rachel, Imielinski, Marcin, Banerji, Shantanu, Berger, Alice H., Lawrence, Michael S., Zhang, Jinghui, Pho, Nam H., Walker, Sarah R., Winckler, Wendy, Getz, Gad, Frank, David, Hahn, William C., Eck, Michael J., Mani, D. R., Jaffe, Jacob D., Carr, Steven A., Wong, Kwok-Kin, and Meyerson, Matthew

Published
2012

9. The use of topicalNitrosomonas eutrophafor cosmetic improvement of facial wrinkles

Author

Suzana Saric-Bosanac, Simran Dhaliwal, Iryna Rybak, Larry Weiss, Alexandra R. Vaughn, Raja K Sivamani, Paloma N. Reiter, Manisha Notay, Connie C. Li, Ambrogio Lauren Nicole, Megha Trivedi, and W. Burney

Subjects
Adult, Male, medicine.medical_specialty, Cosmetic Techniques, Dermatology, Nitrosomonas eutropha, Administration, Cutaneous, law.invention, Young Adult, 030207 dermatology & venereal diseases, 03 medical and health sciences, Probiotic, 0302 clinical medicine, law, Photography, medicine, Humans, Rejuvenation, Prospective Studies, Nitrosomonas, Wrinkle, Skin, Aerosols, High concentration, biology, business.industry, Probiotics, Significant difference, Facial wrinkles, Middle Aged, equipment and supplies, Glabella, biology.organism_classification, Skin Aging, Treatment Outcome, medicine.anatomical_structure, Face, 030220 oncology & carcinogenesis, Forehead, Female, medicine.symptom, business
Abstract

Background Both topical and oral probiotics are becoming widely used. There is increasing interest in the cosmetic potential in topical probiotics. Nitrosomonas eutropha is an ammonia-oxidizing bacteria. Aim The purpose of this study was to assess whether there is any improvement in facial wrinkles with the use of Nitrosomonas eutropha, a topical probiotic. Methods In this prospective study, high-resolution photographs were obtained in twenty-nine participants at baseline and after using topical Nitrosomonas eutropha for seven days. Results There was a significant difference in wrinkle depth and severity in the high concentration probiotic group. There was also a statistically significant improvement in pigmentation of the forehead and glabella in the higher concentration group. Conclusions Nitrosomonas eutropha may have aesthetic benefits in terms of reducing the appearance of wrinkles. Larger studies with longer treatment and follow-up periods are required.

Published
2019

10. A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers

Author

Lee, Ryan S., Stewart, Chip, Carter, Scott L., Ambrogio, Lauren, Cibulskis, Kristian, Sougnez, Carrie, Lawrence, Michael S., Auclair, Daniel, Mora, Jaume, Golub, Todd R., Biegel, Jaclyn A., Getz, Gad, and Roberts, Charles W.M.

Subjects
Pediatrics, Genomics, Cancer -- Genetic aspects, Health care industry
Abstract

Cancer is principally considered a genetic disease, and numerous mutations are thought essential to drive its growth. However, the existence of genomically stable cancers and the emergence of mutations in [...]

Published
2012
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11. Exome sequencing, ANGPTL3, mutations, and familial combined hypolipidemia

Author

Musunuru, Kiran, Pirruccello, James P., Ron Do, Peloso, Gina M., Guiducci, Candace, Sougnez, Carrie, Barry, Andrew J., Fennell, Tim, Banks, Erik, Ambrogio, Lauren, Garimella, Kiran V., Fisher, Sheila, Abreu, Justin, Cibulskis, Kristian, Kernytsky, Andrew, Rudzicz, Nicholas, Engert, James C., DePristo, Mark A., Daly, Mark J., Gonzalez, Elena, Cohen, Jonathan C., Schonfeld, Gustav, Gabriel, Stacey B., Pin Yue, Kathiresan, Sekar, Hobbs, Helen H., and Altshuler, David

Subjects
Gene mutations -- Analysis, Hyperlipidemia -- Genetic aspects, Hyperlipidemia -- Causes of, Cholesterol, LDL -- Health aspects, Cholesterol metabolism -- Genetic aspects
Abstract

All protein-coding regions of the genome (the 'exome') are sequenced in two family members with combined hypolipidemia, marked by extremely low plasma levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol and triglycerides. The analysis of ANGPTL3 (the angiopoietinlike 3 protein) mutations has highlighted a role for the gene in LDL cholesterol metabolism in humans and has displayed the usefulness of exome sequencing for identification of novel genetic causes of inherited disorders.

Published
2010

12. Landscape of genomic alterations in cervical carcinomas

Author

Ojesina, Akinyemi I., Lichtenstein, Lee, Freeman, Samuel S., Pedamallu, Chandra Sekhar, Imaz-Rosshandler, Ivan, Pugh, Trevor J., Cherniack, Andrew D., Ambrogio, Lauren, Cibulskis, Kristian, Bertelsen, Bjørn, Romero-Cordoba, Sandra, Treviño, Victor, Vazquez-Santillan, Karla, Guadarrama, Alberto Salido, Wright, Alexi A., Rosenberg, Mara W., Duke, Fujiko, Kaplan, Bethany, Wang, Rui, Nickerson, Elizabeth, Walline, Heather M., Lawrence, Michael S., Stewart, Chip, Carter, Scott L., McKenna, Aaron, Rodriguez-Sanchez, Iram P., Espinosa-Castilla, Magali, Woie, Kathrine, Bjorge, Line, Wik, Elisabeth, Halle, Mari K., Hoivik, Erling A., Krakstad, Camilla, Gabiño, Nayeli Belem, Gómez-Macías, Gabriela Sofia, Valdez-Chapa, Lezmes D., Garza-Rodríguez, María Lourdes, Maytorena, German, Vazquez, Jorge, Rodea, Carlos, Cravioto, Adrian, Cortes, Maria L., Greulich, Heidi, Crum, Christopher P., Neuberg, Donna S., Hidalgo-Miranda, Alfredo, Escareno, Claudia Rangel, Akslen, Lars A., Carey, Thomas E., Vintermyr, Olav K., Gabriel, Stacey B., Barrera-Saldaña, Hugo A., Melendez-Zajgla, Jorge, Getz, Gad, Salvesen, Helga B., and Meyerson, Matthew

Published
2014
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13. Mutational heterogeneity in cancer and the search for new cancer-associated genes

Author

Lawrence, Michael S., Stojanov, Petar, Polak, Paz, Kryukov, Gregory V., Cibulskis, Kristian, Sivachenko, Andrey, Carter, Scott L., Stewart, Chip, Mermel, Craig H., Roberts, Steven A., Kiezun, Adam, Hammerman, Peter S., McKenna, Aaron, Drier, Yotam, Zou, Lihua, Ramos, Alex H., Pugh, Trevor J., Stransky, Nicolas, Helman, Elena, Kim, Jaegil, Sougnez, Carrie, Ambrogio, Lauren, Nickerson, Elizabeth, Shefler, Erica, Cortés, Maria L., Auclair, Daniel, Saksena, Gordon, Voet, Douglas, Noble, Michael, DiCara, Daniel, Lin, Pei, Lichtenstein, Lee, Heiman, David I., Fennell, Timothy, Imielinski, Marcin, Hernandez, Bryan, Hodis, Eran, Baca, Sylvan, Dulak, Austin M., Lohr, Jens, Landau, Dan-Avi, Wu, Catherine J., Melendez-Zajgla, Jorge, Hidalgo-Miranda, Alfredo, Koren, Amnon, McCarroll, Steven A., Mora, Jaume, Lee, Ryan S., Crompton, Brian, Onofrio, Robert, Parkin, Melissa, Winckler, Wendy, Ardlie, Kristin, Gabriel, Stacey B., Roberts, Charles W. M., Biegel, Jaclyn A., Stegmaier, Kimberly, Bass, Adam J., Garraway, Levi A., Meyerson, Matthew, Golub, Todd R., Gordenin, Dmitry A., Sunyaev, Shamil, Lander, Eric S., and Getz, Gad

Published
2013
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14. Melanoma genome sequencing reveals frequent PREX2 mutations

Author

Berger, Michael F., Hodis, Eran, Heffernan, Timothy P., Deribe, Yonathan Lissanu, Lawrence, Michael S., Protopopov, Alexei, Ivanova, Elena, Watson, Ian R., Nickerson, Elizabeth, Ghosh, Papia, Zhang, Hailei, Zeid, Rhamy, Ren, Xiaojia, Cibulskis, Kristian, Sivachenko, Andrey Y., Wagle, Nikhil, Sucker, Antje, Sougnez, Carrie, Onofrio, Robert, Ambrogio, Lauren, Auclair, Daniel, Fennell, Timothy, Carter, Scott L., Drier, Yotam, Stojanov, Petar, Singer, Meredith A., Voet, Douglas, Jing, Rui, Saksena, Gordon, Barretina, Jordi, Ramos, Alex H., Pugh, Trevor J., Stransky, Nicolas, Parkin, Melissa, Winckler, Wendy, Mahan, Scott, Ardlie, Kristin, Baldwin, Jennifer, Wargo, Jennifer, Schadendorf, Dirk, Meyerson, Matthew, Gabriel, Stacey B., Golub, Todd R., Wagner, Stephan N., Lander, Eric S., Getz, Gad, Chin, Lynda, and Garraway, Levi A.

Published
2012
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15. The genomic complexity of primary human prostate cancer

Author

Berger, Michael F., Lawrence, Michael S., Demichelis, Francesca, Drier, Yotam, Cibulskis, Kristian, Sivachenko, Andrey Y., Sboner, Andrea, Esgueva, Raquel, Pflueger, Dorothee, Sougnez, Carrie, Onofrio, Robert, Carter, Scott L., Park, Kyung, Habegger, Lukas, Ambrogio, Lauren, Fennell, Timothy, Parkin, Melissa, Saksena, Gordon, Voet, Douglas, Ramos, Alex H., Pugh, Trevor J., Wilkinson, Jane, Fisher, Sheila, Winckler, Wendy, Mahan, Scott, Ardlie, Kristin, Baldwin, Jennifer, Simons, Jonathan W., Kitabayashi, Naoki, MacDonald, Theresa Y., Kantoff, Philip W., Chin, Lynda, Gabriel, Stacey B., Gerstein, Mark B., Golub, Todd R., Meyerson, Matthew, Tewari, Ashutosh, Lander, Eric S., Getz, Gad, Rubin, Mark A., and Garraway, Levi A.

Published
2011
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16. 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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17. The use of topicalNitrosomonas eutrophafor cosmetic improvement of facial wrinkles

Author

Notay, Manisha, primary, Saric‐Bosanac, Suzana, additional, Vaughn, Alexandra R., additional, Dhaliwal, Simran, additional, Trivedi, Megha, additional, Reiter, Paloma N., additional, Rybak, Iryna, additional, Li, Connie C., additional, Weiss, Larry B., additional, Ambrogio, Lauren, additional, Burney, Waqas, additional, and Sivamani, Raja K., additional

Published
2019
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18. The use of topical Nitrosomonas eutropha for cosmetic improvement of facial wrinkles.

Author

Notay, Manisha, Saric‐Bosanac, Suzana, Vaughn, Alexandra R., Dhaliwal, Simran, Trivedi, Megha, Reiter, Paloma N., Rybak, Iryna, Li, Connie C., Weiss, Larry B., Ambrogio, Lauren, Burney, Waqas, and Sivamani, Raja K.

Subjects
AMMONIA-oxidizing bacteria, PROBIOTICS, ANIMAL coloration, LONGITUDINAL method
Abstract

Background: Both topical and oral probiotics are becoming widely used. There is increasing interest in the cosmetic potential in topical probiotics. Nitrosomonas eutropha is an ammonia‐oxidizing bacteria. Aim: The purpose of this study was to assess whether there is any improvement in facial wrinkles with the use of Nitrosomonas eutropha, a topical probiotic. Methods: In this prospective study, high‐resolution photographs were obtained in twenty‐nine participants at baseline and after using topical Nitrosomonas eutropha for seven days. Results: There was a significant difference in wrinkle depth and severity in the high concentration probiotic group. There was also a statistically significant improvement in pigmentation of the forehead and glabella in the higher concentration group. Conclusions: Nitrosomonas eutropha may have aesthetic benefits in terms of reducing the appearance of wrinkles. Larger studies with longer treatment and follow‐up periods are required. [ABSTRACT FROM AUTHOR]

Published
2020
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19. A glimpse into the somatic mutation landscape of melanoma through exome sequencing of 121 tumor-normal pairs

Author

Hodis, Eran, Watson, Ian, Theurillat, Jean-Philippe, Zou, Lihua, Place, Chelsea, Nickerson, Elizabeth, Auclair, Daniel, Cibulskis, Kristian, Sivachenko, Andrey, Kryukov, Gregory, Stransky, Nicolas, Ramos, Alex H., Voet, Douglas, Lawrence, Michael S., Stojanov, Petar, Saksena, Gordon, McKenna, Aaron, Carter, Scott L., Pugh, Trevor, Noble, Michael, Lin, Pei, Lichtenstein, Lee, Zupko, Robert, Sougnez, Carrie, Guiducci, Candace, Onofrio, Robert C., Ambrogio, Lauren, Fennell, Timothy, Chong, Kelly, Winckler, Wendy, Ardlie, Kristin, Lander, Eric S., Golub, Todd, Meyerson, Matthew, Gabriel, Stacey B., Getz, Gad, Wagner, Stefan, Schadendorf, Dirk, Hoon, Dave S. B., Chin, Lynda, and Garraway, Levi A.

Subjects
Medizin
Published
2012

20. The Genomic Landscape of Pediatric Ewing Sarcoma

Author

Crompton, Brian D., primary, Stewart, Chip, additional, Taylor-Weiner, Amaro, additional, Alexe, Gabriela, additional, Kurek, Kyle C., additional, Calicchio, Monica L., additional, Kiezun, Adam, additional, Carter, Scott L., additional, Shukla, Sachet A., additional, Mehta, Swapnil S., additional, Thorner, Aaron R., additional, de Torres, Carmen, additional, Lavarino, Cinzia, additional, Suñol, Mariona, additional, McKenna, Aaron, additional, Sivachenko, Andrey, additional, Cibulskis, Kristian, additional, Lawrence, Michael S., additional, Stojanov, Petar, additional, Rosenberg, Mara, additional, Ambrogio, Lauren, additional, Auclair, Daniel, additional, Seepo, Sara, additional, Blumenstiel, Brendan, additional, DeFelice, Matthew, additional, Imaz-Rosshandler, Ivan, additional, Schwarz-Cruz y Celis, Angela, additional, Rivera, Miguel N., additional, Rodriguez-Galindo, Carlos, additional, Fleming, Mark D., additional, Golub, Todd R., additional, Getz, Gad, additional, Mora, Jaume, additional, and Stegmaier, Kimberly, additional

Published
2014
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21. Abstract 999: The genomic landscape of pediatric Ewing sarcoma

Author

Crompton, Brian, primary, Stewart, Chip, additional, Taylor-Weiner, Amaro, additional, Alexa, Gabriela, additional, Kurek, Kyle, additional, Calicchio, Monica, additional, Kiezun, Adam, additional, Carter, Scott, additional, Shukla, Sachet, additional, Mehta, Swapnil, additional, Thorner, Aaron, additional, Torres, Carmen de, additional, Lavarino, Cinzia, additional, Sunol, Mariona, additional, McKenna, Aaron, additional, Sivachenko, Andrey, additional, Cibulskis, Kristian, additional, Lawrence, Michael, additional, Ambrogio, Lauren, additional, Auclair, Daniel, additional, Rosshandler, Ivan, additional, Celis, Angela Schwarz-Cruz y, additional, Rivera, Miguel, additional, Rodriguez-Galindo, Carlos, additional, Fleming, Mark, additional, Golub, Todd, additional, Getz, Gad, additional, Mora, Jaume, additional, and Stegmaier, Kimberly, additional

Published
2014
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22. Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

Author

Shern, Jack F., primary, Chen, Li, additional, Chmielecki, Juliann, additional, Wei, Jun S., additional, Patidar, Rajesh, additional, Rosenberg, Mara, additional, Ambrogio, Lauren, additional, Auclair, Daniel, additional, Wang, Jianjun, additional, Song, Young K., additional, Tolman, Catherine, additional, Hurd, Laura, additional, Liao, Hongling, additional, Zhang, Shile, additional, Bogen, Dominik, additional, Brohl, Andrew S., additional, Sindiri, Sivasish, additional, Catchpoole, Daniel, additional, Badgett, Thomas, additional, Getz, Gad, additional, Mora, Jaume, additional, Anderson, James R., additional, Skapek, Stephen X., additional, Barr, Frederic G., additional, Meyerson, Matthew, additional, Hawkins, Douglas S., additional, and Khan, Javed, additional

Published
2014
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23. Landscape of genomic alterations in cervical carcinomas

Author

Ojesina, Akinyemi I., primary, Lichtenstein, Lee, additional, Freeman, Samuel S., additional, Pedamallu, Chandra Sekhar, additional, Imaz-Rosshandler, Ivan, additional, Pugh, Trevor J., additional, Cherniack, Andrew D., additional, Ambrogio, Lauren, additional, Cibulskis, Kristian, additional, Bertelsen, Bjørn, additional, Romero-Cordoba, Sandra, additional, Treviño, Victor, additional, Vazquez-Santillan, Karla, additional, Guadarrama, Alberto Salido, additional, Wright, Alexi A., additional, Rosenberg, Mara W., additional, Duke, Fujiko, additional, Kaplan, Bethany, additional, Wang, Rui, additional, Nickerson, Elizabeth, additional, Walline, Heather M., additional, Lawrence, Michael S., additional, Stewart, Chip, additional, Carter, Scott L., additional, McKenna, Aaron, additional, Rodriguez-Sanchez, Iram P., additional, Espinosa-Castilla, Magali, additional, Woie, Kathrine, additional, Bjorge, Line, additional, Wik, Elisabeth, additional, Halle, Mari K., additional, Hoivik, Erling A., additional, Krakstad, Camilla, additional, Gabiño, Nayeli Belem, additional, Gómez-Macías, Gabriela Sofia, additional, Valdez-Chapa, Lezmes D., additional, Garza-Rodríguez, María Lourdes, additional, Maytorena, German, additional, Vazquez, Jorge, additional, Rodea, Carlos, additional, Cravioto, Adrian, additional, Cortes, Maria L., additional, Greulich, Heidi, additional, Crum, Christopher P., additional, Neuberg, Donna S., additional, Hidalgo-Miranda, Alfredo, additional, Escareno, Claudia Rangel, additional, Akslen, Lars A., additional, Carey, Thomas E., additional, Vintermyr, Olav K., additional, Gabriel, Stacey B., additional, Barrera-Saldaña, Hugo A., additional, Melendez-Zajgla, Jorge, additional, Getz, Gad, additional, Salvesen, Helga B., additional, and Meyerson, Matthew, additional

Published
2013
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24. Abstract 4604: Landscape of human and viral genomic alterations in cervical carcinomas.

Author

Ojesina, Akinyemi I., primary, Lichtenstein, Lee, additional, Ambrogio, Lauren, additional, Cibulskis, Kristian, additional, Freeman, Samuel, additional, Pedamallu, Chandra Sekhar, additional, Bertelsen, Bjørn, additional, Imaz, Ivan, additional, Vazquez, Karla, additional, Salido Guadarrama, Alberto, additional, Treviño, Victor, additional, Romero-Cordoba, Sandra, additional, Duke, Fujiko, additional, Kaplan, Bethany, additional, Rodriguez, Iram, additional, Espinosa Castilla, Magali, additional, Woie, Katherine, additional, Bjorge, Line, additional, Wik, Elisabeth, additional, Halle, Mari K., additional, Høivik, Erling, additional, Krakstad, Camilla, additional, Gómez Macías, Gabriela, additional, de Lourdes Garza Rodríguez, María, additional, Vazquez, Jorge, additional, Rodea, Carlos, additional, Cravioto, Adrian, additional, Cortes, Maria L., additional, Greulich, Heidi, additional, Crum, Christopher P., additional, Akslen, Lars, additional, Barrera Saldaña, Hugo, additional, Melendez-Zajgla, Jorge, additional, Getz, Gad, additional, Salvesen, Helga B., additional, and Meyerson, Matthew L., additional

Published
2013
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25. Abstract 3806: Progressive biallelic loss of TP53 is associated with progression of pleuropulmonary blastoma initiated by germline loss and somatic mutation of DICER1.

Author

Pugh, Trevor J., primary, Yu, Weiying, additional, Yang, Jiandong, additional, Ambrogio, Lauren, additional, Carter, Scott L., additional, Kiezun, Adam, additional, McKenna, Aaron, additional, Giannikopoulos, Petros, additional, Getz, Gad, additional, Messinger, Yoav, additional, Meyerson, Matthew, additional, and Hill, D. Ashley, additional

Published
2013
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26. Abstract 2570: An integrated germline analysis platform for comprehensive clinical cancer genomics.

Author

Van Allen, Eliezer M., primary, Wagle, Nikhil, additional, Keizun, Adam, additional, Kryukov, Gregory, additional, McKenna, Aaron, additional, Huang, Franklin, additional, Hiller, Elaine, additional, Rainville, Irene, additional, Auclair, Daniel, additional, Ambrogio, Lauren, additional, Gray, Stacy, additional, Joffe, Steven, additional, Getz, Gad, additional, Garber, Judy, additional, and Garraway, Levi, additional

Published
2013
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27. Abstract 3152: CanSeq: prospective clinical whole-exome sequencing of FFPE tumor samples.

Author

Wagle, Nikhil, primary, Van Allen, Eliezer, additional, Perrin, Danielle, additional, Friedrich, Dennis, additional, Fisher, Sheila, additional, Kryukov, Gregory, additional, Ambrogio, Lauren, additional, Auclair, Daniel, additional, Gray, Stacy, additional, Joffe, Steven, additional, Janne, Pasi, additional, Garber, Judy, additional, Macconaill, Laura, additional, Lindeman, Neal, additional, Rollins, Barrett, additional, Kantoff, Phillip, additional, Getz, Gad, additional, Gabriel, Stacey, additional, and Garraway, Levi A., additional

Published
2013
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29. 1314 RECURRENT MUTATIONS IN SPOP DEFINE A DISTINCT MOLECULAR CLASS OF PROSTATE CANCER

Author

Barbieri, Christopher, primary, Baca, Sylvan, additional, Demichelis, Francesca, additional, Lawrence, Michael, additional, Blattner, Mija, additional, Theurillat, Jean-Philippe, additional, Boysen, Gunther, additional, Stojanov, Petar, additional, Van Allen, Eli, additional, Stransky, Nico, additional, Nickerson, Elizabeth, additional, Park, Kyung, additional, Kitabayashi, Naoki, additional, MacDonald, Theresa, additional, Vuong, Terry, additional, Auclair, Daniel, additional, Onofrio, Robert, additional, Guiducci, Candace, additional, Cibulskis, Kristian, additional, Sivachenko, Andrey, additional, Carter, Scott, additional, Ambrogio, Lauren, additional, Parkin, Melissa, additional, White, Thomas, additional, Saksena, Gordon, additional, Voet, Douglas, additional, Ramos, Alex H., additional, Winckler, Wendy, additional, Hussain, Wasay, additional, Wilkinson, Jane, additional, Ardlie, Kristin, additional, Banerjee, Samprit, additional, Baldwin, Jennifer, additional, Mosquera, Juan Miguel, additional, Gabriel, Stacey B., additional, Kantoff, Philip W., additional, Golub, Todd R., additional, Meyerson, Matthew, additional, Lander, Eric S., additional, Getz, Gad, additional, Nelson, Peter, additional, Garraway, Levi A., additional, Tewari, Ashutosh, additional, and Rubin, Mark A., additional

Published
2012
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30. Abstract 5056: A glimpse into the somatic mutation landscape of melanoma through exome sequencing of 121 tumor-normal pairs

Author

Hodis, Eran, primary, Watson, Ian, additional, Theurillat, Jean-Philippe, additional, Zou, Lihua, additional, Place, Chelsea, additional, Nickerson, Elizabeth, additional, Auclair, Daniel, additional, Cibulskis, Kristian, additional, Sivachenko, Andrey, additional, Kryukov, Gregory, additional, Stransky, Nicolas, additional, Ramos, Alex H., additional, Voet, Douglas, additional, Lawrence, Michael S., additional, Stojanov, Petar, additional, Saksena, Gordon, additional, McKenna, Aaron, additional, Carter, Scott L., additional, Pugh, Trevor, additional, Noble, Michael, additional, Lin, Pei, additional, Lichtenstein, Lee, additional, Zupko, Robert, additional, Sougnez, Carrie, additional, Guiducci, Candace, additional, Onofrio, Robert C., additional, Ambrogio, Lauren, additional, Fennell, Timothy, additional, Chong, Kelly, additional, Winckler, Wendy, additional, Ardlie, Kristin, additional, Lander, Eric S., additional, Golub, Todd, additional, Meyerson, Matthew, additional, Gabriel, Stacey B., additional, Getz, Gad, additional, Wagner, Stefan, additional, Schadendorf, Dirk, additional, Hoon, Dave S. B., additional, Chin, Lynda, additional, and Garraway, Levi A., additional

Published
2012
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31. Predicting Relapse in Patients With Medulloblastoma by Integrating Evidence From Clinical and Genomic Features

Author

Tamayo, Pablo, primary, Cho, Yoon-Jae, additional, Tsherniak, Aviad, additional, Greulich, Heidi, additional, Ambrogio, Lauren, additional, Schouten-van Meeteren, Netteke, additional, Zhou, Tianni, additional, Buxton, Allen, additional, Kool, Marcel, additional, Meyerson, Matthew, additional, Pomeroy, Scott L., additional, and Mesirov, Jill P., additional

Published
2011
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32. Abstract 3925: Characterization of complex chromosomal aberrations in prostate cancer from whole genome sequencing

Author

Berger, Michael F., primary, Lawrence, Michael S., additional, Demichelis, Francesca, additional, Drier, Yotam, additional, Cibulskis, Kristian, additional, Sivachenko, Andrey Y., additional, Sboner, Andrea, additional, Esgueva, Raquel, additional, Pflueger, Dorothee, additional, Sougnez, Carrie, additional, Onofrio, Robert, additional, Carter, Scott L., additional, Park, Kyung, additional, Habegger, Lukas, additional, Ambrogio, Lauren, additional, Fennell, Timothy, additional, Parkin, Melissa, additional, Saksena, Gordon, additional, Voet, Douglas, additional, Ramos, Alex H., additional, Pugh, Trevor J., additional, Wilkinson, Jane, additional, Fisher, Sheila, additional, Winckler, Wendy, additional, Mahan, Scott, additional, Ardlie, Kristin, additional, Baldwin, Jennifer, additional, Simons, Jonathan W., additional, Kitabayashi, Naoki, additional, MacDonald, Theresa Y., additional, Kantoff, Philip W., additional, Chin, Lynda, additional, Gabriel, Stacey B., additional, Gerstein, Mark B., additional, Golub, Todd R., additional, Meyerson, Matthew, additional, Tewari, Ashutosh, additional, Lander, Eric S., additional, Getz, Gad, additional, Rubin, Mark A., additional, and Garraway, Levi A., additional

Published
2011
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33. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

Author

Fisher, Sheila, primary, Barry, Andrew, additional, Abreu, Justin, additional, Minie, Brian, additional, Nolan, Jillian, additional, Delorey, Toni M, additional, Young, Geneva, additional, Fennell, Timothy J, additional, Allen, Alexander, additional, Ambrogio, Lauren, additional, Berlin, Aaron M, additional, Blumenstiel, Brendan, additional, Cibulskis, Kristian, additional, Friedrich, Dennis, additional, Johnson, Ryan, additional, Juhn, Frank, additional, Reilly, Brian, additional, Shammas, Ramy, additional, Stalker, John, additional, Sykes, Sean M, additional, Thompson, Jon, additional, Walsh, John, additional, Zimmer, Andrew, additional, Zwirko, Zac, additional, Gabriel, Stacey, additional, Nicol, Robert, additional, and Nusbaum, Chad, additional

Published
2011
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34. Exome Sequencing,ANGPTL3Mutations, and Familial Combined Hypolipidemia

Author

Musunuru, Kiran, primary, Pirruccello, James P., additional, Do, Ron, additional, Peloso, Gina M., additional, Guiducci, Candace, additional, Sougnez, Carrie, additional, Garimella, Kiran V., additional, Fisher, Sheila, additional, Abreu, Justin, additional, Barry, Andrew J., additional, Fennell, Tim, additional, Banks, Eric, additional, Ambrogio, Lauren, additional, Cibulskis, Kristian, additional, Kernytsky, Andrew, additional, Gonzalez, Elena, additional, Rudzicz, Nicholas, additional, Engert, James C., additional, DePristo, Mark A., additional, Daly, Mark J., additional, Cohen, Jonathan C., additional, Hobbs, Helen H., additional, Altshuler, David, additional, Schonfeld, Gustav, additional, Gabriel, Stacey B., additional, Yue, Pin, additional, and Kathiresan, Sekar, additional

Published
2010
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35. Abstract 1139: Complete characterization of prostate cancer genomes by massively parallel sequencing

Author

Berger, Michael F., primary, Lawrence, Michael S., additional, Cibulskis, Kristian, additional, Pflueger, Dorothee, additional, Demichelis, Francesca, additional, Sougnez, Carrie, additional, Onofrio, Robert C., additional, Ambrogio, Lauren, additional, Fennell, Timothy, additional, Parkin, Melissa, additional, Carter, Scott L., additional, Saksena, Gordon, additional, Sivachenko, Andrey, additional, Voet, Douglas, additional, Wilkinson, Jane, additional, Fisher, Sheila, additional, Winckler, Wendy, additional, Ardlie, Kristin, additional, Chant, John, additional, Baldwin, Jennifer, additional, Gerstein, Mark, additional, Golub, Todd R., additional, Meyerson, Matthew, additional, Tewari, Ashutosh K., additional, Gabriel, Stacey B., additional, Lander, Eric S., additional, Getz, Gad, additional, Rubin, Mark A., additional, and Garraway, Levi A., additional

Published
2010
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36. Integrative Genomic Approaches Identify IKBKE as a Breast Cancer Oncogene

Author

Boehm, Jesse S., primary, Zhao, Jean J., additional, Yao, Jun, additional, Kim, So Young, additional, Firestein, Ron, additional, Dunn, Ian F., additional, Sjostrom, Sarah K., additional, Garraway, Levi A., additional, Weremowicz, Stanislawa, additional, Richardson, Andrea L., additional, Greulich, Heidi, additional, Stewart, Carly J., additional, Mulvey, Laura A., additional, Shen, Rhine R., additional, Ambrogio, Lauren, additional, Hirozane-Kishikawa, Tomoko, additional, Hill, David E., additional, Vidal, Marc, additional, Meyerson, Matthew, additional, Grenier, Jennifer K., additional, Hinkle, Greg, additional, Root, David E., additional, Roberts, Thomas M., additional, Lander, Eric S., additional, Polyak, Kornelia, additional, and Hahn, William C., additional

Published
2007
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37. Mutational heterogeneity in cancer and the search for new cancer genes

Author

Lawrence, Michael S., Stojanov, Petar, Polak, Paz, Kryukov, Gregory V., Cibulskis, Kristian, Sivachenko, Andrey, Carter, Scott L., Stewart, Chip, Mermel, Craig H., Roberts, Steven A., Kiezun, Adam, Hammerman, Peter S., McKenna, Aaron, Drier, Yotam, Zou, Lihua, Ramos, Alex H., Pugh, Trevor J., Stransky, Nicolas, Helman, Elena, Kim, Jaegil, Sougnez, Carrie, Ambrogio, Lauren, Nickerson, Elizabeth, Shefler, Erica, Cortés, Maria L., Auclair, Daniel, Saksena, Gordon, Voet, Douglas, Noble, Michael, DiCara, Daniel, Lin, Pei, Lichtenstein, Lee, Heiman, David I., Fennell, Timothy, Imielinski, Marcin, Hernandez, Bryan, Hodis, Eran, Baca, Sylvan, Dulak, Austin M., Lohr, Jens, Landau, Dan-Avi, Wu, Catherine J., Melendez-Zajgla, Jorge, Hidalgo-Miranda, Alfredo, Koren, Amnon, McCarroll, Steven A., Mora, Jaume, Crompton, Brian, Onofrio, Robert, Parkin, Melissa, Winckler, Wendy, Ardlie, Kristin, Gabriel, Stacey B., Roberts, Charles W. M., Biegel, Jaclyn A., Stegmaier, Kimberly, Bass, Adam J., Garraway, Levi A., Meyerson, Matthew, Golub, Todd R., Gordenin, Dmitry A., Sunyaev, Shamil, Lander, Eric S., and Getz, Gad

Abstract

Major international projects are now underway aimed at creating a comprehensive catalog of all genes responsible for the initiation and progression of cancer. These studies involve sequencing of matched tumor–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here, we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false positive findings that overshadow true driver events. Here, we show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumor-normal pairs and discover extraordinary variation in (i) mutation frequency and spectrum within cancer types, which shed light on mutational processes and disease etiology, and (ii) mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and allow true cancer genes to rise to attention.

Published
2014
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38. Mapping Copy Number Variation by Population Scale Genome Sequencing

Author

Mills, Ryan Edward, Handsaker, Robert E, Korn, Joshua, Nemesh, James, Shi, Xinghua, Lee, Charles, McCarroll, Steven A., Altshuler, David Matthew, Gabriel, Stacey B., Lander, Eric Steven, Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., Daly, Mark Joseph, DePristo, Mark A., Ball, Aaron D., Banks, Eric, Browning, Brian L., Garimella, Kiran V., Grossman, Sharon Rachel, Hanna, Matt, Hartl, Chris, Kernytsky, Andrew M., Li, Heng, Maguire, Jared R., McKenna, Aaron, Philippakis, Anthony Andrew, Poplin, Ryan E., Price, Alkes, Rivas, Manuel A., Sabeti, Pardis Christine, Schaffner, Stephen, Shlyakhter, Ilya, and Wilkinson, Jane

Subjects
genetics and genomics, molecular biology, evolution
Abstract

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies., Organismic and Evolutionary Biology

Published
2011
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39. A Map of Human Genome Variation from Population Scale Sequencing

Author

Altshuler, David Matthew, Lander, Eric Steven, Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Gabriel, Stacey B., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., Lee, Charles, Mills, Ryan Edward, Shi, Xinghua, Daly, Mark Joseph, DePristo, Mark A., Ball, Aaron D., Banks, Eric, Browning, Brian L., Garimella, Kiran V., Grossman, Sharon Rachel, Handsaker, Robert E, Hanna, Matt, Hartl, Chris, Kernytsky, Andrew M., Korn, Joshua M., Li, Heng, Maguire, Jared R., McCarroll, Steven A., Nemesh, James C., McKenna, Aaron, Philippakis, Anthony Andrew, Poplin, Ryan E., Price, Alkes, Rivas, Manuel A., Sabeti, Pardis Christine, Schaffner, Stephen, and Shlyakhter, Ilya

Subjects
wide association, gene-expression, recombination hotspots, meiotic recombination, genotype imputation, rare variants, haplotype map, nucleotide, diseases
Abstract

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother–father–child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately \(10^{−8}\) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research., Organismic and Evolutionary Biology, Other Research Unit

Published
2010
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40. Demographic history and rare allele sharing among human populations

Author

Gravel, Simon, Henn, Brenna M., Gutenkunst, Ryan N., Indap, Amit R., Marth, Gabor T., Clark, Andrew G., Yu, Fuli, Gibbs, Richard A., Bustamante, Carlos D., Altshuler, David L., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Collins, Francis S., De La Vega, Francisco M., Donnelly, Peter, Egholm, Michael, Flicek, Paul, Gabriel, Stacey B., 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., Deiros, David, Metzker, Mike, Muzny, Donna, Reid, Jeff, Wheeler, David, Li, Jingxiang, Jian, Min, Li, Guoqing, Li, Ruiqiang, Liang, Huiqing, Tian, Geng, Wang, Bo, Wang, Jian, Wang, Wei, Yang, Huanming, Zhang, Xiuqing, Zheng, Huisong, Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., 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, 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, 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, Dooling, David, Fulton, Lucinda, Fulton, Robert, Weinstock, George, 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, Jin, Fang, Xiaodong, Guo, Xiaosen, Li, Yingrui, Luo, Ruibang, Tai, Shuaishuai, Wu, Honglong, Zheng, Hancheng, Zheng, Xiaole, Zhou, Yan, Garrison, Erik P., Huang, Weichun, Indap, Amit, Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, 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., Boyko, Adam, Degenhardt, Jeremiah, Kaganovich, Mark, Keinan, Alon, Lacroute, Phil, Ma, Xin, Reynolds, Andy, Clarke, Laura, 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., Bauer, Markus, Cheetham, R. Keira, Cox, Tony, Eberle, Michael, James, Terena, Kahn, Scott, Murray, Lisa, Ye, Kai, 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., 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, Auton, Adam, Iqbal, Zamin, Lunter, Gerton, Marchini, Jonathan L., Moutsianas, Loukas, Myers, Simon, Tumian, Afidalina, 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., Melton, S. Cord, Li, Yun, Anderson, Paul, Blackwell, Tom, Chen, Wei, Cookson, William O., Ding, Jun, Kang, Hyun Min, 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, Kidd, Jeffrey M., Sahinalp, S. Cenk, Sudmant, Peter H., 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., Le, Si Quang, 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, Mu, Xinmeng Jasmine, Urban, Alexander E., Zhang, Zhengdong, Coafra, Cristian, Dinh, Huyen, Kovar, Christie, Lee, Sandy, Nazareth, Lynne, Wilkinson, Jane, Coffey, Allison, Scott, Carol, Gharani, Neda, Kaye, Jane S., Kent, Alastair, Li, Taosha, McGuire, Amy L., Ossorio, Pilar N., Rotimi, Charles N., Su, Yeyang, Toji, Lorraine H., TylerSmith, Chris, 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., Peterson, Jane L., Gravel, Simon, Henn, Brenna M., Gutenkunst, Ryan N., Indap, Amit R., Marth, Gabor T., Clark, Andrew G., Yu, Fuli, Gibbs, Richard A., Bustamante, Carlos D., Altshuler, David L., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Collins, Francis S., De La Vega, Francisco M., Donnelly, Peter, Egholm, Michael, Flicek, Paul, Gabriel, Stacey B., 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., Deiros, David, Metzker, Mike, Muzny, Donna, Reid, Jeff, Wheeler, David, Li, Jingxiang, Jian, Min, Li, Guoqing, Li, Ruiqiang, Liang, Huiqing, Tian, Geng, Wang, Bo, Wang, Jian, Wang, Wei, Yang, Huanming, Zhang, Xiuqing, Zheng, Huisong, Ambrogio, Lauren, Bloom, Toby, Cibulskis, Kristian, Fennell, Tim J., Jaffe, David B., Shefler, Erica, Sougnez, Carrie L., 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, 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, 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, Dooling, David, Fulton, Lucinda, Fulton, Robert, Weinstock, George, 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, Jin, Fang, Xiaodong, Guo, Xiaosen, Li, Yingrui, Luo, Ruibang, Tai, Shuaishuai, Wu, Honglong, Zheng, Hancheng, Zheng, Xiaole, Zhou, Yan, Garrison, Erik P., Huang, Weichun, Indap, Amit, Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, 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., Boyko, Adam, Degenhardt, Jeremiah, Kaganovich, Mark, Keinan, Alon, Lacroute, Phil, Ma, Xin, Reynolds, Andy, Clarke, Laura, 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., Bauer, Markus, Cheetham, R. Keira, Cox, Tony, Eberle, Michael, James, Terena, Kahn, Scott, Murray, Lisa, Ye, Kai, 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., 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, Auton, Adam, Iqbal, Zamin, Lunter, Gerton, Marchini, Jonathan L., Moutsianas, Loukas, Myers, Simon, Tumian, Afidalina, 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., Melton, S. Cord, Li, Yun, Anderson, Paul, Blackwell, Tom, Chen, Wei, Cookson, William O., Ding, Jun, Kang, Hyun Min, 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, Kidd, Jeffrey M., Sahinalp, S. Cenk, Sudmant, Peter H., 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., Le, Si Quang, 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, Mu, Xinmeng Jasmine, Urban, Alexander E., Zhang, Zhengdong, Coafra, Cristian, Dinh, Huyen, Kovar, Christie, Lee, Sandy, Nazareth, Lynne, Wilkinson, Jane, Coffey, Allison, Scott, Carol, Gharani, Neda, Kaye, Jane S., Kent, Alastair, Li, Taosha, McGuire, Amy L., Ossorio, Pilar N., Rotimi, Charles N., Su, Yeyang, Toji, Lorraine H., TylerSmith, Chris, 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.

Abstract

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence.

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