Attenzione: i dati modificati non sono ancora stati salvati. Per confermare inserimenti o cancellazioni di voci è necessario confermare con il tasto SALVA/INSERISCI in fondo alla pagina
IRIS Institutional Research Information System - AIR Archivio Istituzionale della Ricerca
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. The dataset created by this analysis includes 3.5 million somatic variants and forms the basis for PanCan Atlas papers. The results have been made available to the research community along with the methods used to generate them. This project is the result of collaboration from a number of institutes and demonstrates how team science drives extremely large genomics projects.
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines / K. Ellrott, M.H. Bailey, G. Saksena, K.R. Covington, C. Kandoth, C. Stewart, J. Hess, M. Singer, K.E. Chiotti, M. Mclellan, H.J. Sofia, C. Hutter, G. Getz, D. Wheeler, L. Ding, S.J. Caesar-Johnson, J.A. Demchok, I. Felau, M. Kasapi, M.L. Ferguson, C.M. Hutter, H.J. Sofia, R. Tarnuzzer, Z. Wang, L. Yang, J.C. Zenklusen, J.(. Zhang, S. Chudamani, J. Liu, L. Lolla, R. Naresh, T. Pihl, Q. Sun, Y. Wan, W. Ye, J. Cho, T. Defreitas, S. Frazer, N. Gehlenborg, G. Getz, D.I. Heiman, J. Kim, M.S. Lawrence, P. Lin, S. Meier, M.S. Noble, G. Saksena, D. Voet, H. Zhang, B. Bernard, N. Chambwe, V. Dhankani, T. Knijnenburg, R. Kramer, K. Leinonen, Y. Liu, M. Miller, S. Reynolds, I. Shmulevich, V. Thorsson, W. Zhang, R. Akbani, B.M. Broom, A.M. Hegde, J. Zhenlin, R.S. Kanchi, A. Korkut, L. Jun, H. Liang, S. Ling, W. Liu, L. Yiling, G.B. Mills, N. Kwok-Shing, A. Rao, M. Ryan, J. Wang, J.N. Weinstein, J. Zhang, A. Abeshouse, J. Armenia, D. Chakravarty, W.K. Chatila, I. de Bruijn, J. Gao, B.E. Gross, Z.J. Heins, R. Kundra, L. Konnor, M. Ladanyi, A. Luna, M.G. Nissan, A. Ochoa, S.M. Phillips, E. Reznik, F. Sanchez-Vega, C. Sander, N. Schultz, R. Sheridan, S.O. Sumer, Y. Sun, B.S. Taylor, J. Wang, H. Zhang, P. Anur, M. Peto, P. Spellman, C. Benz, J.M. Stuart, C.K. Wong, C. Yau, D.N. Hayes, N. Parker, M.D. Wilkerson, A. Ally, M. Balasundaram, R. Bowlby, D. Brooks, R. Carlsen, E. Chuah, N. Dhalla, R. Holt, S.J.M. Jones, K. Kasaian, D. Lee, M. Yussanne, M.A. Marra, M. Mayo, R.A. Moore, A.J. Mungall, K. Mungall, A.G. Robertson, S. Sadeghi, J.E. Schein, P. Sipahimalani, A. Tam, N. Thiessen, K. Tse, T. Wong, A.C. Berger, R. Beroukhim, A.D. Cherniack, C. Cibulskis, S.B. Gabriel, G.F. Gao, H. Gavin, M. Meyerson, S.E. Schumacher, J. Shih, M.H. Kucherlapati, R.S. Kucherlapati, S. Baylin, L. Cope, L. Danilova, M.S. Bootwalla, P.H. Lai, D.T. Maglinte, D.J. Van Den Berg, D.J. Weisenberger, J.T. Auman, S. Balu, T. Bodenheimer, C. Fan, K.A. Hoadley, A.P. Hoyle, S.R. Jefferys, C.D. Jones, S. Meng, P.A. Mieczkowski, L.E. Mose, A.H. Perou, C.M. Perou, J. Roach, Y. Shi, J.V. Simons, T. Skelly, M.G. Soloway, D. Tan, U. Veluvolu, H. Fan, T. Hinoue, P.W. Laird, H. Shen, W. Zhou, M. Bellair, K. Chang, K. Covington, C.J. Creighton, H. Dinh, H. Doddapaneni, L.A. Donehower, J. Drummond, R.A. Gibbs, R. Glenn, W. Hale, Y. Han, H. Jianhong, V. Korchina, S. Lee, L. Lewis, L. Wei, X. Liu, M. Morgan, D. Morton, D. Muzny, J. Santibanez, M. Sheth, E. Shinbrot, L. Wang, M. Wang, D.A. Wheeler, X. Liu, F. Zhao, J. Hess, E.L. Appelbaum, M. Bailey, M.G. Cordes, L. Ding, C.C. Fronick, L.A. Fulton, R.S. Fulton, C. Kandoth, E.R. Mardis, M.D. Mclellan, C.A. Miller, H.K. Schmidt, R.K. Wilson, D. Crain, E. Curley, J. Gardner, K. Lau, D. Mallery, S. Morris, J. Paulauskis, R. Penny, C. Shelton, T. Shelton, M. Sherman, E. Thompson, P. Yena, J. Bowen, J.M. Gastier-Foster, M. Gerken, K.M. Leraas, T.M. Lichtenberg, N.C. Ramirez, L. Wise, E. Zmuda, N. Corcoran, T. Costello, C. Hovens, A.L. Carvalho, A.C. de Carvalho, J.H. Fregnani, A. Longatto-Filho, R.M. Reis, C. Scapulatempo-Neto, H.C.S. Silveira, D.O. Vidal, A. Burnette, J. Eschbacher, B. Hermes, A. Noss, R. Singh, M.L. Anderson, P.D. Castro, M. Ittmann, D. Huntsman, B. Kohl, L. Xuan, R. Thorp, C. Andry, E.R. Duffy, V. Lyadov, O. Paklina, G. Setdikova, A. Shabunin, M. Tavobilov, C. Mcpherson, R. Warnick, R. Berkowitz, D. Cramer, C. Feltmate, N. Horowitz, A. Kibel, M. Muto, C.P. Raut, A. Malykh, J.S. Barnholtz-Sloan, W. Barrett, K. Devine, J. Fulop, Q.T. Ostrom, K. Shimmel, Y. Wolinsky, A.E. Sloan, A. De Rose, F. Giuliante, M. Goodman, B.Y. Karlan, C.H. Hagedorn, J. Eckman, J. Harr, J. Myers, K. Tucker, L.A. Zach, B. Deyarmin, H. Hai, L. Kvecher, C. Larson, R.J. Mural, S. Somiari, A. Vicha, T. Zelinka, J. Bennett, M. Iacocca, B. Rabeno, P. Swanson, M. Latour, L. Lacombe, B. Têtu, A. Bergeron, M. Mcgraw, S.M. Staugaitis, J. Chabot, H. Hibshoosh, A. Sepulveda, S. Tao, T. Wang, O. Potapova, O. Voronina, L. Desjardins, O. Mariani, S. Roman-Roman, X. Sastre, M. Stern, F. Cheng, S. Signoretti, A. Berchuck, D. Bigner, E. Lipp, J. Marks, S. Mccall, R. Mclendon, A. Secord, A. Sharp, M. Behera, D.J. Brat, A. Chen, K. Delman, S. Force, F. Khuri, K. Magliocca, S. Maithel, J.J. Olson, T. Owonikoko, A. Pickens, S. Ramalingam, D.M. Shin, G. Sica, E.G. Van Meir, H. Zhang, W. Eijckenboom, A. Gillis, E. Korpershoek, L. Looijenga, W. Oosterhuis, H. Stoop, K.E. van Kessel, E.C. Zwarthoff, C. Calatozzolo, L. Cuppini, S. Cuzzubbo, F. Dimeco, G. Finocchiaro, L. Mattei, A. Perin, B. Pollo, C. Chen, J. Houck, P. Lohavanichbutr, A. Hartmann, C. Stoehr, R. Stoehr, H. Taubert, S. Wach, B. Wullich, W. Kycler, D. Murawa, M. Wiznerowicz, K. Chung, W.J. Edenfield, J. Martin, E. Baudin, G. Bubley, R. Bueno, A. De Rienzo, W.G. Richards, S. Kalkanis, T. Mikkelsen, H. Noushmehr, L. Scarpace, N. Girard, M. Aymerich, E. Campo, E. Giné, A.L. Guillermo, N. Van Bang, P.T. Hanh, B.D. Phu, Y. Tang, H. Colman, K. Evason, P.R. Dottino, J.A. Martignetti, H. Gabra, H. Juhl, T. Akeredolu, S. Stepa, D. Hoon, K. Ahn, K.J. Kang, F. Beuschlein, A. Breggia, M. Birrer, D. Bell, M. Borad, A.H. Bryce, E. Castle, V. Chandan, J. Cheville, J.A. Copland, M. Farnell, T. Flotte, N. Giama, H. Thai, M. Kendrick, J. Kocher, K. Kopp, C. Moser, D. Nagorney, D. O’Brien, B.P. O’Neill, T. Patel, G. Petersen, F. Que, M. Rivera, L. Roberts, R. Smallridge, T. Smyrk, M. Stanton, R.H. Thompson, M. Torbenson, J.D. Yang, L. Zhang, F. Brimo, J.A. Ajani, A.M. Angulo Gonzalez, C. Behrens, J. Bondaruk, R. Broaddus, B. Czerniak, B. Esmaeli, J. Fujimoto, J. Gershenwald, C. Guo, A.J. Lazar, C. Logothetis, F. Meric-Bernstam, C. Moran, L. Ramondetta, D. Rice, A. Sood, P. Tamboli, T. Thompson, P. Troncoso, A. Tsao, I. Wistuba, C. Carter, L. Haydu, P. Hersey, V. Jakrot, H. Kakavand, R. Kefford, K. Lee, G. Long, G. Mann, M. Quinn, R. Saw, R. Scolyer, K. Shannon, A. Spillane, J. Stretch, M. Synott, J. Thompson, J. Wilmott, H. Al-Ahmadie, T.A. Chan, R. Ghossein, A. Gopalan, D.A. Levine, V. Reuter, S. Singer, B. Singh, N.V. Tien, T. Broudy, C. Mirsaidi, P. Nair, P. Drwiega, J. Miller, J. Smith, H. Zaren, J. Park, N.P. Hung, E. Kebebew, W.M. Linehan, A.R. Metwalli, K. Pacak, P.A. Pinto, M. Schiffman, L.S. Schmidt, C.D. Vocke, N. Wentzensen, R. Worrell, H. Yang, M. Moncrieff, C. Goparaju, J. Melamed, H. Pass, N. Botnariuc, I. Caraman, M. Cernat, I. Chemencedji, A. Clipca, S. Doruc, G. Gorincioi, S. Mura, M. Pirtac, I. Stancul, D. Tcaciuc, M. Albert, I. Alexopoulou, A. Arnaout, J. Bartlett, J. Engel, S. Gilbert, J. Parfitt, H. Sekhon, G. Thomas, D.M. Rassl, R.C. Rintoul, C. Bifulco, R. Tamakawa, W. Urba, N. Hayward, H. Timmers, A. Antenucci, F. Facciolo, G. Grazi, M. Marino, R. Merola, R. de Krijger, A. Gimenez-Roqueplo, A. Piché, S. Chevalier, G. Mckercher, K. Birsoy, G. Barnett, C. Brewer, C. Farver, T. Naska, N.A. Pennell, D. Raymond, C. Schilero, K. Smolenski, F. Williams, C. Morrison, J.A. Borgia, M.J. Liptay, M. Pool, C.W. Seder, K. Junker, L. Omberg, M. Dinkin, G. Manikhas, D. Alvaro, M.C. Bragazzi, V. Cardinale, G. Carpino, E. Gaudio, D. Chesla, S. Cottingham, M. Dubina, F. Moiseenko, R. Dhanasekaran, K. Becker, K. Janssen, J. Slotta-Huspenina, M.H. Abdel-Rahman, D. Aziz, S. Bell, C.M. Cebulla, A. Davis, R. Duell, J.B. Elder, J. Hilty, B. Kumar, J. Lang, N.L. Lehman, R. Mandt, P. Nguyen, R. Pilarski, K. Rai, L. Schoenfield, K. Senecal, P. Wakely, P. Hansen, R. Lechan, J. Powers, A. Tischler, W.E. Grizzle, K.C. Sexton, A. Kastl, J. Henderson, S. Porten, J. Waldmann, M. Fassnacht, S.L. Asa, D. Schadendorf, M. Couce, M. Graefen, H. Huland, G. Sauter, T. Schlomm, R. Simon, P. Tennstedt, O. Olabode, M. Nelson, O. Bathe, P.R. Carroll, J.M. Chan, P. Disaia, P. Glenn, R.K. Kelley, C.N. Landen, J. Phillips, M. Prados, J. Simko, K. Smith-McCune, S. Vandenberg, K. Roggin, A. Fehrenbach, A. Kendler, S. Sifri, R. Steele, A. Jimeno, F. Carey, I. Forgie, M. Mannelli, M. Carney, B. Hernandez, B. Campos, C. Herold-Mende, C. Jungk, A. Unterberg, A. von Deimling, A. Bossler, J. Galbraith, L. Jacobus, M. Knudson, T. Knutson, M. Deqin, M. Milhem, R. Sigmund, A.K. Godwin, R. Madan, H.G. Rosenthal, C. Adebamowo, S.N. Adebamowo, A. Boussioutas, D. Beer, T. Giordano, A. Mes-Masson, F. Saad, T. Bocklage, L. Landrum, R. Mannel, K. Moore, K. Moxley, R. Postier, J. Walker, R. Zuna, M. Feldman, F. Valdivieso, R. Dhir, J. Luketich, E.M. Mora Pinero, M. Quintero-Aguilo, C.G. Carlotti, J.S. Dos Santos, R. Kemp, A. Sankarankuty, D. Tirapelli, J. Catto, K. Agnew, E. Swisher, J. Creaney, B. Robinson, C.S. Shelley, E.M. Godwin, S. Kendall, C. Shipman, C. Bradford, T. Carey, A. Haddad, J. Moyer, L. Peterson, M. Prince, L. Rozek, G. Wolf, R. Bowman, K.M. Fong, I. Yang, R. Korst, W.K. Rathmell, J.L. Fantacone-Campbell, J.A. Hooke, A.J. Kovatich, C.D. Shriver, J. Dipersio, B. Drake, R. Govindan, S. Heath, T. Ley, B. Van Tine, P. Westervelt, M.A. Rubin, J.I. Lee, N.D. Aredes, A. Mariamidze. - In: CELL SYSTEMS. - ISSN 2405-4712. - 6:3(2018 Mar 28), pp. 271-281.e7. [10.1016/j.cels.2018.03.002]
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
Ellrott, Kyle
;Bailey, Matthew H.;Saksena, Gordon;Covington, Kyle R.;Kandoth, Cyriac;Stewart, Chip;Hess, Julian;Ma, Singer;Chiotti, Kami E.;McLellan, Michael;Sofia, Heidi J.;Hutter, Carolyn;Getz, Gad;Wheeler, David;Ding, Li;Caesar-Johnson, Samantha J.;Demchok, John A.;Felau, Ina;Kasapi, Melpomeni;Ferguson, Martin L.;Hutter, Carolyn M.;Sofia, Heidi J.;Tarnuzzer, Roy;Wang, Zhining;Yang, Liming;Zenklusen, Jean C.;Zhang, Jiashan (Julia);Chudamani, Sudha;Liu, Jia;Lolla, Laxmi;Naresh, Rashi;Pihl, Todd;Sun, Qiang;Wan, Yunhu;Wu, Ye;Cho, Juok;DeFreitas, Timothy;Frazer, Scott;Gehlenborg, Nils;Getz, Gad;Heiman, David I.;Kim, Jaegil;Lawrence, Michael S.;Lin, Pei;Meier, Sam;Noble, Michael S.;Saksena, Gordon;Voet, Doug;Zhang, Hailei;Bernard, Brady;Chambwe, Nyasha;Dhankani, Varsha;Knijnenburg, Theo;Kramer, Roger;Leinonen, Kalle;Liu, Yuexin;Miller, Michael;Reynolds, Sheila;Shmulevich, Ilya;Thorsson, Vesteinn;Zhang, Wei;Akbani, Rehan;Broom, Bradley M.;Hegde, Apurva M.;Ju, Zhenlin;Kanchi, Rupa S.;Korkut, Anil;Li, Jun;Liang, Han;Ling, Shiyun;Liu, Wenbin;Lu, Yiling;Mills, Gordon B.;Ng, Kwok-Shing;Rao, Arvind;Ryan, Michael;Wang, Jing;Weinstein, John N.;Zhang, Jiexin;Abeshouse, Adam;Armenia, Joshua;Chakravarty, Debyani;Chatila, Walid K.;de Bruijn, Ino;Gao, Jianjiong;Gross, Benjamin E.;Heins, Zachary J.;Kundra, Ritika;La, Konnor;Ladanyi, Marc;Luna, Augustin;Nissan, Moriah G.;Ochoa, Angelica;Phillips, Sarah M.;Reznik, Ed;Sanchez-Vega, Francisco;Sander, Chris;Schultz, Nikolaus;Sheridan, Robert;Sumer, S. Onur;Sun, Yichao;Taylor, Barry S.;Wang, Jioajiao;Zhang, Hongxin;Anur, Pavana;Peto, Myron;Spellman, Paul;Benz, Christopher;Stuart, Joshua M.;Wong, Christopher K.;Yau, Christina;Hayes, D. Neil;Parker, null;Wilkerson, Matthew D.;Ally, Adrian;Balasundaram, Miruna;Bowlby, Reanne;Brooks, Denise;Carlsen, Rebecca;Chuah, Eric;Dhalla, Noreen;Holt, Robert;Jones, Steven J. M.;Kasaian, Katayoon;Lee, Darlene;Ma, Yussanne;Marra, Marco A.;Mayo, Michael;Moore, Richard A.;Mungall, Andrew J.;Mungall, Karen;Robertson, A. Gordon;Sadeghi, Sara;Schein, Jacqueline E.;Sipahimalani, Payal;Tam, Angela;Thiessen, Nina;Tse, Kane;Wong, Tina;Berger, Ashton C.;Beroukhim, Rameen;Cherniack, Andrew D.;Cibulskis, Carrie;Gabriel, Stacey B.;Gao, Galen F.;Ha, Gavin;Meyerson, Matthew;Schumacher, Steven E.;Shih, Juliann;Kucherlapati, Melanie H.;Kucherlapati, Raju S.;Baylin, Stephen;Cope, Leslie;Danilova, Ludmila;Bootwalla, Moiz S.;Lai, Phillip H.;Maglinte, Dennis T.;Van Den Berg, David J.;Weisenberger, Daniel J.;Auman, J. Todd;Balu, Saianand;Bodenheimer, Tom;Fan, Cheng;Hoadley, Katherine A.;Hoyle, Alan P.;Jefferys, Stuart R.;Jones, Corbin D.;Meng, Shaowu;Mieczkowski, Piotr A.;Mose, Lisle E.;Perou, Amy H.;Perou, Charles M.;Roach, Jeffrey;Shi, Yan;Simons, Janae V.;Skelly, Tara;Soloway, Matthew G.;Tan, Donghui;Veluvolu, Umadevi;Fan, Huihui;Hinoue, Toshinori;Laird, Peter W.;Shen, Hui;Zhou, Wanding;Bellair, Michelle;Chang, Kyle;Covington, Kyle;Creighton, Chad J.;Dinh, Huyen;Doddapaneni, HarshaVardhan;Donehower, Lawrence A.;Drummond, Jennifer;Gibbs, Richard A.;Glenn, Robert;Hale, Walker;Han, Yi;Hu, Jianhong;Korchina, Viktoriya;Lee, Sandra;Lewis, Lora;Li, Wei;Liu, Xiuping;Morgan, Margaret;Morton, Donna;Muzny, Donna;Santibanez, Jireh;Sheth, Margi;Shinbrot, Eve;Wang, Linghua;Wang, Min;Wheeler, David A.;Xi, Liu;Zhao, Fengmei;Hess, Julian;Appelbaum, Elizabeth L.;Bailey, Matthew;Cordes, Matthew G.;Ding, Li;Fronick, Catrina C.;Fulton, Lucinda A.;Fulton, Robert S.;Kandoth, Cyriac;Mardis, Elaine R.;McLellan, Michael D.;Miller, Christopher A.;Schmidt, Heather K.;Wilson, Richard K.;Crain, Daniel;Curley, Erin;Gardner, Johanna;Lau, Kevin;Mallery, David;Morris, Scott;Paulauskis, Joseph;Penny, Robert;Shelton, Candace;Shelton, Troy;Sherman, Mark;Thompson, Eric;Yena, Peggy;Bowen, Jay;Gastier-Foster, Julie M.;Gerken, Mark;Leraas, Kristen M.;Lichtenberg, Tara M.;Ramirez, Nilsa C.;Wise, Lisa;Zmuda, Erik;Corcoran, Niall;Costello, Tony;Hovens, Christopher;Carvalho, Andre L.;de Carvalho, Ana C.;Fregnani, José H.;Longatto-Filho, Adhemar;Reis, Rui M.;Scapulatempo-Neto, Cristovam;Silveira, Henrique C. S.;Vidal, Daniel O.;Burnette, Andrew;Eschbacher, Jennifer;Hermes, Beth;Noss, Ardene;Singh, Rosy;Anderson, Matthew L.;Castro, Patricia D.;Ittmann, Michael;Huntsman, David;Kohl, Bernard;Le, Xuan;Thorp, Richard;Andry, Chris;Duffy, Elizabeth R.;Lyadov, Vladimir;Paklina, Oxana;Setdikova, Galiya;Shabunin, Alexey;Tavobilov, Mikhail;McPherson, Christopher;Warnick, Ronald;Berkowitz, Ross;Cramer, Daniel;Feltmate, Colleen;Horowitz, Neil;Kibel, Adam;Muto, Michael;Raut, Chandrajit P.;Malykh, Andrei;Barnholtz-Sloan, Jill S.;Barrett, Wendi;Devine, Karen;Fulop, Jordonna;Ostrom, Quinn T.;Shimmel, Kristen;Wolinsky, Yingli;Sloan, Andrew E.;De Rose, Agostino;Giuliante, Felice;Goodman, Marc;Karlan, Beth Y.;Hagedorn, Curt H.;Eckman, John;Harr, Jodi;Myers, Jerome;Tucker, Kelinda;Zach, Leigh Anne;Deyarmin, Brenda;Hu, Hai;Kvecher, Leonid;Larson, Caroline;Mural, Richard J.;Somiari, Stella;Vicha, Ales;Zelinka, Tomas;Bennett, Joseph;Iacocca, Mary;Rabeno, Brenda;Swanson, Patricia;Latour, Mathieu;Lacombe, Louis;Têtu, Bernard;Bergeron, Alain;McGraw, Mary;Staugaitis, Susan M.;Chabot, John;Hibshoosh, Hanina;Sepulveda, Antonia;Su, Tao;Wang, Timothy;Potapova, Olga;Voronina, Olga;Desjardins, Laurence;Mariani, Odette;Roman-Roman, Sergio;Sastre, Xavier;Stern, Marc-Henri;Cheng, Feixiong;Signoretti, Sabina;Berchuck, Andrew;Bigner, Darell;Lipp, Eric;Marks, Jeffrey;McCall, Shannon;McLendon, Roger;Secord, Angeles;Sharp, Alexis;Behera, Madhusmita;Brat, Daniel J.;Chen, Amy;Delman, Keith;Force, Seth;Khuri, Fadlo;Magliocca, Kelly;Maithel, Shishir;Olson, Jeffrey J.;Owonikoko, Taofeek;Pickens, Alan;Ramalingam, Suresh;Shin, Dong M.;Sica, Gabriel;Van Meir, Erwin G.;Zhang, Hongzheng;Eijckenboom, Wil;Gillis, Ad;Korpershoek, Esther;Looijenga, Leendert;Oosterhuis, Wolter;Stoop, Hans;van Kessel, Kim E.;Zwarthoff, Ellen C.;Calatozzolo, Chiara;Cuppini, Lucia;Cuzzubbo, Stefania;F. Dimeco;Finocchiaro, Gaetano;Mattei, Luca;Perin, Alessandro;Pollo, Bianca;Chen, Chu;Houck, John;Lohavanichbutr, Pawadee;Hartmann, Arndt;Stoehr, Christine;Stoehr, Robert;Taubert, Helge;Wach, Sven;Wullich, Bernd;Kycler, Witold;Murawa, Dawid;Wiznerowicz, Maciej;Chung, Ki;Edenfield, W. Jeffrey;Martin, Julie;Baudin, Eric;Bubley, Glenn;Bueno, Raphael;De Rienzo, Assunta;Richards, William G.;Kalkanis, Steven;Mikkelsen, Tom;Noushmehr, Houtan;Scarpace, Lisa;Girard, Nicolas;Aymerich, Marta;Campo, Elias;Giné, Eva;Guillermo, Armando López;Van Bang, Nguyen;Hanh, Phan Thi;Phu, Bui Duc;Tang, Yufang;Colman, Howard;Evason, Kimberley;Dottino, Peter R.;Martignetti, John A.;Gabra, Hani;Juhl, Hartmut;Akeredolu, Teniola;Stepa, Serghei;Hoon, Dave;Ahn, Keunsoo;Kang, Koo Jeong;Beuschlein, Felix;Breggia, Anne;Birrer, Michael;Bell, Debra;Borad, Mitesh;Bryce, Alan H.;Castle, Erik;Chandan, Vishal;Cheville, John;Copland, John A.;Farnell, Michael;Flotte, Thomas;Giama, Nasra;Ho, Thai;Kendrick, Michael;Kocher, Jean-Pierre;Kopp, Karla;Moser, Catherine;Nagorney, David;O’Brien, Daniel;O’Neill, Brian Patrick;Patel, Tushar;Petersen, Gloria;Que, Florencia;Rivera, Michael;Roberts, Lewis;Smallridge, Robert;Smyrk, Thomas;Stanton, Melissa;Thompson, R. Houston;Torbenson, Michael;Yang, Ju Dong;Zhang, Lizhi;Brimo, Fadi;Ajani, Jaffer A.;Angulo Gonzalez, Ana Maria;Behrens, Carmen;Bondaruk, Jolanta;Broaddus, Russell;Czerniak, Bogdan;Esmaeli, Bita;Fujimoto, Junya;Gershenwald, Jeffrey;Guo, Charles;Lazar, Alexander J.;Logothetis, Christopher;Meric-Bernstam, Funda;Moran, Cesar;Ramondetta, Lois;Rice, David;Sood, Anil;Tamboli, Pheroze;Thompson, Timothy;Troncoso, Patricia;Tsao, Anne;Wistuba, Ignacio;Carter, Candace;Haydu, Lauren;Hersey, Peter;Jakrot, Valerie;Kakavand, Hojabr;Kefford, Richard;Lee, Kenneth;Long, Georgina;Mann, Graham;Quinn, Michael;Saw, Robyn;Scolyer, Richard;Shannon, Kerwin;Spillane, Andrew;Stretch, Jonathan;Synott, Maria;Thompson, John;Wilmott, James;Al-Ahmadie, Hikmat;Chan, Timothy A.;Ghossein, Ronald;Gopalan, Anuradha;Levine, Douglas A.;Reuter, Victor;Singer, Samuel;Singh, Bhuvanesh;Tien, Nguyen Viet;Broudy, Thomas;Mirsaidi, Cyrus;Nair, Praveen;Drwiega, Paul;Miller, Judy;Smith, Jennifer;Zaren, Howard;Park, Joong-Won;Hung, Nguyen Phi;Kebebew, Electron;Linehan, W. Marston;Metwalli, Adam R.;Pacak, Karel;Pinto, Peter A.;Schiffman, Mark;Schmidt, Laura S.;Vocke, Cathy D.;Wentzensen, Nicolas;Worrell, Robert;Yang, Hannah;Moncrieff, Marc;Goparaju, Chandra;Melamed, Jonathan;Pass, Harvey;Botnariuc, Natalia;Caraman, Irina;Cernat, Mircea;Chemencedji, Inga;Clipca, Adrian;Doruc, Serghei;Gorincioi, Ghenadie;Mura, Sergiu;Pirtac, Maria;Stancul, Irina;Tcaciuc, Diana;Albert, Monique;Alexopoulou, Iakovina;Arnaout, Angel;Bartlett, John;Engel, Jay;Gilbert, Sebastien;Parfitt, Jeremy;Sekhon, Harman;Thomas, George;Rassl, Doris M.;Rintoul, Robert C.;Bifulco, Carlo;Tamakawa, Raina;Urba, Walter;Hayward, Nicholas;Timmers, Henri;Antenucci, Anna;Facciolo, Francesco;Grazi, Gianluca;Marino, Mirella;Merola, Roberta;de Krijger, Ronald;Gimenez-Roqueplo, Anne-Paule;Piché, Alain;Chevalier, Simone;McKercher, Ginette;Birsoy, Kivanc;Barnett, Gene;Brewer, Cathy;Farver, Carol;Naska, Theresa;Pennell, Nathan A.;Raymond, Daniel;Schilero, Cathy;Smolenski, Kathy;Williams, Felicia;Morrison, Carl;Borgia, Jeffrey A.;Liptay, Michael J.;Pool, Mark;Seder, Christopher W.;Junker, Kerstin;Omberg, Larsson;Dinkin, Mikhail;Manikhas, George;Alvaro, Domenico;Bragazzi, Maria Consiglia;Cardinale, Vincenzo;Carpino, Guido;Gaudio, Eugenio;Chesla, David;Cottingham, Sandra;Dubina, Michael;Moiseenko, Fedor;Dhanasekaran, Renumathy;Becker, Karl-Friedrich;Janssen, Klaus-Peter;Slotta-Huspenina, Julia;Abdel-Rahman, Mohamed H.;Aziz, Dina;Bell, Sue;Cebulla, Colleen M.;Davis, Amy;Duell, Rebecca;Elder, J. Bradley;Hilty, Joe;Kumar, Bahavna;Lang, James;Lehman, Norman L.;Mandt, Randy;Nguyen, Phuong;Pilarski, Robert;Rai, Karan;Schoenfield, Lynn;Senecal, Kelly;Wakely, Paul;Hansen, Paul;Lechan, Ronald;Powers, James;Tischler, Arthur;Grizzle, William E.;Sexton, Katherine C.;Kastl, Alison;Henderson, Joel;Porten, Sima;Waldmann, Jens;Fassnacht, Martin;Asa, Sylvia L.;Schadendorf, Dirk;Couce, Marta;Graefen, Markus;Huland, Hartwig;Sauter, Guido;Schlomm, Thorsten;Simon, Ronald;Tennstedt, Pierre;Olabode, Oluwole;Nelson, Mark;Bathe, Oliver;Carroll, Peter R.;Chan, June M.;Disaia, Philip;Glenn, Pat;Kelley, Robin K.;Landen, Charles N.;Phillips, Joanna;Prados, Michael;Simko, Jeffry;Smith-McCune, Karen;VandenBerg, Scott;Roggin, Kevin;Fehrenbach, Ashley;Kendler, Ady;Sifri, Suzanne;Steele, Ruth;Jimeno, Antonio;Carey, Francis;Forgie, Ian;Mannelli, Massimo;Carney, Michael;Hernandez, Brenda;Campos, Benito;Herold-Mende, Christel;Jungk, Christin;Unterberg, Andreas;von Deimling, Andreas;Bossler, Aaron;Galbraith, Joseph;Jacobus, Laura;Knudson, Michael;Knutson, Tina;Ma, Deqin;Milhem, Mohammed;Sigmund, Rita;Godwin, Andrew K.;Madan, Rashna;Rosenthal, Howard G.;Adebamowo, Clement;Adebamowo, Sally N.;Boussioutas, Alex;Beer, David;Giordano, Thomas;Mes-Masson, Anne-Marie;Saad, Fred;Bocklage, Therese;Landrum, Lisa;Mannel, Robert;Moore, Kathleen;Moxley, Katherine;Postier, Russel;Walker, Joan;Zuna, Rosemary;Feldman, Michael;Valdivieso, Federico;Dhir, Rajiv;Luketich, James;Mora Pinero, Edna M.;Quintero-Aguilo, Mario;Carlotti, Carlos Gilberto;Dos Santos, Jose Sebastião;Kemp, Rafael;Sankarankuty, Ajith;Tirapelli, Daniela;Catto, James;Agnew, Kathy;Swisher, Elizabeth;Creaney, Jenette;Robinson, Bruce;Shelley, Carl Simon;Godwin, Eryn M.;Kendall, Sara;Shipman, Cassaundra;Bradford, Carol;Carey, Thomas;Haddad, Andrea;Moyer, Jeffey;Peterson, Lisa;Prince, Mark;Rozek, Laura;Wolf, Gregory;Bowman, Rayleen;Fong, Kwun M.;Yang, Ian;Korst, Robert;Rathmell, W. Kimryn;Fantacone-Campbell, J. Leigh;Hooke, Jeffrey A.;Kovatich, Albert J.;Shriver, Craig D.;DiPersio, John;Drake, Bettina;Govindan, Ramaswamy;Heath, Sharon;Ley, Timothy;Van Tine, Brian;Westervelt, Peter;Rubin, Mark A.;Lee, Jung Il;Aredes, Natália D.;Mariamidze, Armaz
2018
Abstract
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. The dataset created by this analysis includes 3.5 million somatic variants and forms the basis for PanCan Atlas papers. The results have been made available to the research community along with the methods used to generate them. This project is the result of collaboration from a number of institutes and demonstrates how team science drives extremely large genomics projects.
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/586850
Citazioni
361
441
427
social impact
Conferma cancellazione
Sei sicuro che questo prodotto debba essere cancellato?
simulazione ASN
Il report seguente simula gli indicatori relativi alla propria produzione scientifica in relazione alle soglie ASN 2023-2025 del proprio SC/SSD. Si ricorda che il superamento dei valori soglia (almeno 2 su 3) è requisito necessario ma non sufficiente al conseguimento dell'abilitazione. La simulazione si basa sui dati IRIS e sugli indicatori bibliometrici alla data indicata e non tiene conto di eventuali periodi di congedo obbligatorio, che in sede di domanda ASN danno diritto a incrementi percentuali dei valori. La simulazione può differire dall'esito di un’eventuale domanda ASN sia per errori di catalogazione e/o dati mancanti in IRIS, sia per la variabilità dei dati bibliometrici nel tempo. Si consideri che Anvur calcola i valori degli indicatori all'ultima data utile per la presentazione delle domande.