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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
Cell Systems, Volume 6, No. 3, Year 2018
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Description
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. The MC3 is a variant calling project of over 10,000 cancer exome samples from 33 cancer types. Over three million somatic variants were detected using seven different methods developed from institutions across the United States. These variants formed the basis for the PanCan Atlas papers. © 2018 The Authors
Authors & Co-Authors
Saksena, Gordon
United States, Cambridge
Harvard University
Stewart, Chip
United States, Cambridge
Harvard University
Sofia, Heidi J.
United States, Bethesda
National Institutes of Health Nih
Hutter, Carolyn M.
United States, Bethesda
National Institutes of Health Nih
Getz, Gad A.
United States, Cambridge
Harvard University
United States, Boston
Massachusetts General Hospital
United States, Boston
Harvard Medical School
Wheeler, David A.
United States, Houston
Baylor College of Medicine
Caesar-Johnson, Samantha J.
Unknown Affiliation
Demchok, John A.
Unknown Affiliation
Felau, Ina
Unknown Affiliation
Kasapi, Melpomeni
Unknown Affiliation
Ferguson, Martin L.
Unknown Affiliation
Tarnuzzer, Roy W.
Unknown Affiliation
Zenklusen, Jean Claude
Unknown Affiliation
Chudamani, Sudha
Unknown Affiliation
Liu, Jia
Unknown Affiliation
Lolla, Laxmi
Unknown Affiliation
Naresh, Rashi
Unknown Affiliation
Pihl, Todd D.
Unknown Affiliation
Sun, Qiang
Unknown Affiliation
Wan, Yunhu
Unknown Affiliation
Wu, Ye
Unknown Affiliation
Cho, Juok
Unknown Affiliation
DeFreitas, Timothy
Unknown Affiliation
Frazer, Scott
Unknown Affiliation
Gehlenborg, Nils
Unknown Affiliation
Heiman, David I.
Unknown Affiliation
Kim, Jaegil
Unknown Affiliation
Lawrence, Michael S.
Unknown Affiliation
Lin, Pei
Unknown Affiliation
Meier, Samuel R.
Unknown Affiliation
Noble, Michael S.
Unknown Affiliation
Voet, Doug
Unknown Affiliation
Zhang, Hailei
Unknown Affiliation
Bernard, Brady M.
Unknown Affiliation
Chambwe, Nyasha
Unknown Affiliation
Dhankani, Varsha
Unknown Affiliation
Knijnenburg, Theo A.
Unknown Affiliation
Kramer, Roger W.
Unknown Affiliation
Leinonen, Kalle
Unknown Affiliation
Liu, Yuexin
Unknown Affiliation
Miller, Michael B.
Unknown Affiliation
Reynolds, Sheila M.
Unknown Affiliation
Shmulevich, Ilya
Unknown Affiliation
Thorsson, Vesteinn
Unknown Affiliation
Zhang, Wei
Unknown Affiliation
Akbani, Rehan
Unknown Affiliation
Broom, Bradley M.
Unknown Affiliation
Hegde, Apurva M.
Unknown Affiliation
Ju, Zhenlin
Unknown Affiliation
Kanchi, Rupa S.
Unknown Affiliation
Korkut, Anil
Unknown Affiliation
Li, Jun
Unknown Affiliation
Liang, Han
Unknown Affiliation
Ling, Shiyun
Unknown Affiliation
Liu, Wenbin
Unknown Affiliation
Lu, Yiling
Unknown Affiliation
Mills, Gordon B.
Unknown Affiliation
Ng, Kwokshing
Unknown Affiliation
Rao, Arvind U.K.
Unknown Affiliation
Ryan, Michael C.
Unknown Affiliation
Wang, Jing
Unknown Affiliation
Armenia, Joshua
Unknown Affiliation
Chatila, Walid K.
Unknown Affiliation
de Bruijn, Ino
Unknown Affiliation
Sánchez-Vega, Francisco
Unknown Affiliation
Schultz, Nikolaus D.
Unknown Affiliation
Yau, Christina
Unknown Affiliation
Bowlby, Reanne
Unknown Affiliation
Brooks, Denise B.
Unknown Affiliation
Jones, Steven J.M.
Unknown Affiliation
Ma, Yussanne P.
Unknown Affiliation
Marra, Marco A.
Unknown Affiliation
Moore, Richard A.
Unknown Affiliation
Mungall, Andrew J.
Unknown Affiliation
Mungall, Karen L.
Unknown Affiliation
Robertson, Andrew Gordon
Unknown Affiliation
Schein, Jacqueline E.
Unknown Affiliation
Berger, Ashton C.
Unknown Affiliation
Beroukhim, Rameen
Unknown Affiliation
Cherniack, Andrew D.
Unknown Affiliation
Gabriel, Stacey Bolk
Unknown Affiliation
Ha, Gavin
Unknown Affiliation
Schumacher, Steven E.
Unknown Affiliation
Xu, Jian M.
Unknown Affiliation
van den Berg, David J.
Unknown Affiliation
Hoadley, Katherine A.
Unknown Affiliation
Jones, Corbin D.
Unknown Affiliation
Roach, Jeffrey M.
Unknown Affiliation
Fan, Huihui
Unknown Affiliation
Laird, Peter W.
Unknown Affiliation
Shen, Hui
Unknown Affiliation
Chang, Kyle
Unknown Affiliation
Creighton, Chad J.
Unknown Affiliation
Dinh, Huyen H.
Unknown Affiliation
Doddapaneni, Harshavardhan
Unknown Affiliation
Drummond, Jennifer A.
Unknown Affiliation
Gibbs, Richard A.L.
Unknown Affiliation
Hale, Walker
Unknown Affiliation
Han, Yi
Unknown Affiliation
Korchina, Viktoriya
Unknown Affiliation
Lee, Sandra L.
Unknown Affiliation
Lewis, Lora R.
Unknown Affiliation
Li, Wei
Unknown Affiliation
Morgan, Margaret B.
Unknown Affiliation
Muzny, Donna Marie
Unknown Affiliation
Wang, Linghua
Unknown Affiliation
Fronick, Catrina C.
Unknown Affiliation
Fulton, Robert S.
Unknown Affiliation
Mardis, Elaine R.
Unknown Affiliation
Wilson, Richard K.
Unknown Affiliation
Paulauskis, Joseph D.
Unknown Affiliation
Bowen, Jay
Unknown Affiliation
Gastier-Foster, Julie M.
Unknown Affiliation
Lichtenberg, Tara M.
Unknown Affiliation
Ramirez, Nilsa C.
Unknown Affiliation
Zmuda, Erik J.
Unknown Affiliation
Corcoran, Niall M.
Unknown Affiliation
Hovens, Christopher M.
Unknown Affiliation
Humberto Fregnani, Jose
Unknown Affiliation
Longatto-Filho, Adhemar
Unknown Affiliation
Reis, Rui Manuel Vieira
Unknown Affiliation
Castro, Patricia D.
Unknown Affiliation
Ittmann, Michael M.
Unknown Affiliation
Huntsman, David G.
Unknown Affiliation
Warnick, Ronald E.
Unknown Affiliation
Cramer, Daniel William
Unknown Affiliation
Kibel, Adam S.
Unknown Affiliation
Barnholtz-Sloan, Jill S.
Unknown Affiliation
De Rose, Agostino Maria
Unknown Affiliation
Giuliante, Felice
Unknown Affiliation
Goodman, Marc T.
Unknown Affiliation
Karlan, Beth Y.
Unknown Affiliation
Somiari, Stella B.
Unknown Affiliation
Lacombe, Louis
Unknown Affiliation
Chabot, John A.
Unknown Affiliation
Desjardins, Laurence C.
Unknown Affiliation
Sastre-Garau, Xavier X.
Unknown Affiliation
Stern, Marc Henri
Unknown Affiliation
Signoretti, Sabina
Unknown Affiliation
Berchuck, Andrew
Unknown Affiliation
Brat, Daniel J.
Unknown Affiliation
Delman, Keith A.
Unknown Affiliation
Khuri, Fadlo R.
Unknown Affiliation
Magliocca, Kelly R.
Unknown Affiliation
Owonikoko, Taofeek Kunle
Unknown Affiliation
Ramalingam, Suresh S.
Unknown Affiliation
Shin, Dongmoon
Unknown Affiliation
Looijenga, Leendert H.J.
Unknown Affiliation
Oosterhuis, Wolter J.W.
Unknown Affiliation
Chen, Chu
Unknown Affiliation
Houck, John
Unknown Affiliation
Hartmann, Arndt
Unknown Affiliation
Stoehr, Robert
Unknown Affiliation
Wullich, Bernd
Unknown Affiliation
Noushmehr, Houtan
Unknown Affiliation
Girard, Nicolas
Unknown Affiliation
Campo, Elías
Unknown Affiliation
Colman, Howard
Unknown Affiliation
Martignetti, John A.
Unknown Affiliation
Gabra, H.
Unknown Affiliation
Akeredolu, Teniola
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Birrer, Michael J.
Unknown Affiliation
Borad, Mitesh J.
Unknown Affiliation
Copland, John A.
Unknown Affiliation
Ho, Thai Huu
Unknown Affiliation
Patel, Tushar P.
Unknown Affiliation
Olson, Gloria Moy
Unknown Affiliation
Roberts, Lewis Rowland
Unknown Affiliation
Smallridge, Robert C.
Unknown Affiliation
Torbenson, Michael S.
Unknown Affiliation
Yang, Ju Dong
Unknown Affiliation
Brimo, Fadi
Unknown Affiliation
Fujimoto, Jyunya
Unknown Affiliation
Lazar, A. J.
Unknown Affiliation
Logothetis, Christopher J.
Unknown Affiliation
Meric-Bernstam, Funda
Unknown Affiliation
Moran, César A.
Unknown Affiliation
Rimner, Andreas C.
Unknown Affiliation
Sood, Anil K.
Unknown Affiliation
Tamboli, Pheroze
Unknown Affiliation
Tsao, Anne S.
Unknown Affiliation
Wistuba, Ignacio Ivans
Unknown Affiliation
Lee, Kenneth K.W.
Unknown Affiliation
Long, Georgina V.
Unknown Affiliation
Scolyer, Richard A.
Unknown Affiliation
Spillane, Andrew John
Unknown Affiliation
Wilmott, James S.
Unknown Affiliation
Chan, Timothy A.
Unknown Affiliation
Levine, Douglas A.
Unknown Affiliation
Smith, Jennifer Anne
Unknown Affiliation
Kebebew, Electron K.
Unknown Affiliation
Linehan, W. Marston
Unknown Affiliation
Pacak, Karel
Unknown Affiliation
Pinto, Peter A.
Unknown Affiliation
Schiffman, Mark H.
Unknown Affiliation
Wentzensen, Nicolas A.
Unknown Affiliation
Pass, Harvey Ira
Unknown Affiliation
Bartlett, John M.S.
Unknown Affiliation
Gilbert, Sebastien
Unknown Affiliation
Sekhon, Harman S.
Unknown Affiliation
Hayward, Nicholas K.
Unknown Affiliation
Gimenez-Roqueplo, Anne Paule
Unknown Affiliation
Birsoy, Kivanç
Unknown Affiliation
Barnett, Gene H.
Unknown Affiliation
Brewer, Cathy J.
Unknown Affiliation
Farver, Carol F.
Unknown Affiliation
Pennell, Nathan A.
Unknown Affiliation
Morrison, Carl D.
Unknown Affiliation
Omberg, Larsson
Unknown Affiliation
Manikhas, Georgiy Moiseevich
Unknown Affiliation
Alvaro, Domenico
Unknown Affiliation
Cardinale, Vincenzo
Unknown Affiliation
Dubina, Michael V.
Unknown Affiliation
Dhanasekaran, Renumathy
Unknown Affiliation
Slotta-Huspenina, Julia B.
Unknown Affiliation
Abdel-Rahman, Mohamed H.
Unknown Affiliation
Cebulla, Colleen M.
Unknown Affiliation
Lehman, Norman L.
Unknown Affiliation
Pilarski, Robert T.
Unknown Affiliation
Rai, Karan
Unknown Affiliation
Schoenfield, Lynn R.
Unknown Affiliation
Grizzle, William E.
Unknown Affiliation
Porten, Sima P.
Unknown Affiliation
Asa, Sylvia L.
Unknown Affiliation
Schadendorf, Dirk
Unknown Affiliation
Graefen, Markus
Unknown Affiliation
Huland, Hartwig
Unknown Affiliation
Sauter, Guido
Unknown Affiliation
Schlomm, Thorsten
Unknown Affiliation
Simon, Ronald
Unknown Affiliation
Tennstedt, Pierre
Unknown Affiliation
Bathe, Oliver F.
Unknown Affiliation
Carroll, Peter R.
Unknown Affiliation
Chan, June Maylin L.
Unknown Affiliation
DiSaia, Philip John
Unknown Affiliation
Kelley, Robin Kate
Unknown Affiliation
Phillips, Joanna J.
Unknown Affiliation
Simko, Jeffry P.
Unknown Affiliation
Smith-McCune, Karen K.
Unknown Affiliation
Carney, Michael E.
Unknown Affiliation
Hernandez, Brenda Y.
Unknown Affiliation
Herold-Mende, Christel C.
Unknown Affiliation
Unterberg, Andreas Wilhelm
Unknown Affiliation
von Deimling, Andreas
Unknown Affiliation
Godwin, Andrew K.
Unknown Affiliation
Adebamowo, Clement
Unknown Affiliation
Adebamowo, Sally N.
Unknown Affiliation
Boussioutas, Alex
Unknown Affiliation
Mès-Masson, Anne Marie
Unknown Affiliation
Saad, Fred
Unknown Affiliation
Walker, Joan L.
Unknown Affiliation
Zuna, Rosemary E.
Unknown Affiliation
Feldman, Michael D.
Unknown Affiliation
Dhir, Rajiv J.
Unknown Affiliation
Luketich, James D.
Unknown Affiliation
Agnew, Kathy J.
Unknown Affiliation
Creaney, Jenette
Unknown Affiliation
Robinson, Bruce Gregory
Unknown Affiliation
Shelley, Carl Simon
Unknown Affiliation
Bradford, Carol R.
Unknown Affiliation
Carey, Thomas E.
Unknown Affiliation
Fong, Kwun Meng
Unknown Affiliation
Yang, Ian A.
Unknown Affiliation
Hooke, Jeffrey A.
Unknown Affiliation
Kovatich, Albert J.
Unknown Affiliation
Shriver, Craig D.
Unknown Affiliation
DIpersio, John F.
Unknown Affiliation
Drake, Bettina Fisher
Unknown Affiliation
Van Tine, Brian A.
Unknown Affiliation
Rubin, Mark A.
Unknown Affiliation
Statistics
Citations: 422
Authors: 270
Affiliations: 9
Identifiers
Doi:
10.1016/j.cels.2018.03.002
ISSN:
24054712
Research Areas
Cancer
Genetics And Genomics
Infectious Diseases