Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

被引：1500

作者：

Imielinski, Marcin ^{[1
,2
,3
,5
]}

Berger, Alice H. ^{[1
,5
]}

Hammerman, Peter S. ^{[1
,5
]}

Hernandez, Bryan ^{[1
]}

Pugh, Trevor J. ^{[1
,5
]}

Hodis, Eran ^{[1
]}

Cho, Jeonghee ^{[6
]}

Suh, James ^{[7
]}

Capelletti, Marzia ^{[5
]}

Sivachenko, Andrey ^{[1
]}

Sougnez, Carrie ^{[1
]}

Auclair, Daniel ^{[1
]}

Lawrence, Michael S. ^{[1
]}

Stojanov, Petar ^{[1
,5
]}

Cibulskis, Kristian ^{[1
]}

Choi, Kyusam ^{[6
]}

de Waal, Luc ^{[1
,5
]}

Sharifnia, Tanaz ^{[1
,5
]}

Brooks, Angela ^{[1
,5
]}

Greulich, Heidi ^{[1
,5
]}

Banerji, Shantanu ^{[1
,5
]}

Zander, Thomas ^{[9
,10
,12
]}

Seidel, Danila ^{[9
,10
]}

Leenders, Frauke ^{[9
,10
]}

Ansen, Sascha ^{[9
,10
]}

Ludwig, Corinna ^{[9
,10
]}

Engel-Riedel, Walburga ^{[9
,10
]}

Stoelben, Erich ^{[9
,10
]}

Wolf, Juergen ^{[9
,10
]}

Goparju, Chandra ^{[8
]}

Thompson, Kristin ^{[1
]}

Winckler, Wendy ^{[1
]}

Kwiatkowski, David ^{[5
]}

Johnson, Bruce E. ^{[5
]}

Jaenne, Pasi A. ^{[5
]}

Miller, Vincent A. ^{[13
]}

Pao, William ^{[15
]}

Travis, William D. ^{[14
]}

Pass, Harvey I. ^{[8
]}

Gabriel, Stacey B. ^{[1
]}

Lander, Eric S. ^{[1
,4
,16
]}

Thomas, Roman K. ^{[9
,10
,11
,12
,17
,18
]}

Garraway, Levi A. ^{[1
,5
]}

Getz, Gad ^{[1
]}

Meyerson, Matthew ^{[1
,3
,5
]}

机构：

[1] Broad Inst Harvard & MIT, Cambridge, MA 02142 USA

[2] Massachusetts Gen Hosp, Dept Pathol, Boston, MA 02114 USA

[3] Harvard Univ, Sch Med, Dept Pathol, Boston, MA 02115 USA

[4] Harvard Univ, Sch Med, Dept Syst Biol, Boston, MA 02115 USA

[5] Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA

[6] Samsung Med Ctr, Samsung Res Inst, Seoul 135967, South Korea

[7] NYU, Langone Med Ctr, Dept Pathol, New York, NY 10016 USA

[8] NYU, Langone Med Ctr, Dept Cardiothorac Surg, New York, NY 10016 USA

[9] Univ Cologne, Dept Internal Med, D-50924 Cologne, Germany

[10] Univ Cologne, Ctr Integrated Oncol, D-50924 Cologne, Germany

[11] Univ Cologne, Lab Translat Canc Genom Koln Bonn, D-50924 Cologne, Germany

[12] Max Planck Inst Neurol Res, D-50924 Cologne, Germany

[13] Mem Sloan Kettering Canc Ctr, Dept Med, Thorac Oncol Serv, New York, NY 10065 USA

[14] Mem Sloan Kettering Canc Ctr, Dept Pathol, New York, NY 10065 USA

[15] Vanderbilt Ingram Canc Ctr, Div Hematol Oncol, Nashville, TN 37232 USA

[16] MIT, Dept Biol, Cambridge, MA 02142 USA

[17] Univ Cologne, Dept Translat Genom, D-50931 Cologne, Germany

[18] Univ Cologne, Dept Pathol, D-50937 Cologne, Germany

来源：

CELL | 2012年 / 150卷 / 06期

关键词：

GROWTH-FACTOR RECEPTOR; SOMATIC MUTATIONS; GENE-MUTATIONS; CANCER; GENOME; EGFR; LANDSCAPE; GEFITINIB; PATTERNS; REVEALS;

D O I：

10.1016/j.cell.2012.08.029

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.

引用

页码：1107 / 1120

页数：14

共 56 条

[1] A method and server for predicting damaging missense mutations
Adzhubei, Ivan A.
Schmidt, Steffen
Peshkin, Leonid
Ramensky, Vasily E.
Gerasimova, Anna
Bork, Peer
Kondrashov, Alexey S.
Sunyaev, Shamil R.
[J]. NATURE METHODS, 2010, 7 (04) : 248 - 249
[2] [Anonymous], 2012, CANCER
[3] Sequence analysis of mutations and translocations across breast cancer subtypes
Banerji, Shantanu
Cibulskis, Kristian
Rangel-Escareno, Claudia
Brown, Kristin K.
Carter, Scott L.
Frederick, Abbie M.
Lawrence, Michael S.
Sivachenko, Andrey Y.
Sougnez, Carrie
Zou, Lihua
Cortes, Maria L.
Fernandez-Lopez, Juan C.
Peng, Shouyong
Ardlie, Kristin G.
Auclair, Daniel
Bautista-Pina, Veronica
Duke, Fujiko
Francis, Joshua
Jung, Joonil
Maffuz-Aziz, Antonio
Onofrio, Robert C.
Parkin, Melissa
Pho, Nam H.
Quintanar-Jurado, Valeria
Ramos, Alex H.
Rebollar-Vega, Rosa
Rodriguez-Cuevas, Sergio
Romero-Cordoba, Sandra L.
Schumacher, Steven E.
Stransky, Nicolas
Thompson, Kristin M.
Uribe-Figueroa, Laura
Baselga, Jose
Beroukhim, Rameen
Polyak, Kornelia
Sgroi, Dennis C.
Richardson, Andrea L.
Jimenez-Sanchez, Gerardo
Lander, Eric S.
Gabriel, Stacey B.
Garraway, Levi A.
Golub, Todd R.
Melendez-Zajgla, Jorge
Toker, Alex
Getz, Gad
Hidalgo-Miranda, Alfredo
Meyerson, Matthew
[J]. NATURE, 2012, 486 (7403) : 405 - 409
[4] The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Barretina, Jordi
Caponigro, Giordano
Stransky, Nicolas
Venkatesan, Kavitha
Margolin, Adam A.
Kim, Sungjoon
Wilson, Christopher J.
Lehar, Joseph
Kryukov, Gregory V.
Sonkin, Dmitriy
Reddy, Anupama
Liu, Manway
Murray, Lauren
Berger, Michael F.
Monahan, John E.
Morais, Paula
Meltzer, Jodi
Korejwa, Adam
Jane-Valbuena, Judit
Mapa, Felipa A.
Thibault, Joseph
Bric-Furlong, Eva
Raman, Pichai
Shipway, Aaron
Engels, Ingo H.
Cheng, Jill
Yu, Guoying K.
Yu, Jianjun
Aspesi, Peter, Jr.
de Silva, Melanie
Jagtap, Kalpana
Jones, Michael D.
Wang, Li
Hatton, Charles
Palescandolo, Emanuele
Gupta, Supriya
Mahan, Scott
Sougnez, Carrie
Onofrio, Robert C.
Liefeld, Ted
MacConaill, Laura
Winckler, Wendy
Reich, Michael
Li, Nanxin
Mesirov, Jill P.
Gabriel, Stacey B.
Getz, Gad
Ardlie, Kristin
Chan, Vivien
Myer, Vic E.
[J]. NATURE, 2012, 483 (7391) : 603 - 607
[5] Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
Bass, Adam J.
Lawrence, Michael S.
Brace, Lear E.
Ramos, Alex H.
Drier, Yotam
Cibulskis, Kristian
Sougnez, Carrie
Voet, Douglas
Saksena, Gordon
Sivachenko, Andrey
Jing, Rui
Parkin, Melissa
Pugh, Trevor
Verhaak, Roel G.
Stransky, Nicolas
Boutin, Adam T.
Barretina, Jordi
Solit, David B.
Vakiani, Evi
Shao, Wenlin
Mishina, Yuji
Warmuth, Markus
Jimenez, Jose
Chiang, Derek Y.
Signoretti, Sabina
Kaelin, William G., Jr.
Spardy, Nicole
Hahn, William C.
Hoshida, Yujin
Ogino, Shuji
DePinho, Ronald A.
Chin, Lynda
Garraway, Levi A.
Fuchs, Charles S.
Baselga, Jose
Tabernero, Josep
Gabriel, Stacey
Lander, Eric S.
Getz, Gad
Meyerson, Matthew
[J]. NATURE GENETICS, 2011, 43 (10) : 964 - U67
[6] Integrated genomic analyses of ovarian carcinoma
Bell, D.
Berchuck, A.
Birrer, M.
Chien, J.
Cramer, D. W.
Dao, F.
Dhir, R.
DiSaia, P.
Gabra, H.
Glenn, P.
Godwin, A. K.
Gross, J.
Hartmann, L.
Huang, M.
Huntsman, D. G.
Iacocca, M.
Imielinski, M.
Kalloger, S.
Karlan, B. Y.
Levine, D. A.
Mills, G. B.
Morrison, C.
Mutch, D.
Olvera, N.
Orsulic, S.
Park, K.
Petrelli, N.
Rabeno, B.
Rader, J. S.
Sikic, B. I.
Smith-McCune, K.
Sood, A. K.
Bowtell, D.
Penny, R.
Testa, J. R.
Chang, K.
Dinh, H. H.
Drummond, J. A.
Fowler, G.
Gunaratne, P.
Hawes, A. C.
Kovar, C. L.
Lewis, L. R.
Morgan, M. B.
Newsham, I. F.
Santibanez, J.
Reid, J. G.
Trevino, L. R.
Wu, Y. -Q.
Wang, M.
[J]. NATURE, 2011, 474 (7353) : 609 - 615
[7] Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, David R.
Balasubramanian, Shankar
Swerdlow, Harold P.
Smith, Geoffrey P.
Milton, John
Brown, Clive G.
Hall, Kevin P.
Evers, Dirk J.
Barnes, Colin L.
Bignell, Helen R.
Boutell, Jonathan M.
Bryant, Jason
Carter, Richard J.
Cheetham, R. Keira
Cox, Anthony J.
Ellis, Darren J.
Flatbush, Michael R.
Gormley, Niall A.
Humphray, Sean J.
Irving, Leslie J.
Karbelashvili, Mirian S.
Kirk, Scott M.
Li, Heng
Liu, Xiaohai
Maisinger, Klaus S.
Murray, Lisa J.
Obradovic, Bojan
Ost, Tobias
Parkinson, Michael L.
Pratt, Mark R.
Rasolonjatovo, Isabelle M. J.
Reed, Mark T.
Rigatti, Roberto
Rodighiero, Chiara
Ross, Mark T.
Sabot, Andrea
Sankar, Subramanian V.
Scally, Aylwyn
Schroth, Gary P.
Smith, Mark E.
Smith, Vincent P.
Spiridou, Anastassia
Torrance, Peta E.
Tzonev, Svilen S.
Vermaas, Eric H.
Walter, Klaudia
Wu, Xiaolin
Zhang, Lu
Alam, Mohammed D.
Anastasi, Carole
[J]. NATURE, 2008, 456 (7218) : 53 - 59
[8] Melanoma genome sequencing reveals frequent PREX2 mutations
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
Garraway, Levi A.
[J]. NATURE, 2012, 485 (7399) : 502 - 506
[9] The genomic complexity of primary human prostate cancer
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.
Garraway, Levi A.
[J]. NATURE, 2011, 470 (7333) : 214 - 220
[10] ROS1 Rearrangements Define a Unique Molecular Class of Lung Cancers
Bergethon, Kristin
Shaw, Alice T.
Ou, Sai-Hong Ignatius
Katayama, Ryohei
Lovly, Christine M.
McDonald, Nerina T.
Massion, Pierre P.
Siwak-Tapp, Christina
Gonzalez, Adriana
Fang, Rong
Mark, Eugene J.
Batten, Julie M.
Chen, Haiquan
Wilner, Keith D.
Kwak, Eunice L.
Clark, Jeffrey W.
Carbone, David P.
Ji, Hongbin
Engelman, Jeffrey A.
Mino-Kenudson, Mari
Pao, William
Iafrate, A. John
[J]. JOURNAL OF CLINICAL ONCOLOGY, 2012, 30 (08) : 863 - 870

← 1 2 3 4 5 6 →