Mutational Landscape of Aggressive Prostate Tumors in African American Men

被引:58
作者
Lindquist, Karla J. [1 ]
Paris, Pamela L. [2 ]
Hoffmann, Thomas J. [1 ,3 ]
Cardin, Niall J. [1 ]
Kazma, Remi [1 ]
Mefford, Joel A. [1 ]
Simko, Jeffrey P. [2 ]
Ngo, Vy [2 ]
Chen, Yalei [4 ]
Levin, Albert M. [4 ]
Chitale, Dhananjay [4 ]
Helfand, Brian T. [5 ]
Catalona, William J. [5 ]
Rybicki, Benjamin A. [4 ]
Witte, John S. [1 ,2 ,3 ,6 ]
机构
[1] Univ Calif San Francisco, Dept Epidemiol & Biostat, San Francisco, CA 94143 USA
[2] Univ Calif San Francisco, Dept Urol, San Francisco, CA USA
[3] Univ Calif San Francisco, Dept Human Genet, San Francisco, CA 94143 USA
[4] Henry Ford Hlth Syst, Dept Publ Hlth Sci, Detroit, MI USA
[5] Northwestern Univ, Robert H Lurie Comprehens Canc Ctr, Chicago, IL 60611 USA
[6] Univ Calif San Francisco, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA
基金
美国国家卫生研究院;
关键词
CANCER GENOMICS; GENES; ANCESTRY; RECURRENCE; DELETION; LOCI;
D O I
10.1158/0008-5472.CAN-15-1787
中图分类号
R73 [肿瘤学];
学科分类号
100214 ;
摘要
Prostate cancer is the most frequently diagnosed and second most fatal nonskin cancer among men in the United States. African American men are two times more likely to develop and die of prostate cancer compared with men of other ancestries. Previous whole genome or exome tumor-sequencing studies of prostate cancer have primarily focused on men of European ancestry. In this study, we sequenced and characterized somatic mutations in aggressive (Gleason >= 7, stage >= T2b) prostate tumors from 24 African American patients. We describe the locations and prevalence of small somatic mutations (up to 50 bases in length), copy number aberrations, and structural rearrangements in the tumor genomes compared with patient-matched normal genomes. We observed several mutation patterns consistent with previous studies, such as large copy number aberrations in chromosome 8 and complex rearrangement chains. However, TMPRSS2-ERG gene fusions and PTEN losses occurred in only 21% and 8% of the African American patients, respectively, far less common than in patients of European ancestry. We also identified mutations that appeared specific to or more common in African American patients, including a novel CDC27-OAT gene fusion occurring in 17% of patients. The genomic aberrations reported in this study warrant further investigation of their biologic significant role in the incidence and clinical outcomes of prostate cancer in African Americans.
引用
收藏
页码:1860 / 1868
页数:9
相关论文
共 43 条
[1]   The Molecular Taxonomy of Primary Prostate Cancer [J].
Abeshouse, Adam ;
Ahn, Jaeil ;
Akbani, Rehan ;
Ally, Adrian ;
Amin, Samirkumar ;
Andry, Christopher D. ;
Annala, Matti ;
Aprikian, Armen ;
Armenia, Joshua ;
Arora, Arshi ;
Auman, J. Todd ;
Balasundaram, Miruna ;
Balu, Saianand ;
Barbieri, Christopher E. ;
Bauer, Thomas ;
Benz, Christopher C. ;
Bergeron, Alain ;
Beroukhim, Rameen ;
Berrios, Mario ;
Bivol, Adrian ;
Bodenheimer, Tom ;
Boice, Lori ;
Bootwalla, Moiz S. ;
dos Reis, Rodolfo Borges ;
Boutros, Paul C. ;
Bowen, Jay ;
Bowlby, Reanne ;
Boyd, Jeffrey ;
Bradley, Robert K. ;
Breggia, Anne ;
Brimo, Fadi ;
Bristow, Christopher A. ;
Brooks, Denise ;
Broom, Bradley M. ;
Bryce, Alan H. ;
Bubley, Glenn ;
Burks, Eric ;
Butterfield, Yaron S. N. ;
Button, Michael ;
Canes, David ;
Carlotti, Carlos G. ;
Carlsen, Rebecca ;
Carmel, Michel ;
Carroll, Peter R. ;
Carter, Scott L. ;
Cartun, Richard ;
Carver, Brett S. ;
Chan, June M. ;
Chang, Matthew T. ;
Chen, Yu .
CELL, 2015, 163 (04) :1011-1025
[2]   A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer [J].
Al Olama, Ali Amin ;
Kote-Jarai, Zsofia ;
Berndt, Sonja I. ;
Conti, David V. ;
Schumacher, Fredrick ;
Han, Ying ;
Benlloch, Sara ;
Hazelett, Dennis J. ;
Wang, Zhaoming ;
Saunders, Ed ;
Leongamornlert, Daniel ;
Lindstrom, Sara ;
Jugurnauth-Little, Sara ;
Dadaev, Tokhir ;
Tymrakiewicz, Malgorzata ;
Stram, Daniel O. ;
Rand, Kristin ;
Wan, Peggy ;
Stram, Alex ;
Sheng, Xin ;
Pooler, Loreall C. ;
Park, Karen ;
Xia, Lucy ;
Tyrer, Jonathan ;
Kolonel, Laurence N. ;
Le Marchand, Loic ;
Hoover, Robert N. ;
Machiela, Mitchell J. ;
Yeager, Merideth ;
Burdette, Laurie ;
Chung, Charles C. ;
Hutchinson, Amy ;
Yu, Kai ;
Goh, Chee ;
Ahmed, Mahbubl ;
Govindasami, Koveela ;
Guy, Michelle ;
Tammela, Teuvo L. J. ;
Auvinen, Anssi ;
Wahlfors, Tlina ;
Schleutker, Johanna ;
Visakorpi, Tapio ;
Leinonen, Katri A. ;
Xu, Jianfeng ;
Aly, Markus ;
Donovan, Jenny ;
Travis, Ruth C. ;
Key, Tim J. ;
Siddiq, Afshan ;
Canzian, Federico .
NATURE GENETICS, 2014, 46 (10) :1103-1109
[3]   Signatures of mutational processes in human cancer [J].
Alexandrov, Ludmil B. ;
Nik-Zainal, Serena ;
Wedge, David C. ;
Aparicio, Samuel A. J. R. ;
Behjati, Sam ;
Biankin, Andrew V. ;
Bignell, Graham R. ;
Bolli, Niccolo ;
Borg, Ake ;
Borresen-Dale, Anne-Lise ;
Boyault, Sandrine ;
Burkhardt, Birgit ;
Butler, Adam P. ;
Caldas, Carlos ;
Davies, Helen R. ;
Desmedt, Christine ;
Eils, Roland ;
Eyfjord, Jorunn Erla ;
Foekens, John A. ;
Greaves, Mel ;
Hosoda, Fumie ;
Hutter, Barbara ;
Ilicic, Tomislav ;
Imbeaud, Sandrine ;
Imielinsk, Marcin ;
Jaeger, Natalie ;
Jones, David T. W. ;
Jones, David ;
Knappskog, Stian ;
Kool, Marcel ;
Lakhani, Sunil R. ;
Lopez-Otin, Carlos ;
Martin, Sancha ;
Munshi, Nikhil C. ;
Nakamura, Hiromi ;
Northcott, Paul A. ;
Pajic, Marina ;
Papaemmanuil, Elli ;
Paradiso, Angelo ;
Pearson, John V. ;
Puente, Xose S. ;
Raine, Keiran ;
Ramakrishna, Manasa ;
Richardson, Andrea L. ;
Richter, Julia ;
Rosenstiel, Philip ;
Schlesner, Matthias ;
Schumacher, Ton N. ;
Span, Paul N. ;
Teague, Jon W. .
NATURE, 2013, 500 (7463) :415-+
[4]   An integrated map of genetic variation from 1,092 human genomes [J].
Altshuler, David M. ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Donnelly, Peter ;
Eichler, Evan E. ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Green, Eric D. ;
Hurles, Matthew E. ;
Knoppers, Bartha M. ;
Korbel, Jan O. ;
Lander, Eric S. ;
Lee, Charles ;
Lehrach, Hans ;
Mardis, Elaine R. ;
Marth, Gabor T. ;
McVean, Gil A. ;
Nickerson, Deborah A. ;
Schmidt, Jeanette P. ;
Sherry, Stephen T. ;
Wang, Jun ;
Wilson, Richard K. ;
Gibbs, Richard A. ;
Dinh, Huyen ;
Kovar, Christie ;
Lee, Sandra ;
Lewis, Lora ;
Muzny, Donna ;
Reid, Jeff ;
Wang, Min ;
Wang, Jun ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Li, Zhuo ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Su, Zhe ;
Tai, Shuaishuai ;
Tang, Meifang .
NATURE, 2012, 491 (7422) :56-65
[5]  
[Anonymous], NHLBI GO EX SEQ PROJ
[6]   Punctuated Evolution of Prostate Cancer Genomes [J].
Baca, Sylvan C. ;
Prandi, Davide ;
Lawrence, Michael S. ;
Mosquera, Juan Miguel ;
Romanel, Alessandro ;
Drier, Yotam ;
Park, Kyung ;
Kitabayashi, Naoki ;
MacDonald, Theresa Y. ;
Ghandi, Mahmoud ;
Van Allen, Eliezer ;
Kryukov, Gregory V. ;
Sboner, Andrea ;
Theurillat, Jean-Philippe ;
Soong, T. David ;
Nickerson, Elizabeth ;
Auclair, Daniel ;
Tewari, Ashutosh ;
Beltran, Himisha ;
Onofrio, Robert C. ;
Boysen, Gunther ;
Guiducci, Candace ;
Barbieri, Christopher E. ;
Cibulskis, Kristian ;
Sivachenko, Andrey ;
Carter, Scott L. ;
Saksena, Gordon ;
Voet, Douglas ;
Ramos, Alex H. ;
Winckler, Wendy ;
Cipicchio, Michelle ;
Ardlie, Kristin ;
Kantoff, Philip W. ;
Berger, Michael F. ;
Gabriel, Stacey B. ;
Golub, Todd R. ;
Meyerson, Matthew ;
Lander, Eric S. ;
Elemento, Olivier ;
Getz, Gad ;
Demichelis, Francesca ;
Rubin, Mark A. ;
Garraway, Levi A. .
CELL, 2013, 153 (03) :666-677
[7]   Evidence of chromosomal instability in prostate cancer determined by spectral karyotyping (SKY) and interphase FISH analysis [J].
Beheshti, B ;
Park, PC ;
Sweet, JM ;
Trachtenberg, J ;
Jewett, MAS ;
Squire, JA .
NEOPLASIA, 2001, 3 (01) :62-69
[8]   The genomic complexity of primary human prostate cancer [J].
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. .
NATURE, 2011, 470 (7333) :214-220
[9]   Spatial genomic heterogeneity within localized, multifocal prostate cancer [J].
Boutros, Paul C. ;
Fraser, Michael ;
Harding, Nicholas J. ;
de Borja, Richard ;
Trudel, Dominique ;
Lalonde, Emilie ;
Meng, Alice ;
Hennings-Yeomans, Pablo H. ;
McPherson, Andrew ;
Sabelnykova, Veronica Y. ;
Zia, Amin ;
Fox, Natalie S. ;
Livingstone, Julie ;
Shiah, Yu-Jia ;
Wang, Jianxin ;
Beck, Timothy A. ;
Have, Cherry L. ;
Chong, Taryne ;
Sam, Michelle ;
Johns, Jeremy ;
Timms, Lee ;
Buchner, Nicholas ;
Wong, Ada ;
Watson, John D. ;
Simmons, Trent T. ;
P'ng, Christine ;
Zafarana, Gaetano ;
Nguyen, Francis ;
Luo, Xuemei ;
Chu, Kenneth C. ;
Prokopec, Stephenie D. ;
Sykes, Jenna ;
Dal Pra, Alan ;
Berlin, Alejandro ;
Brown, Andrew ;
Chan-Seng-Yue, Michelle A. ;
Yousif, Fouad ;
Denroche, Robert E. ;
Chong, Lauren C. ;
Chen, Gregory M. ;
Jung, Esther ;
Fung, Clement ;
Starmans, Maud H. W. ;
Chen, Hanbo ;
Govind, Shaylan K. ;
Hawley, James ;
D'Costa, Alister ;
Pintilie, Melania ;
Waggott, Daryl ;
Hach, Faraz .
NATURE GENETICS, 2015, 47 (07) :736-+
[10]   Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads [J].
Carnevali, Paolo ;
Baccash, Jonathan ;
Halpern, Aaron L. ;
Nazarenko, Igor ;
Nilsen, Geoffrey B. ;
Pant, Krishna P. ;
Ebert, Jessica C. ;
Brownley, Anushka ;
Morenzoni, Matt ;
Karpinchyk, Vitali ;
Martin, Bruce ;
Ballinger, Dennis G. ;
Drmanac, Radoje .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (03) :279-292