Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns

被引：255

作者：

Schuh, Anna ^{[1
]}

Becq, Jennifer ^{[2
]}

Humphray, Sean ^{[2
]}

Alexa, Adrian ^{[2
]}

Burns, Adam

Clifford, Ruth

Feller, Stephan M. ^{[3
]}

Grocock, Russell ^{[2
]}

Henderson, Shirley

Khrebtukova, Irina ^{[4
]}

Kingsbury, Zoya ^{[2
]}

Luo, Shujun ^{[4
]}

McBride, David ^{[2
]}

Murray, Lisa ^{[2
]}

Menju, Toshi ^{[3
,5
]}

Timbs, Adele

Ross, Mark ^{[2
]}

Taylor, Jenny

Bentley, David ^{[2
]}

机构：

[1] Univ Oxford, Oxford NIHR Biomed Res Ctr, Mol Diagnost Lab, Oxford OX3 9DS, England

[2] Illumina Cambridge Ltd, Saffron Walden, Essex, England

[3] Univ Oxford, Biol Syst Architecture Grp, Dept Oncol, Weatherall Inst Mol Med, Oxford OX3 9DS, England

[4] Illumina Inc, Hayward, CA USA

[5] Kyoto Univ, Dept Thorac Surg, Grad Sch Med, Kyoto, Japan

来源：

BLOOD | 2012年 / 120卷 / 20期

关键词：

ADJUVANT CHEMOTHERAPY; SOMATIC MUTATIONS; CANCER; FLUDARABINE; CYCLOPHOSPHAMIDE; IDENTIFICATION; TRASTUZUMAB; SIGNATURES; RITUXIMAB; CATALOG;

D O I：

10.1182/blood-2012-05-433540

中图分类号：

R5 [内科学];

学科分类号：

1002 ; 100201 ;

摘要：

Chronic lymphocytic leukemia is characterized by relapse after treatment and chemotherapy resistance. Similarly, in other malignancies leukemia cells accumulate mutations during growth, forming heterogeneous cell populations that are subject to Darwinian selection and may respond differentially to treatment. There is therefore a clinical need to monitor changes in the subclonal composition of cancers during disease progression. Here, we use whole-genome sequencing to track subclonal heterogeneity in 3 chronic lymphocytic leukemia patients subjected to repeated cycles of therapy. We reveal different somatic mutation profiles in each patient and use these to establish probable hierarchical patterns of subclonal evolution, to identify subclones that decline or expand over time, and to detect founder mutations. We show that clonal evolution patterns are heterogeneous in individual patients. We conclude that genome sequencing is a powerful and sensitive approach to monitor disease progression repeatedly at the molecular level. If applied to future clinical trials, this approach might eventually influence treatment strategies as a tool to individualize and direct cancer treatment. (Blood. 2012; 120(20): 4191-4196)

引用

页码：4191 / 4196

页数：6

共 38 条

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Amado, Rafael G. ;

Wolf, Michael ;

Peeters, Marc ;

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Siena, Salvatore ;

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van Delft, Frederik W. ;

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Davies, Helen ;

Edkins, Sarah ;

Hardy, Claire ;

Latimer, Calli ;

Teague, Jon ;

Andrews, Jenny ;

Barthorpe, Syd ;

Beare, Dave ;

Buck, Gemma ;

Campbell, Peter J. ;

Forbes, Simon ;

Jia, Mingming ;

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Kok, Chai Yin ;

Lau, King Wai ;

Leroy, Catherine ;

Lin, Meng-Lay ;

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Maguire, Simon ;

McLay, Kirsten ;

Menzies, Andrew ;

Mironenko, Tatiana ;

Mulderrig, Lee ;

Mudie, Laura ;

O'Meara, Sarah ;

Pleasance, Erin ;

Rajasingham, Arjunan ;

Shepherd, Rebecca ;

Smith, Raffaella ;

Stebbings, Lucy ;

Stephens, Philip ;

Tang, Gurpreet ;

Tarpey, Patrick S. ;

Turrell, Kelly ;

Dykema, Karl J. ;

Khoo, Sok Kean ;

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Young, Margaret A. ;

Lamprecht, Tamara ;

McLellan, Michael D. ;

McMichael, Joshua F. ;

Wallis, John W. ;

Lu, Charles ;

Shen, Dong ;

Harris, Christopher C. ;

Dooling, David J. ;

Fulton, Robert S. ;

Fulton, Lucinda L. ;

Chen, Ken ;

Schmidt, Heather ;

Kalicki-Veizer, Joelle ;

Magrini, Vincent J. ;

Cook, Lisa ;

McGrath, Sean D. ;

Vickery, Tammi L. ;

Wendl, Michael C. ;

Heath, Sharon ;

Watson, Mark A. ;

Link, Daniel C. ;

Tomasson, Michael H. ;

Shannon, William D. ;

Payton, Jacqueline E. ;

Kulkarni, Shashikant ;

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Ding, Li ;

Ellis, Matthew J. ;

Li, Shunqiang ;

Larson, David E. ;

Chen, Ken ;

Wallis, Johnw. ;

Harris, Christopher C. ;

McLellan, Michael D. ;

Fulton, Robert S. ;

Fulton, Lucinda L. ;

Abbott, Rachel M. ;

Hoog, Jeremy ;

Dooling, David J. ;

Koboldt, Daniel C. ;

Schmidt, Heather ;

Kalicki, Joelle ;

Zhang, Qunyuan ;

Chen, Lei ;

Lin, Ling ;

Wendl, Michael C. ;

McMichael, Joshua F. ;

Magrini, Vincent J. ;

Cook, Lisa ;

McGrath, Sean D. ;

Vickery, Tammi L. ;

Appelbaum, Elizabeth ;

DeSchryver, Katherine ;

Davies, Sherri ;

Guintoli, Therese ;

Lin, Li ;

Crowder, Robert ;

Tao, Yu ;

Snider, Jacqueline E. ;

Smith, Scott M. ;

Dukes, Adam F. ;

Sanderson, Gabriel E. ;

Pohl, Craig S. ;

Delehaunty, Kim D. ;

Fronick, Catrina C. ;

Pape, Kimberley A. ;

Reed, Jerry S. ;

Robinson, Jody S. ;

Hodges, Jennifer S. ;

Schierding, William ;

Dees, Nathan D. ;

Shen, Dong ;

Locke, Devin P. ;

Wiechert, Madeline E. ;

Eldred, James M. ;

Peck, Josh B. .

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Ellis, Matthew J. ;

Ding, Li ;

Shen, Dong ;

Luo, Jingqin ;

Suman, Vera J. ;

Wallis, John W. ;

Van Tine, Brian A. ;

Hoog, Jeremy ;

Goiffon, Reece J. ;

Goldstein, Theodore C. ;

Ng, Sam ;

Lin, Li ;

Crowder, Robert ;

Snider, Jacqueline ;

Ballman, Karla ;

Weber, Jason ;

Chen, Ken ;

Koboldt, Daniel C. ;

Kandoth, Cyriac ;

Schierding, William S. ;

McMichael, Joshua F. ;

Miller, Christopher A. ;

Lu, Charles ;

Harris, Christopher C. ;

McLellan, Michael D. ;

Wendl, Michael C. ;

DeSchryver, Katherine ;

Allred, D. Craig ;

Esserman, Laura ;

Unzeitig, Gary ;

Margenthaler, Julie ;

Babiera, G. V. ;

Marcom, P. Kelly ;

Guenther, J. M. ;

Leitch, Marilyn ;

Hunt, Kelly ;

Olson, John ;

Tao, Yu ;

Maher, Christopher A. ;

Fulton, Lucinda L. ;

Fulton, Robert S. ;

Harrison, Michelle ;

Oberkfell, Ben ;

Du, Feiyu ;

Demeter, Ryan ;

Vickery, Tammi L. ;

Elhammali, Adnan ;

Piwnica-Worms, Helen ;

McDonald, Sandra ;

Watson, Mark .

NATURE, 2012, 486 (7403) :353-360

← 1 2 3 4 →

共 38 条

[1] Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer [J].

Amado, Rafael G. ;

Wolf, Michael ;

Peeters, Marc ;

Van Cutsem, Eric ;

Siena, Salvatore ;

Freeman, Daniel J. ;

Juan, Todd ;

Sikorski, Robert ;

Suggs, Sid ;

Radinsky, Robert ;

Patterson, Scott D. ;

Chang, David D. .

JOURNAL OF CLINICAL ONCOLOGY, 2008, 26 (10) :1626-1634

[2] Genetic variegation of clonal architecture and propagating cells in leukaemia [J].

Anderson, Kristina ;

Lutz, Christoph ;

van Delft, Frederik W. ;

Bateman, Caroline M. ;

Guo, Yanping ;

Colman, Susan M. ;

Kempski, Helena ;

Moorman, Anthony V. ;

Titley, Ian ;

Swansbury, John ;

Kearney, Lyndal ;

Enver, Tariq ;

Greaves, Mel .

NATURE, 2011, 469 (7330) :356-+

[3] Accurate whole human genome sequencing using reversible terminator chemistry [J].

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 .

NATURE, 2008, 456 (7218) :53-59

[4] Signatures of mutation and selection in the cancer genome [J].

Bignell, Graham R. ;

Greenman, Chris D. ;

Davies, Helen ;

Butler, Adam P. ;

Edkins, Sarah ;

Andrews, Jenny M. ;

Buck, Gemma ;

Chen, Lina ;

Beare, David ;

Latimer, Calli ;

Widaa, Sara ;

Hinton, Jonathon ;

Fahey, Ciara ;

Fu, Beiyuan ;

Swamy, Sajani ;

Dalgliesh, Gillian L. ;

Teh, Bin T. ;

Deloukas, Panos ;

Yang, Fengtang ;

Campbell, Peter J. ;

Futreal, P. Andrew ;

Stratton, Michael R. .

NATURE, 2010, 463 (7283) :893-U61

[5] Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing [J].

Campbell, Peter J. ;

Stephens, Philip J. ;

Pleasance, Erin D. ;

O'Meara, Sarah ;

Li, Heng ;

Santarius, Thomas ;

Stebbings, Lucy A. ;

Leroy, Catherine ;

Edkins, Sarah ;

Hardy, Claire ;

Teague, Jon W. ;

Menzies, Andrew ;

Goodhead, Ian ;

Turner, Daniel J. ;

Clee, Christopher M. ;

Quail, Michael A. ;

Cox, Antony ;

Brown, Clive ;

Durbin, Richard ;

Hurles, Matthew E. ;

Edwards, Paul A. W. ;

Bignell, Graham R. ;

Stratton, Michael R. ;

Futreal, P. Andrew .

NATURE GENETICS, 2008, 40 (06) :722-729

[6] Initial genome sequencing and analysis of multiple myeloma [J].

Chapman, Michael A. ;

Lawrence, Michael S. ;

Keats, Jonathan J. ;

Cibulskis, Kristian ;

Sougnez, Carrie ;

Schinzel, Anna C. ;

Harview, Christina L. ;

Brunet, Jean-Philippe ;

Ahmann, Gregory J. ;

Adli, Mazhar ;

Anderson, Kenneth C. ;

Ardlie, Kristin G. ;

Auclair, Daniel ;

Baker, Angela ;

Bergsagel, P. Leif ;

Bernstein, Bradley E. ;

Drier, Yotam ;

Fonseca, Rafael ;

Gabriel, Stacey B. ;

Hofmeister, Craig C. ;

Jagannath, Sundar ;

Jakubowiak, Andrzej J. ;

Krishnan, Amrita ;

Levy, Joan ;

Liefeld, Ted ;

Lonial, Sagar ;

Mahan, Scott ;

Mfuko, Bunmi ;

Monti, Stefano ;

Perkins, Louise M. ;

Onofrio, Robb ;

Pugh, Trevor J. ;

Rajkumar, S. Vincent ;

Ramos, Alex H. ;

Siegel, David S. ;

Sivachenko, Andrey ;

Stewart, A. Keith ;

Trudel, Suzanne ;

Vij, Ravi ;

Voet, Douglas ;

Winckler, Wendy ;

Zimmerman, Todd ;

Carpten, John ;

Trent, Jeff ;

Hahn, William C. ;

Garraway, Levi A. ;

Meyerson, Matthew ;

Lander, Eric S. ;

Getz, Gad ;

Golub, Todd R. .

NATURE, 2011, 471 (7339) :467-472

[7] Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes [J].

Dalgliesh, Gillian L. ;

Furge, Kyle ;

Greenman, Chris ;

Chen, Lina ;

Bignell, Graham ;

Butler, Adam ;

Davies, Helen ;

Edkins, Sarah ;

Hardy, Claire ;

Latimer, Calli ;

Teague, Jon ;

Andrews, Jenny ;

Barthorpe, Syd ;

Beare, Dave ;

Buck, Gemma ;

Campbell, Peter J. ;

Forbes, Simon ;

Jia, Mingming ;

Jones, David ;

Knott, Henry ;

Kok, Chai Yin ;

Lau, King Wai ;

Leroy, Catherine ;

Lin, Meng-Lay ;

McBride, David J. ;

Maddison, Mark ;

Maguire, Simon ;

McLay, Kirsten ;

Menzies, Andrew ;

Mironenko, Tatiana ;

Mulderrig, Lee ;

Mudie, Laura ;

O'Meara, Sarah ;

Pleasance, Erin ;

Rajasingham, Arjunan ;

Shepherd, Rebecca ;

Smith, Raffaella ;

Stebbings, Lucy ;

Stephens, Philip ;

Tang, Gurpreet ;

Tarpey, Patrick S. ;

Turrell, Kelly ;

Dykema, Karl J. ;

Khoo, Sok Kean ;

Petillo, David ;

Wondergem, Bill ;

Anema, John ;

Kahnoski, Richard J. ;

Teh, Bin Tean ;

Stratton, Michael R. .

NATURE, 2010, 463 (7279) :360-363

[8] Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing [J].

Ding, Li ;

Ley, Timothy J. ;

Larson, David E. ;

Miller, Christopher A. ;

Koboldt, Daniel C. ;

Welch, John S. ;

Ritchey, Julie K. ;

Young, Margaret A. ;

Lamprecht, Tamara ;

McLellan, Michael D. ;

McMichael, Joshua F. ;

Wallis, John W. ;

Lu, Charles ;

Shen, Dong ;

Harris, Christopher C. ;

Dooling, David J. ;

Fulton, Robert S. ;

Fulton, Lucinda L. ;

Chen, Ken ;

Schmidt, Heather ;

Kalicki-Veizer, Joelle ;

Magrini, Vincent J. ;

Cook, Lisa ;

McGrath, Sean D. ;

Vickery, Tammi L. ;

Wendl, Michael C. ;

Heath, Sharon ;

Watson, Mark A. ;

Link, Daniel C. ;

Tomasson, Michael H. ;

Shannon, William D. ;

Payton, Jacqueline E. ;

Kulkarni, Shashikant ;

Westervelt, Peter ;

Walter, Matthew J. ;

Graubert, Timothy A. ;

Mardis, Elaine R. ;

Wilson, Richard K. ;

DiPersio, John F. .

NATURE, 2012, 481 (7382) :506-510

[9] Genome remodelling in a basal-like breast cancer metastasis and xenograft [J].

Ding, Li ;

Ellis, Matthew J. ;

Li, Shunqiang ;

Larson, David E. ;

Chen, Ken ;

Wallis, Johnw. ;

Harris, Christopher C. ;

McLellan, Michael D. ;

Fulton, Robert S. ;

Fulton, Lucinda L. ;

Abbott, Rachel M. ;

Hoog, Jeremy ;

Dooling, David J. ;

Koboldt, Daniel C. ;

Schmidt, Heather ;

Kalicki, Joelle ;

Zhang, Qunyuan ;

Chen, Lei ;

Lin, Ling ;

Wendl, Michael C. ;

McMichael, Joshua F. ;

Magrini, Vincent J. ;

Cook, Lisa ;

McGrath, Sean D. ;

Vickery, Tammi L. ;

Appelbaum, Elizabeth ;

DeSchryver, Katherine ;

Davies, Sherri ;

Guintoli, Therese ;

Lin, Li ;

Crowder, Robert ;

Tao, Yu ;

Snider, Jacqueline E. ;

Smith, Scott M. ;

Dukes, Adam F. ;

Sanderson, Gabriel E. ;

Pohl, Craig S. ;

Delehaunty, Kim D. ;

Fronick, Catrina C. ;

Pape, Kimberley A. ;

Reed, Jerry S. ;

Robinson, Jody S. ;

Hodges, Jennifer S. ;

Schierding, William ;

Dees, Nathan D. ;

Shen, Dong ;

Locke, Devin P. ;

Wiechert, Madeline E. ;

Eldred, James M. ;

Peck, Josh B. .

NATURE, 2010, 464 (7291) :999-1005

[10] Whole-genome analysis informs breast cancer response to aromatase inhibition [J].

Ellis, Matthew J. ;

Ding, Li ;

Shen, Dong ;

Luo, Jingqin ;

Suman, Vera J. ;

Wallis, John W. ;

Van Tine, Brian A. ;

Hoog, Jeremy ;

Goiffon, Reece J. ;

Goldstein, Theodore C. ;

Ng, Sam ;

Lin, Li ;

Crowder, Robert ;

Snider, Jacqueline ;

Ballman, Karla ;

Weber, Jason ;

Chen, Ken ;

Koboldt, Daniel C. ;

Kandoth, Cyriac ;

Schierding, William S. ;

McMichael, Joshua F. ;

Miller, Christopher A. ;

Lu, Charles ;

Harris, Christopher C. ;

McLellan, Michael D. ;

Wendl, Michael C. ;

DeSchryver, Katherine ;

Allred, D. Craig ;

Esserman, Laura ;

Unzeitig, Gary ;

Margenthaler, Julie ;

Babiera, G. V. ;

Marcom, P. Kelly ;

Guenther, J. M. ;

Leitch, Marilyn ;

Hunt, Kelly ;

Olson, John ;

Tao, Yu ;

Maher, Christopher A. ;

Fulton, Lucinda L. ;

Fulton, Robert S. ;

Harrison, Michelle ;

Oberkfell, Ben ;

Du, Feiyu ;

Demeter, Ryan ;

Vickery, Tammi L. ;

Elhammali, Adnan ;

Piwnica-Worms, Helen ;

McDonald, Sandra ;

Watson, Mark .

NATURE, 2012, 486 (7403) :353-360

← 1 2 3 4 →