Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers

被引：15

作者：

Borad, Mitesh J. ^{[1
,2
,3
]}

Egan, Jan B. ^{[3
]}

Condjella, Rachel M. ^{[2
]}

Liang, Winnie S. ^{[4
]}

Fonseca, Rafael ^{[1
,2
,3
]}

Ritacca, Nicole R. ^{[2
]}

McCullough, Ann E. ^{[5
]}

Barrett, Michael T. ^{[2
,4
]}

Hunt, Katherine S. ^{[1
]}

Champion, Mia D. ^{[3
,6
]}

Patel, Maitray D. ^{[7
]}

Young, Scott W. ^{[7
]}

Silva, Alvin C. ^{[7
]}

Ho, Thai H. ^{[1
,2
,3
]}

Halfdanarson, Thorvardur R. ^{[1
,2
,3
]}

McWilliams, Robert R. ^{[3
,8
]}

Lazaridis, Konstantinos N. ^{[3
]}

Ramanathan, Ramesh K. ^{[1
,2
]}

Baker, Angela ^{[4
]}

Aldrich, Jessica ^{[4
]}

Kurdoglu, Ahmet ^{[4
]}

Izatt, Tyler ^{[4
]}

Christoforides, Alexis ^{[4
]}

Cherni, Irene ^{[4
]}

Nasser, Sara ^{[4
]}

Reiman, Rebecca ^{[4
]}

Cuyugan, Lori ^{[4
]}

McDonald, Jacquelyn ^{[4
]}

Adkins, Jonathan ^{[4
]}

Mastrian, Stephen D. ^{[4
]}

Valdez, Riccardo ^{[5
]}

Jaroszewski, Dawn E. ^{[9
]}

Von Hoff, Daniel D. ^{[4
]}

Craig, David W. ^{[4
]}

Stewart, A. Keith ^{[1
,2
,3
]}

Carpten, John D. ^{[4
]}

Bryce, Alan H. ^{[1
,2
,3
]}

机构：

[1] Mayo Clin, Div Hematol Oncol, Scottsdale, AZ USA

[2] Mayo Clin, Canc Ctr, Scottsdale, AZ USA

[3] Mayo Clin, Ctr Individualized Med, Rochester, MN USA

[4] Translat Genom Res Inst, Phoenix, AZ USA

[5] Mayo Clin, Dept Pathol, Scottsdale, AZ USA

[6] Mayo Clin, Dept Biomed Stat & Informat, Scottsdale, AZ USA

[7] Mayo Clin, Dept Radiol, Scottsdale, AZ USA

[8] Mayo Clin, Canc Ctr, Rochester, MN USA

[9] Mayo Clin, Dept Cardiovasc Surg, Scottsdale, AZ USA

来源：

SCIENTIFIC REPORTS | 2016年 / 6卷

关键词：

MOLECULAR TUMOR BOARD; FRAMEWORK; DNA; TRIALS; EXOME; HETEROGENEITY; BIOMARKERS; GENES;

D O I：

10.1038/s41598-016-0021-4

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

DNA focused panel sequencing has been rapidly adopted to assess therapeutic targets in advanced/refractory cancer. Integrated Genomic Profiling (IGP) utilising DNA/RNA with tumour/normal comparisons in a Clinical Laboratory Improvement Amendments (CLIA) compliant setting enables a single assay to provide: therapeutic target prioritisation, novel target discovery/application and comprehensive germline assessment. A prospective study in 35 advanced/refractory cancer patients was conducted using CLIA-compliant IGP. Feasibility was assessed by estimating time to results (TTR), prioritising/assigning putative therapeutic targets, assessing drug access, ascertaining germline alterations, and assessing patient preferences/perspectives on data use/reporting. Therapeutic targets were identified using biointelligence/pathway analyses and interpreted by a Genomic Tumour Board. Seventy-five percent of cases harboured 1-3 therapeutically targetable mutations/case (median 79 mutations of potential functional significance/case). Median time to CLIA-validated results was 116 days with CLIA-validation of targets achieved in 21/22 patients. IGP directed treatment was instituted in 13 patients utilising on/off label FDA approved drugs (n = 9), clinical trials (n = 3) and single patient IND (n = 1). Preliminary clinical efficacy was noted in five patients (two partial response, three stable disease). Although barriers to broader application exist, including the need for wider availability of therapies, IGP in a CLIA-framework is feasible and valuable in selection/prioritisation of anti-cancer therapeutic targets.

引用

页数：12

共 40 条

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Liang, Winnie S. ;

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McCullough, Ann E. ;

Barrett, Michael T. ;

Hunt, Katherine ;

Patel, Maitray D. ;

Young, Scott W. ;

Collins, Joseph M. ;

Silva, Alvin C. ;

Condjella, Rachel M. ;

Block, Matthew ;

McWilliams, Robert R. ;

Lazaridis, Konstantinos N. ;

Klee, Eric W. ;

Bible, Keith C. ;

Harris, Pamela ;

Oliver, Gavin R. ;

Bhavsar, Jaysheel D. ;

Nair, Asha A. ;

Middha, Sumit ;

Asmann, Yan ;

Kocher, Jean-Pierre ;

Schahl, Kimberly ;

Kipp, Benjamin R. ;

Fritcher, Emily G. Barr ;

Baker, Angela ;

Aldrich, Jessica ;

Kurdoglu, Ahmet ;

Izatt, Tyler ;

Christoforides, Alexis ;

Cherni, Irene ;

Nasser, Sara ;

Reiman, Rebecca ;

Phillips, Lori ;

McDonald, Jackie ;

Adkins, Jonathan ;

Mastrian, Stephen D. ;

Placek, Pamela ;

Watanabe, Aprill T. ;

LoBello, Janine ;

Han, Haiyong ;

Von Hoff, Daniel ;

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Meyerson, M. ;

Aldape, K. ;

Bigner, D. ;

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Kahn, A. ;

Penny, R. ;

Ferguson, M. L. ;

Gerhard, D. S. ;

Getz, G. ;

Brennan, C. ;

Taylor, B. S. ;

Winckler, W. ;

Park, P. ;

Ladanyi, M. ;

Hoadley, K. A. ;

Verhaak, R. G. W. ;

Hayes, D. N. ;

Spellman, Paul T. ;

Absher, D. ;

Weir, B. A. ;

Ding, L. ;

Wheeler, D. ;

Lawrence, M. S. ;

Cibulskis, K. ;

Mardis, E. ;

Zhang, Jinghui ;

Wilson, R. K. ;

Donehower, L. ;

Wheeler, D. A. ;

Purdom, E. ;

Wallis, J. ;

Laird, P. W. ;

Herman, J. G. ;

Schuebel, K. E. ;

Weisenberger, D. J. ;

Baylin, S. B. ;

Schultz, N. ;

Yao, Jun ;

Wiedemeyer, R. ;

Weinstein, J. ;

Sander, C. ;

Gibbs, R. A. ;

Gray, J. ;

Kucherlapati, R. ;

Lander, E. S. ;

Myers, R. M. ;

Perou, C. M. ;

McLendon, Roger .

NATURE, 2008, 455 (7216) :1061-1068

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Dawson, Sarah-Jane ;

Tsui, Dana W. Y. ;

Murtaza, Muhammed ;

Biggs, Heather ;

Rueda, Oscar M. ;

Chin, Suet-Feung ;

Dunning, Mark J. ;

Gale, Davina ;

Forshew, Tim ;

Mahler-Araujo, Betania ;

Rajan, Sabrina ;

Humphray, Sean ;

Becq, Jennifer ;

Halsall, David ;

Wallis, Matthew ;

Bentley, David ;

Caldas, Carlos ;

Rosenfeld, Nitzan .

NEW ENGLAND JOURNAL OF MEDICINE, 2013, 368 (13) :1199-1209

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DePristo, Mark A. ;

Banks, Eric ;

Poplin, Ryan ;

Garimella, Kiran V. ;

Maguire, Jared R. ;

Hartl, Christopher ;

Philippakis, Anthony A. ;

del Angel, Guillermo ;

Rivas, Manuel A. ;

Hanna, Matt ;

McKenna, Aaron ;

Fennell, Tim J. ;

Kernytsky, Andrew M. ;

Sivachenko, Andrey Y. ;

Cibulskis, Kristian ;

Gabriel, Stacey B. ;

Altshuler, David ;

Daly, Mark J. .

NATURE GENETICS, 2011, 43 (05) :491-+

← 1 2 3 4 →

共 40 条

[1] A method and server for predicting damaging missense mutations [J].

Adzhubei, Ivan A. ;

Schmidt, Steffen ;

Peshkin, Leonid ;

Ramensky, Vasily E. ;

Gerasimova, Anna ;

Bork, Peer ;

Kondrashov, Alexey S. ;

Sunyaev, Shamil R. .

NATURE METHODS, 2010, 7 (04) :248-249

[2] Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER) [J].

Andre, Fabrice ;

Bachelot, Thomas ;

Commo, Frederic ;

Campone, Mario ;

Arnedos, Monica ;

Dieras, Veronique ;

Lacroix-Triki, Magali ;

Lacroix, Ludovic ;

Cohen, Pascale ;

Gentien, David ;

Adelaide, Jose ;

Dalenc, Florence ;

Goncalves, Anthony ;

Levy, Christelle ;

Ferrero, Jean-Marc ;

Bonneterre, Jacques ;

Lefeuvre, Claudia ;

Jimenez, Marta ;

Filleron, Thomas ;

Bonnefoi, Herve .

LANCET ONCOLOGY, 2014, 15 (03) :267-274

[3] The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity [J].

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. .

NATURE, 2012, 483 (7391) :603-607

[4] Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response [J].

Beltran, Himisha ;

Eng, Kenneth ;

Mosquera, Juan Miguel ;

Sigaras, Alexandros ;

Romanel, Alessandro ;

Rennert, Hanna ;

Kossai, Myriam ;

Pauli, Chantal ;

Faltas, Bishoy ;

Fontugne, Jacqueline ;

Park, Kyung ;

Banfelder, Jason ;

Prandi, Davide ;

Madhukar, Neel ;

Zhang, Tuo ;

Padilla, Jessica ;

Greco, Noah ;

McNary, Terra J. ;

Herrscher, Erick ;

Wilkes, David ;

MacDonald, Theresa Y. ;

Xue, Hui ;

Vacic, Vladimir ;

Emde, Anne-Katrin ;

Oschwald, Dayna ;

Tan, Adrian Y. ;

Chen, Zhengming ;

Collins, Colin ;

Gleave, Martin E. ;

Wang, Yuzhuo ;

Chakravarty, Dimple ;

Schiffman, Marc ;

Kim, Robert ;

Campagne, Fabien ;

Robinson, Brian D. ;

Nanus, David M. ;

Tagawa, Scott T. ;

Xiang, Jenny Z. ;

Smogorzewska, Agata ;

Demichelis, Francesca ;

Rickman, David S. ;

Sboner, Andrea ;

Elemento, Olivier ;

Rubin, Mark A. .

JAMA ONCOLOGY, 2015, 1 (04) :466-474

[5] Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies [J].

Bettegowda, Chetan ;

Sausen, Mark ;

Leary, Rebecca J. ;

Kinde, Isaac ;

Wang, Yuxuan ;

Agrawal, Nishant ;

Bartlett, Bjarne R. ;

Wang, Hao ;

Luber, Brandon ;

Alani, Rhoda M. ;

Antonarakis, Emmanuel S. ;

Azad, Nilofer S. ;

Bardelli, Alberto ;

Brem, Henry ;

Cameron, John L. ;

Lee, Clarence C. ;

Fecher, Leslie A. ;

Gallia, Gary L. ;

Gibbs, Peter ;

Le, Dung ;

Giuntoli, Robert L. ;

Goggins, Michael ;

Hogarty, Michael D. ;

Holdhoff, Matthias ;

Hong, Seung-Mo ;

Jiao, Yuchen ;

Juhl, Hartmut H. ;

Kim, Jenny J. ;

Siravegna, Giulia ;

Laheru, Daniel A. ;

Lauricella, Calogero ;

Lim, Michael ;

Lipson, Evan J. ;

Marie, Suely Kazue Nagahashi ;

Netto, George J. ;

Oliner, Kelly S. ;

Olivi, Alessandro ;

Olsson, Louise ;

Riggins, Gregory J. ;

Sartore-Bianchi, Andrea ;

Schmidt, Kerstin ;

Shih, Ie-Ming ;

Oba-Shinjo, Sueli Mieko ;

Siena, Salvatore ;

Theodorescu, Dan ;

Tie, Jeanne ;

Harkins, Timothy T. ;

Veronese, Silvio ;

Wang, Tian-Li ;

Weingart, Jon D. .

SCIENCE TRANSLATIONAL MEDICINE, 2014, 6 (224)

[6] Integrated Genomic Characterization Reveals Novel, Therapeutically Relevant Drug Targets in FGFR and EGFR Pathways in Sporadic Intrahepatic Cholangiocarcinoma [J].

Borad, Mitesh J. ;

Champion, Mia D. ;

Egan, Jan B. ;

Liang, Winnie S. ;

Fonseca, Rafael ;

Bryce, Alan H. ;

McCullough, Ann E. ;

Barrett, Michael T. ;

Hunt, Katherine ;

Patel, Maitray D. ;

Young, Scott W. ;

Collins, Joseph M. ;

Silva, Alvin C. ;

Condjella, Rachel M. ;

Block, Matthew ;

McWilliams, Robert R. ;

Lazaridis, Konstantinos N. ;

Klee, Eric W. ;

Bible, Keith C. ;

Harris, Pamela ;

Oliver, Gavin R. ;

Bhavsar, Jaysheel D. ;

Nair, Asha A. ;

Middha, Sumit ;

Asmann, Yan ;

Kocher, Jean-Pierre ;

Schahl, Kimberly ;

Kipp, Benjamin R. ;

Fritcher, Emily G. Barr ;

Baker, Angela ;

Aldrich, Jessica ;

Kurdoglu, Ahmet ;

Izatt, Tyler ;

Christoforides, Alexis ;

Cherni, Irene ;

Nasser, Sara ;

Reiman, Rebecca ;

Phillips, Lori ;

McDonald, Jackie ;

Adkins, Jonathan ;

Mastrian, Stephen D. ;

Placek, Pamela ;

Watanabe, Aprill T. ;

LoBello, Janine ;

Han, Haiyong ;

Von Hoff, Daniel ;

Craig, David W. ;

Stewart, A. Keith ;

Carpten, John D. .

PLOS GENETICS, 2014, 10 (02)

[7] The causes and consequences of genetic heterogeneity in cancer evolution [J].

Burrell, Rebecca A. ;

McGranahan, Nicholas ;

Bartek, Jiri ;

Swanton, Charles .

NATURE, 2013, 501 (7467) :338-345

[8] Comprehensive genomic characterization defines human glioblastoma genes and core pathways [J].

Chin, L. ;

Meyerson, M. ;

Aldape, K. ;

Bigner, D. ;

Mikkelsen, T. ;

VandenBerg, S. ;

Kahn, A. ;

Penny, R. ;

Ferguson, M. L. ;

Gerhard, D. S. ;

Getz, G. ;

Brennan, C. ;

Taylor, B. S. ;

Winckler, W. ;

Park, P. ;

Ladanyi, M. ;

Hoadley, K. A. ;

Verhaak, R. G. W. ;

Hayes, D. N. ;

Spellman, Paul T. ;

Absher, D. ;

Weir, B. A. ;

Ding, L. ;

Wheeler, D. ;

Lawrence, M. S. ;

Cibulskis, K. ;

Mardis, E. ;

Zhang, Jinghui ;

Wilson, R. K. ;

Donehower, L. ;

Wheeler, D. A. ;

Purdom, E. ;

Wallis, J. ;

Laird, P. W. ;

Herman, J. G. ;

Schuebel, K. E. ;

Weisenberger, D. J. ;

Baylin, S. B. ;

Schultz, N. ;

Yao, Jun ;

Wiedemeyer, R. ;

Weinstein, J. ;

Sander, C. ;

Gibbs, R. A. ;

Gray, J. ;

Kucherlapati, R. ;

Lander, E. S. ;

Myers, R. M. ;

Perou, C. M. ;

McLendon, Roger .

NATURE, 2008, 455 (7216) :1061-1068

[9] Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer [J].

Dawson, Sarah-Jane ;

Tsui, Dana W. Y. ;

Murtaza, Muhammed ;

Biggs, Heather ;

Rueda, Oscar M. ;

Chin, Suet-Feung ;

Dunning, Mark J. ;

Gale, Davina ;

Forshew, Tim ;

Mahler-Araujo, Betania ;

Rajan, Sabrina ;

Humphray, Sean ;

Becq, Jennifer ;

Halsall, David ;

Wallis, Matthew ;

Bentley, David ;

Caldas, Carlos ;

Rosenfeld, Nitzan .

NEW ENGLAND JOURNAL OF MEDICINE, 2013, 368 (13) :1199-1209

[10] A framework for variation discovery and genotyping using next-generation DNA sequencing data [J].

DePristo, Mark A. ;

Banks, Eric ;

Poplin, Ryan ;

Garimella, Kiran V. ;

Maguire, Jared R. ;

Hartl, Christopher ;

Philippakis, Anthony A. ;

del Angel, Guillermo ;

Rivas, Manuel A. ;

Hanna, Matt ;

McKenna, Aaron ;

Fennell, Tim J. ;

Kernytsky, Andrew M. ;

Sivachenko, Andrey Y. ;

Cibulskis, Kristian ;

Gabriel, Stacey B. ;

Altshuler, David ;

Daly, Mark J. .

NATURE GENETICS, 2011, 43 (05) :491-+

← 1 2 3 4 →