Drug Sensitivity Prediction From Cell Line-Based Pharmacogenomics Data: Guidelines for Developing Machine Learning Models

IN SOCK JANG, ELIAS CHAIBUB NETO, JUSTIN GUINNEY, STEPHEN H. FRIEND, ADAM A. MARGOLIN, SYSTEMATIC ASSESSMENT OF ANALYTICAL METHODS FOR DRUG SENSITIVITY PREDICTION FROM CANCER CELL LINE DATA pacific symposium on biocomputing. pp. 63- 74 ,(2013) , 10.1142/9789814583220_0007

Christiaan Klijn, Steffen Durinck, Eric W Stawiski, Peter M Haverty, Zhaoshi Jiang, Hanbin Liu, Jeremiah Degenhardt, Oleg Mayba, Florian Gnad, Jinfeng Liu, Gregoire Pau, Jens Reeder, Yi Cao, Kiran Mukhyala, Suresh K Selvaraj, Mamie Yu, Gregory J Zynda, Matthew J Brauer, Thomas D Wu, Robert C Gentleman, Gerard Manning, Robert L Yauch, Richard Bourgon, David Stokoe, Zora Modrusan, Richard M Neve, Frederic J de Sauvage, Jeffrey Settleman, Somasekar Seshagiri, Zemin Zhang, A comprehensive transcriptional portrait of human cancer cell lines Nature Biotechnology. ,vol. 33, pp. 306- 312 ,(2015) , 10.1038/NBT.3080

Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai Juul Birkbak, Andrew C Jin, Andrew H Beck, Hugo JWL Aerts, John Quackenbush, Inconsistency in large pharmacogenomic studies Nature. ,vol. 504, pp. 389- 393 ,(2013) , 10.1038/NATURE12831

Paul Geeleher, Nancy J Cox, R Huang, Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. Genome Biology. ,vol. 15, pp. 1- 12 ,(2014) , 10.1186/GB-2014-15-3-R47

J. L. Sebaugh, Guidelines for accurate EC50/IC50 estimation Pharmaceutical Statistics. ,vol. 10, pp. 128- 134 ,(2011) , 10.1002/PST.426

Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A Margolin, Sungjoon Kim, Christopher J Wilson, Joseph Lehár, Gregory V Kryukov, Dmitriy Sonkin, Anupama Reddy, Manway Liu, Lauren Murray, Michael F Berger, John E Monahan, Paula Morais, Jodi Meltzer, Adam Korejwa, Judit Jané-Valbuena, Felipa A Mapa, Joseph Thibault, Eva Bric-Furlong, Pichai Raman, Aaron Shipway, Ingo H Engels, Jill Cheng, Guoying K Yu, Jianjun Yu, Peter Aspesi, Melanie De Silva, Kalpana Jagtap, Michael D Jones, Li Wang, Charles Hatton, Emanuele Palescandolo, Supriya Gupta, Scott Mahan, Carrie Sougnez, Robert C Onofrio, Ted Liefeld, Laura MacConaill, Wendy Winckler, Michael Reich, Nanxin Li, Jill P Mesirov, Stacey B Gabriel, Gad Getz, Kristin Ardlie, Vivien Chan, Vic E Myer, Barbara L Weber, Jeff Porter, Markus Warmuth, Peter Finan, Jennifer L Harris, Matthew Meyerson, Todd R Golub, Michael P Morrissey, William R Sellers, Robert Schlegel, Levi A Garraway, None, The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Nature. ,vol. 483, pp. 603- 607 ,(2012) , 10.1038/NATURE11003

James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Muhammad Ammad-Ud-Din, Petteri Hintsanen, Suleiman A Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, James J Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray, Gustavo Stolovitzky, None, A community effort to assess and improve drug sensitivity prediction algorithms Nature Biotechnology. ,vol. 32, pp. 1202- 1212 ,(2014) , 10.1038/NBT.2877

Gregory Riddick, Hua Song, Susie Ahn, Jennifer Walling, Diego Borges-Rivera, Wei Zhang, Howard A. Fine, Predicting in vitro drug sensitivity using Random Forests Bioinformatics. ,vol. 27, pp. 220- 224 ,(2011) , 10.1093/BIOINFORMATICS/BTQ628

Jyoti D Patel, Lada Krilov, Sylvia Adams, Carol Aghajanian, Ethan Basch, Marcia S Brose, William L Carroll, Marcos De Lima, Mark R Gilbert, Mark G Kris, John L Marshall, Gregory A Masters, Steven J O'Day, Blasé Polite, Gary K Schwartz, Sunil Sharma, Ian Thompson, Nicholas J Vogelzang, Bruce J Roth, None, Clinical Cancer Advances 2013: Annual Report on Progress Against Cancer From the American Society of Clinical Oncology Journal of Clinical Oncology. ,vol. 32, pp. 129- 160 ,(2014) , 10.1200/JCO.2013.53.7076

Mathew J Garnett, Elena J Edelman, Sonja J Heidorn, Chris D Greenman, Anahita Dastur, King Wai Lau, Patricia Greninger, I Richard Thompson, Xi Luo, Jorge Soares, Qingsong Liu, Francesco Iorio, Didier Surdez, Li Chen, Randy J Milano, Graham R Bignell, Ah T Tam, Helen Davies, Jesse A Stevenson, Syd Barthorpe, Stephen R Lutz, Fiona Kogera, Karl Lawrence, Anne McLaren-Douglas, Xeni Mitropoulos, Tatiana Mironenko, Helen Thi, Laura Richardson, Wenjun Zhou, Frances Jewitt, Tinghu Zhang, Patrick O’Brien, Jessica L Boisvert, Stacey Price, Wooyoung Hur, Wanjuan Yang, Xianming Deng, Adam Butler, Hwan Geun Choi, Jae Won Chang, Jose Baselga, Ivan Stamenkovic, Jeffrey A Engelman, Sreenath V Sharma, Olivier Delattre, Julio Saez-Rodriguez, Nathanael S Gray, Jeffrey Settleman, P Andrew Futreal, Daniel A Haber, Michael R Stratton, Sridhar Ramaswamy, Ultan McDermott, Cyril H Benes, None, Systematic identification of genomic markers of drug sensitivity in cancer cells Nature. ,vol. 483, pp. 570- 575 ,(2012) , 10.1038/NATURE11005