Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies

Oncotarget

Volumn 7, Issue 32, 2016, Pages 51619-51625

  Pozdeyev, Nikita ^a   Yoo, Minjae ^a   Mackie, Ryan ^a   Schweppe, Rebecca E ^a   Tan, Aik Choon ^a   Haugen, Bryan R ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

Cancer; Cell line; Database integration; Drug sensitivity; Pharmacogenomics

Indexed keywords

2 MORPHOLINO 6 (1 THIANTHRENYL) 4 PYRANONE; 5 (2,6 DICHLOROBENZYLSULFONYL) 3 [3,5 DIMETHYL 4 [2 (1 PYRROLIDINYLMETHYL) 1 PYRROLIDINYLCARBONYL] 1H PYRROL 2 YLMETHYLENE] 1,3 DIHYDRO 2H INDOL 2 ONE; 6 [[2 [[4 (2,4 DICHLOROPHENYL) 5 (4 METHYL 1H IMIDAZOL 2 YL) 2 PYRIMIDINYL]AMINO]ETHYL]AMINO]NICOTINONITRILE; AFATINIB; AXITINIB; BEXAROTENE; CRIZOTINIB; DORAMAPIMOD; DOXORUBICIN; ERLOTINIB; GEFITINIB; LAPATINIB; NILOTINIB; OLAPARIB; PACLITAXEL; PARTHENOLIDE; SELUMETINIB; SERDEMETAN; SORAFENIB; TANESPIMYCIN; TOZASERTIB; VELIPARIB; ANTINEOPLASTIC AGENT;

AREA UNDER THE CURVE; ARTICLE; DRUG MECHANISM; DRUG POTENCY; DRUG SENSITIVITY; IC50; IN VITRO STUDY; NEOPLASM; PHARMACOGENOMICS; COMPUTER INTERFACE; DRUG RESISTANCE; GENETIC DATABASE; GENETICS; GENOMICS; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; PHARMACOGENETIC TESTING; PHARMACOGENETICS; PROCEDURES; TUMOR CELL LINE;

ANTINEOPLASTIC AGENTS; CELL LINE, TUMOR; DATA COLLECTION; DATABASES, GENETIC; DRUG RESISTANCE, NEOPLASM; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; NEOPLASMS; PHARMACOGENETICS; PHARMACOGENOMIC TESTING; USER-COMPUTER INTERFACE;

EID: 84982290181     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.10010     Document Type: Article

References (13)

1. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012; 483: 603-607.
2. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 2012; 483: 570-575.
3. Seashore-Ludlow B, Rees MG, Cheah JH, Cokol M, Price E V, Coletti ME, Jones V, Bodycombe NE, Soule CK, Gould J, Alexander B, Li A, Montgomery P et al. Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset. Cancer Discov. 2015; 5: 1210-1223.
4. Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, Ebright RY, Stewart ML, Ito D, Wang S, Bracha AL, Liefeld T, Wawer M et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell. 2013; 154: 1151-1161.
5. Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJ, Quackenbush J. Inconsistency in large pharmacogenomic studies. Nature. 2013; 504: 389-393.
6. Stransky N, Ghandi M, Kryukov GV, Garraway LA, Lehár J, Liu M, Sonkin D, Kauffmann A, Venkatesan K, Edelman EJ, Riester M, Barretina J, Caponigro G et al. Pharmacogenomic agreement between two cancer cell line data sets. Nature. 2015; 528: 84-87.
7. Corcoran RB, Cheng KA, Hata AN, Faber AC, Ebi H, Coffee EM, Greninger P, Brown RD, Godfrey JT, Cohoon TJ, Song Y, Lifshits E, Hung KE et al. Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models. Cancer Cell. 2013; 23: 121-128.
8. Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK. Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat Chem Biol. 2013; 9: 708-714.
9. Shimada K, Hayano M, Pagano NC, Stockwell BR. Cell-Line Selectivity Improves the Predictive Power of Pharmacogenomic Analyses and Helps Identify NADPH as Biomarker for Ferroptosis Sensitivity. Cell Chem Biol. 2016; 23: 225-235.
10. Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DM, Grossmann P, Beck AH, Aerts HJ, Lupien M et al. PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Bioinformatics. 2016; 32: 1244-1246.
11. Ritz C, Streibig JC. Bioassay Analysis using R. J. Stat. Softw. 2005; 12: 1-21.
12. Sebaugh JL, McCray PD. Defining the linear portion of a sigmoidshaped curve: bend points. Pharm. Stat. 2003; 2: 167-174.
13. Sebaugh JL. Guidelines for accurate EC50/IC50 estimation. Pharm. Stat. 2011; 10: 128-134.