Assessment of pharmacogenomic agreement [version 1; referees: 3 approved]
In 2013 we published an analysis demonstrating that drug response data and gene-drug associations reported in two independent large-scale pharmacogenomic screens, Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE), were inconsistent. The GDSC and CCLE investigator...
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2016-05-01
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| Online Access: | http://f1000research.com/articles/5-825/v1 |
| _version_ | 1818970136312283136 |
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| author | Zhaleh Safikhani Nehme El-Hachem Rene Quevedo Petr Smirnov Anna Goldenberg Nicolai Juul Birkbak Christopher Mason Christos Hatzis Leming Shi Hugo JWL Aerts John Quackenbush Benjamin Haibe-Kains |
| author_facet | Zhaleh Safikhani Nehme El-Hachem Rene Quevedo Petr Smirnov Anna Goldenberg Nicolai Juul Birkbak Christopher Mason Christos Hatzis Leming Shi Hugo JWL Aerts John Quackenbush Benjamin Haibe-Kains |
| author_sort | Zhaleh Safikhani |
| collection | DOAJ |
| description | In 2013 we published an analysis demonstrating that drug response data and gene-drug associations reported in two independent large-scale pharmacogenomic screens, Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE), were inconsistent. The GDSC and CCLE investigators recently reported that their respective studies exhibit reasonable agreement and yield similar molecular predictors of drug response, seemingly contradicting our previous findings. Reanalyzing the authors’ published methods and results, we found that their analysis failed to account for variability in the genomic data and more importantly compared different drug sensitivity measures from each study, which substantially deviate from our more stringent consistency assessment. Our comparison of the most updated genomic and pharmacological data from the GDSC and CCLE confirms our published findings that the measures of drug response reported by these two groups are not consistent. We believe that a principled approach to assess the reproducibility of drug sensitivity predictors is necessary before envisioning their translation into clinical settings. |
| first_indexed | 2024-12-20T14:31:41Z |
| format | Article |
| id | doaj.art-4ff889a58ef74aa58f2a2faddabae771 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-20T14:31:41Z |
| publishDate | 2016-05-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-4ff889a58ef74aa58f2a2faddabae7712022-12-21T19:37:35ZengF1000 Research LtdF1000Research2046-14022016-05-01510.12688/f1000research.8705.19367Assessment of pharmacogenomic agreement [version 1; referees: 3 approved]Zhaleh Safikhani0Nehme El-Hachem1Rene Quevedo2Petr Smirnov3Anna Goldenberg4Nicolai Juul Birkbak5Christopher Mason6Christos Hatzis7Leming Shi8Hugo JWL Aerts9John Quackenbush10Benjamin Haibe-Kains11Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, CanadaInstitut de recherches cliniques de Montréal, Montreal, Quebec, H2W 1R7, CanadaDepartment of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, CanadaPrincess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, CanadaDepartment of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, CanadaUniversity College London, London, WC1E 6BT, UKThe Feil Family Brain and Mind Research Institute (BMRI), New York, NY, 10065, USAYale Cancer Center, Yale University, New Haven, CT, 06510, USAUniversity of Arkansas for Medical Sciences, Little Rock, AR, 72205, USADepartment of Radiation Oncology and Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02215, USADepartment of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USADepartment of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, CanadaIn 2013 we published an analysis demonstrating that drug response data and gene-drug associations reported in two independent large-scale pharmacogenomic screens, Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE), were inconsistent. The GDSC and CCLE investigators recently reported that their respective studies exhibit reasonable agreement and yield similar molecular predictors of drug response, seemingly contradicting our previous findings. Reanalyzing the authors’ published methods and results, we found that their analysis failed to account for variability in the genomic data and more importantly compared different drug sensitivity measures from each study, which substantially deviate from our more stringent consistency assessment. Our comparison of the most updated genomic and pharmacological data from the GDSC and CCLE confirms our published findings that the measures of drug response reported by these two groups are not consistent. We believe that a principled approach to assess the reproducibility of drug sensitivity predictors is necessary before envisioning their translation into clinical settings.http://f1000research.com/articles/5-825/v1BioinformaticsGenomicsMethods for Diagnostic & Therapeutic StudiesMolecular PharmacologyPharmacogenomicsPharmacokinetics & Drug DeliveryStatistical Methodologies & Health Informatics |
| spellingShingle | Zhaleh Safikhani Nehme El-Hachem Rene Quevedo Petr Smirnov Anna Goldenberg Nicolai Juul Birkbak Christopher Mason Christos Hatzis Leming Shi Hugo JWL Aerts John Quackenbush Benjamin Haibe-Kains Assessment of pharmacogenomic agreement [version 1; referees: 3 approved] F1000Research Bioinformatics Genomics Methods for Diagnostic & Therapeutic Studies Molecular Pharmacology Pharmacogenomics Pharmacokinetics & Drug Delivery Statistical Methodologies & Health Informatics |
| title | Assessment of pharmacogenomic agreement [version 1; referees: 3 approved] |
| title_full | Assessment of pharmacogenomic agreement [version 1; referees: 3 approved] |
| title_fullStr | Assessment of pharmacogenomic agreement [version 1; referees: 3 approved] |
| title_full_unstemmed | Assessment of pharmacogenomic agreement [version 1; referees: 3 approved] |
| title_short | Assessment of pharmacogenomic agreement [version 1; referees: 3 approved] |
| title_sort | assessment of pharmacogenomic agreement version 1 referees 3 approved |
| topic | Bioinformatics Genomics Methods for Diagnostic & Therapeutic Studies Molecular Pharmacology Pharmacogenomics Pharmacokinetics & Drug Delivery Statistical Methodologies & Health Informatics |
| url | http://f1000research.com/articles/5-825/v1 |
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