Repository logo
  • Log In
    Log in via Symplectic to deposit your publication(s).
Repository logo
  • Communities & Collections
  • Research Outputs
  • Statistics
  • Log In
    Log in via Symplectic to deposit your publication(s).
  1. Home
  2. Faculty of Engineering
  3. Bioengineering
  4. Bioengineering
  5. Predicting synergism of cancer drug combinations using NCI-ALMANAC data
 
  • Details
Predicting synergism of cancer drug combinations using NCI-ALMANAC data
File(s)
Predicting Synergism of Cancer Drug Combinations Using NCI-ALMANAC Data.pdf (3.05 MB)
Published version
Author(s)
Sidorov, Pavel
Naulaerts, Stefan
Ariey-Bonnet, Jérémy
Pasquier, Eddy
Ballester, Pedro J
Type
Journal Article
Abstract
Drug combinations are of great interest for cancer treatment. Unfortunately, the discovery of synergistic combinations by purely experimental means is only feasible on small sets of drugs. In silico modeling methods can substantially widen this search by providing tools able to predict which of all possible combinations in a large compound library are synergistic. Here we investigate to which extent drug combination synergy can be predicted by exploiting the largest available dataset to date (NCI-ALMANAC, with over 290,000 synergy determinations). Each cell line is modeled using primarily two machine learning techniques, Random Forest (RF) and Extreme Gradient Boosting (XGBoost), on the datasets provided by NCI-ALMANAC. This large-scale predictive modeling study comprises more than 5,000 pair-wise drug combinations, 60 cell lines, 4 types of models, and 5 types of chemical features. The application of a powerful, yet uncommonly used, RF-specific technique for reliability prediction is also investigated. The evaluation of these models shows that it is possible to predict the synergy of unseen drug combinations with high accuracy (Pearson correlations between 0.43 and 0.86 depending on the considered cell line, with XGBoost providing slightly better predictions than RF). We have also found that restricting to the most reliable synergy predictions results in at least 2-fold error decrease with respect to employing the best learning algorithm without any reliability estimation. Alkylating agents, tyrosine kinase inhibitors and topoisomerase inhibitors are the drugs whose synergy with other partner drugs are better predicted by the models. Despite its leading size, NCI-ALMANAC comprises an extremely small part of all conceivable combinations. Given their accuracy and reliability estimation, the developed models should drastically reduce the number of required in vitro tests by predicting in silico which of the considered combinations are likely to be synergistic.
Date Issued
2019-07-16
Date Acceptance
2019-07-02
Citation
Frontiers in Chemistry, 2019, 7
URI
http://hdl.handle.net/10044/1/108542
URL
https://doi.org/10.3389/fchem.2019.00509
DOI
https://www.dx.doi.org/10.3389/fchem.2019.00509
ISSN
2296-2646
Publisher
Frontiers Media S.A.
Journal / Book Title
Frontiers in Chemistry
Volume
7
Copyright Statement
Copyright © 2019 Sidorov, Naulaerts, Ariey-Bonnet, Pasquier and Ballester. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
License URL
https://creativecommons.org/licenses/by/4.0/
Identifier
https://doi.org/10.3389/fchem.2019.00509
Publication Status
Published
Article Number
509
Date Publish Online
2019-07-16
About
Spiral Depositing with Spiral Publishing with Spiral Symplectic
Contact us
Open access team Report an issue
Other Services
Scholarly Communications Library Services
logo

Imperial College London

South Kensington Campus

London SW7 2AZ, UK

tel: +44 (0)20 7589 5111

Accessibility Modern slavery statement Cookie Policy

Built with DSpace-CRIS software - Extension maintained and optimized by 4Science

  • Cookie settings
  • Privacy policy
  • End User Agreement
  • Send Feedback