Towards realizing the vision of precision medicine: AI based prediction of clinical drug response

See Chen et al. (doi:10.1093/brain/awab199) for a scientific commentary on this article. De Jong et al. present a retrospectively validated machine learning model linking drug mechanism of action and patients' genetic/clinical/demographic background to anti-epileptic drug response. They identify determinants of poor response and explore their potential utility in clinical trial design for precision medicine.

[1]  P. Kwan,et al.  30 years of second-generation antiseizure medications: impact and future perspectives , 2020, The Lancet Neurology.

[2]  F. Sanz,et al.  The DisGeNET knowledge platform for disease genomics: 2019 update , 2019, Nucleic Acids Res..

[3]  D. De Martini.  Empowering phase II clinical trials to reduce phase III failures , 2019, Pharmaceutical statistics.

[4]  B. Steinhoff,et al.  Levetiracetam and brivaracetam: a review of evidence from clinical trials and clinical experience , 2019, Therapeutic advances in neurological disorders.

[5]  Jianying Hu,et al.  Artificial Intelligence for Clinical Trial Design. , 2019, Trends in pharmacological sciences.

[6]  Yi Guo,et al.  Prediction of antiepileptic drug treatment outcomes of patients with newly diagnosed epilepsy by machine learning , 2019, Epilepsy & Behavior.

[7]  Kim-Anh Lê Cao,et al.  DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays , 2019, Bioinform..

[8]  Tudor Groza,et al.  Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources , 2018, Nucleic Acids Res..

[9]  Gautier Koscielny,et al.  Open Targets Platform: new developments and updates two years on , 2018, Nucleic Acids Res..

[10]  Helen E. Parkinson,et al.  The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 , 2018, Nucleic Acids Res..

[11]  Gregory M. Cooper,et al.  CADD: predicting the deleteriousness of variants throughout the human genome , 2018, Nucleic Acids Res..

[12]  Ying Zhang,et al.  Personalized prediction model for seizure‐free epilepsy with levetiracetam therapy: a retrospective data analysis using support vector machine , 2018, British journal of clinical pharmacology.

[13]  Holger Fröhlich,et al.  From hype to reality: data science enabling personalized medicine , 2018, BMC Medicine.

[14]  E. Giardina,et al.  Application of Precision Medicine in Neurodegenerative Diseases , 2018, Front. Neurol..

[15]  L. A. Lowery,et al.  The Role of the Microtubule Cytoskeleton in Neurodevelopmental Disorders , 2018, Front. Cell. Neurosci..

[16]  R. Peck.  Precision Medicine Is Not Just Genomics: The Right Dose for Every Patient. , 2018, Annual review of pharmacology and toxicology.

[17]  Patrick Kwan,et al.  Treatment Outcomes in Patients With Newly Diagnosed Epilepsy Treated With Established and New Antiepileptic Drugs: A 30-Year Longitudinal Cohort Study , 2017, JAMA neurology.

[18]  Nicolò Cesa-Bianchi,et al.  Advances in Neural Information Processing Systems 31 , 2018, NIPS 2018.

[19]  M. Memo,et al.  Potential Role of Microtubule Stabilizing Agents in Neurodevelopmental Disorders , 2017, International journal of molecular sciences.

[20]  Scott Lundberg,et al.  A Unified Approach to Interpreting Model Predictions , 2017, NIPS.

[21]  Kim-Anh Lê Cao,et al.  mixOmics: An R package for ‘omics feature selection and multiple data integration , 2017, bioRxiv.

[22]  Bernd Bischl,et al.  mlrMBO: A Modular Framework for Model-Based Optimization of Expensive Black-Box Functions , 2017, 1703.03373.

[23]  Steve S. Chung,et al.  Efficacy and tolerability of adjunctive brivaracetam in patients with prior antiepileptic drug exposure: A post-hoc study , 2017, Epilepsy Research.

[24]  Yi-wu Shi,et al.  Epilepsy-associated genes , 2017, Seizure.

[25]  Mariana S. Silva-Alves,et al.  A Prediction Algorithm for Drug Response in Patients with Mesial Temporal Lobe Epilepsy Based on Clinical and Genetic Information , 2017, PloS one.

[26]  Bo Wang,et al.  Failure of Investigational Drugs in Late-Stage Clinical Development and Publication of Trial Results. , 2016, JAMA internal medicine.

[27]  Holger Fröhlich,et al.  Integrating Heterogeneous omics Data via Statistical Inference and Learning Techniques , 2016 .

[28]  Brett A. Becker,et al.  EpimiRBase: a comprehensive database of microRNA-epilepsy associations , 2016, Bioinform..

[29]  Xiaoyu Chen,et al.  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..

[30]  M. Wood,et al.  Brivaracetam: Rationale for discovery and preclinical profile of a selective SV2A ligand for epilepsy treatment , 2016, Epilepsia.

[31]  Teng Jiang,et al.  Toward precision medicine in neurological diseases. , 2016, Annals of translational medicine.

[32]  Tianqi Chen,et al.  XGBoost: A Scalable Tree Boosting System , 2016, KDD.

[33]  Michal Ozery-Flato,et al.  Changing the approach to treatment choice in epilepsy using big data , 2016, Epilepsy & Behavior.

[34]  M. Sperling,et al.  A randomized, double‐blind, placebo‐controlled, multicenter, parallel‐group study to evaluate the efficacy and safety of adjunctive brivaracetam in adult patients with uncontrolled partial‐onset seizures , 2015, Epilepsia.

[35]  C. Begley,et al.  The direct cost of epilepsy in the United States: A systematic review of estimates , 2015, Epilepsia.

[36]  Sergey Ioffe,et al.  Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift , 2015, ICML.

[37]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[38]  Table of Pharmacogenomic Biomarkers in Drug Labeling , 2015 .

[39]  J. Pascussi,et al.  Effect of status epilepticus and antiepileptic drugs on CYP2E1 brain expression , 2014, Neuroscience.

[40]  Michael R. Johnson,et al.  Validation of a multigenic model to predict seizure control in newly treated epilepsy , 2014, Epilepsy Research.

[41]  F. Cendes,et al.  The consequences of refractory epilepsy and its treatment , 2014, Epilepsy & Behavior.

[42]  P. Ryvlin,et al.  Pharmacotherapy for tonic–clonic seizures , 2014, Expert opinion on pharmacotherapy.

[43]  Jing Wang,et al.  CrossMap: a versatile tool for coordinate conversion between genome assemblies , 2014, Bioinform..

[44]  K. Radhakrishnan,et al.  Genetic Association Analysis of ATP Binding Cassette Protein Family Reveals a Novel Association of ABCB1 Genetic Variants with Epilepsy Risk, but Not with Drug-Resistance , 2014, PloS one.

[45]  M. Sperling,et al.  Brivaracetam as adjunctive treatment for uncontrolled partial epilepsy in adults: A phase III randomized, double‐blind, placebo‐controlled trial , 2014, Epilepsia.

[46]  杨凌春,et al.  Broad Institute , 2014 .

[47]  Melissa A. Basford,et al.  Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data , 2013, Nature Biotechnology.

[48]  J. French,et al.  Designing better trials for epilepsy medications: the challenge of heterogeneity , 2013 .

[49]  S. Sisodiya,et al.  P-glycoprotein Expression and Pharmacoresistant Epilepsy: Cause or Consequence? , 2014 .

[50]  A. Sieron,et al.  CYP3A5∗3 and C3435T MDR1 Polymorphisms in Prognostication of Drug-Resistant Epilepsy in Children and Adolescents , 2013, BioMed research international.

[51]  Matthias Blum,et al.  miRmap web: comprehensive microRNA target prediction online , 2013, Nucleic Acids Res..

[52]  R. Kukreti,et al.  A systematic review and meta‐analysis of the role of ABCC2 variants on drug response in patients with epilepsy , 2013, Epilepsia.

[53]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[54]  Nitish Srivastava,et al.  Improving neural networks by preventing co-adaptation of feature detectors , 2012, ArXiv.

[55]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[56]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[57]  G. Cavalleri,et al.  Pharmacogenomics and epilepsy: the road ahead. , 2011, Pharmacogenomics.

[58]  Jorge Gonzalez-Martinez,et al.  Cellular localization and functional significance of CYP3A4 in the human epileptic brain , 2011, Epilepsia.

[59]  F. Vogenberg,et al.  Personalized medicine: part 1: evolution and development into theranostics. , 2010, P & T : a peer-reviewed journal for formulary management.

[60]  Y. Finkelstein,et al.  Predisposition to epilepsy—Does the ABCB1 gene play a role? , 2010, Epilepsia.

[61]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[62]  Trevor Hastie,et al.  Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.

[63]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[64]  I. Johnstone,et al.  Statistical challenges of high-dimensional data , 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[65]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[66]  G. Koren,et al.  Polymorphism of the MDR1/ABCB1 C3435T drug‐transporter and resistance to anticonvulsant drugs: A meta‐analysis , 2009, Epilepsia.

[67]  Richard M Huggins,et al.  Multi-SNP pharmacogenomic classifier is superior to single-SNP models for predicting drug outcome in complex diseases , 2009, Pharmacogenetics and genomics.

[68]  Josemir W Sander,et al.  No major role of common SV2A variation for predisposition or levetiracetam response in epilepsy , 2009, Epilepsy Research.

[69]  Tatiana Nikolskaya,et al.  Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platform. , 2009, Methods in molecular biology.

[70]  Petros Maragos,et al.  Multimodal Processing and Interaction, Audio, Video, Text , 2010 .

[71]  C. Daumas-Duport,et al.  ABC transporters, cytochromes P450 and their main transcription factors: expression at the human blood–brain barrier , 2008, Journal of neurochemistry.

[72]  M. Armstrong,et al.  The Genetics of Adverse Drug Reactions , 2008 .

[73]  Petros Maragos,et al.  Cross-Modal Integration for Performance Improving in Multimedia: A Review , 2008, Multimodal Processing and Interaction.

[74]  U. Klotz.  The Role of Pharmacogenetics in the Metabolism of Antiepileptic Drugs , 2007, Clinical pharmacokinetics.

[75]  M. Yuan,et al.  Model selection and estimation in regression with grouped variables , 2006 .

[76]  F. Monzon.  A Multigene Assay to Predict Recurrence of Tamoxifen-Treated, Node-Negative Breast Cancer , 2006 .

[77]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[78]  M. Cronin,et al.  A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. , 2004, The New England journal of medicine.

[79]  J. C. Baayen,et al.  Expression and Cellular Distribution of Multidrug Resistance–related Proteins in the Hippocampus of Patients with Mesial Temporal Lobe Epilepsy , 2004, Epilepsia.

[80]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[81]  M. Mayberg,et al.  Overexpression of Multiple Drug Resistance Genes in Endothelial Cells from Patients with Refractory Epilepsy , 2001, Epilepsia.

[82]  J. Weide,et al.  The effect of genetic polymorphism of cytochrome P450 CYP2C9 on phenytoin dose requirement. , 2001, Pharmacogenetics.

[83]  Jason Weston,et al.  Gene functional classification from heterogeneous data , 2001, RECOMB.

[84]  P. Kwan,et al.  Early identification of refractory epilepsy. , 2000, The New England journal of medicine.

[85]  R. Tibshirani.  Regression Shrinkage and Selection via the Lasso , 1996 .

[86]  David H. Wolpert,et al.  Stacked generalization , 1992, Neural Networks.

[87]  J. Mockus,et al.  Bayesian approach to global optimization and application to multiobjective and constrained problems , 1991 .