Prediction of human population responses to toxic compounds by a collaborative competition

Federica Eduati; Lara M. Mangravite; Tao Wang; Hao Tang; J. Christopher Bare; Ruili Huang; Thea Norman; Mike Kellen; Michael P. Menden; Jichen Yang; Xiaowei Zhan; Rui Zhong; Guanghua Xiao; Menghang Xia; Nour Abdo; Oksana Kosyk; Stephen Friend; Allen Dearry; Anton Simeonov; Raymond R. Tice; Ivan Rusyn; Fred A. Wright; Gustavo Stolovitzky; Yang Xie; Julio Saez-Rodriguez; Tero Aittokallio; Salvatore Alaimo; Alicia Amadoz; Muhammad Ammad-ud-din; Chloe-Agathe Azencott; Jaume Bacardit; Pelham Barron; Elsa Bernard; Andreas Beyer; Shao Bin; Alena van Boemmel; Karsten Borgwardt; April M. Brys; Brian Caffrey; Jeffrey Chang; Jungsoo Chang; Himanshu Chheda; Eleni G. Christodoulou; Mathieu Clement-Ziza; Trevor Cohen; Marianne Cowherd; Sofie Demeyer; Joaquin Dopazo; Joel D. Elhard; Andre O. Falcao; Alfredo Ferro; David A. Friedenberg; Rosalba Giugno; Yunguo Gong; Jenni W. Gorospe; Courtney A. Granville; Dominik Grimm; Matthias Heinig; Rosa D. Hernansaiz; Petteri Hintsanen; Sepp Hochreiter; Liang-Chin Huang; Matthew Huska; Alok Jaiswal; Yunlong Jiao; Samuel Kaski; Ismeet Kaur; Suleiman Ali Khan; Guenter Klambauer; Natalio Krasnogor; Michael Kuhn; Miron Bartosz Kursa; Rintu Kutum; Nicola Lazzarini; Inhan Lee; Michael K. K. Leung; Weng Khong Lim; Charlie Liu; Felipe Llinares Lopez; Alessandro Mammana; Andreas Mayr; Tom Michoel; Misael Mongiovi; Jonathan D. Moore; John-Patrick Mpindi; Ravi Narasimhan; Stephen O. Opiyo; Gaurav Pandey; Andrea L. Peabody; Juliane Perner; Antti Poso; Alfredo Pulvirenti; Konrad Rawlik; Susanne Reinhardt; Carol G. Riffle; Douglas Ruderfer; Aaron J. Sander; Richard S. Savage; Erwan Scornet; Patricia Sebastian-Leon; Roded Sharan; Carl Johann Simon-Gabriel; Veronique Stoven; Jingchun Sun; Jing Tang; Ana L. Teixeira; Albert Tenesa; Jean-Philippe Vert; Martin Vingron; Thomas Walter; Krister Wennerberg; Sean Whalen; Zofia Wisniewska; Yonghui Wu; Hua Xu; Shihua Zhang; Junfei Zhao; W. Jim Zheng; Dai Ziwei; NIEHS-NCATS-UNC DREAM

doi:10.1038/nbt.3299

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Prediction of human population responses to toxic compounds by a collaborative competition

Journal article

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Peer reviewed

Prediction of human population responses to toxic compounds by a collaborative competition

Federica Eduati, Lara M. Mangravite, Tao Wang, Hao Tang, J. Christopher Bare, Ruili Huang, Thea Norman, Mike Kellen, Michael P. Menden, Jichen Yang, …

Nature biotechnology, Vol.33(9), pp.933-940

01/09/2015

DOI: https://doi.org/10.1038/nbt.3299

PMCID: PMC4568441

PMID: 26258538

Abstract

Biotechnology & Applied Microbiology

Life Sciences & Biomedicine

Science & Technology

The ability to computationally predict the effects of toxic compounds on humans could help address the deficiencies of current chemical safety testing. Here, we report the results from a community-based DREAM challenge to predict toxicities of environmental compounds with potential adverse health effects for human populations. We measured the cytotoxicity of 156 compounds in 884 lymphoblastoid cell lines for which genotype and transcriptional data are available as part of the Tox21 1000 Genomes Project. The challenge participants developed algorithms to predict interindividual variability of toxic response from genomic profiles and population-level cytotoxicity data from structural attributes of the compounds. 179 submitted predictions were evaluated against an experimental data set to which participants were blinded. Individual cytotoxicity predictions were better than random, with modest correlations (Pearson's r < 0.28), consistent with complex trait genomic prediction. In contrast, predictions of population-level response to different compounds were higher (r < 0.66). The results highlight the possibility of predicting health risks associated with unknown compounds, although risk estimation accuracy remains suboptimal.

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Title: Prediction of human population responses to toxic compounds by a collaborative competition
Creators - without role: Federica Eduati - European Bioinformat Inst, European Mol Biol Lab, Cambridge, England
Lara M. Mangravite - Sage Bionetworks
Tao Wang - College Station Medical Center
Hao Tang - College Station Medical Center
J. Christopher Bare - Sage Bionetworks
Ruili Huang - NIH, Div Preclin Innovat, Chem Genom Ctr, Natl Ctr Adv Translat Sci, Rockville, MD USA
Thea Norman - Sage Bionetworks
Mike Kellen - Sage Bionetworks
Michael P. Menden - European Bioinformat Inst, European Mol Biol Lab, Cambridge, England
Jichen Yang - College Station Medical Center
Xiaowei Zhan - Biostat
Rui Zhong - College Station Medical Center
Guanghua Xiao - College Station Medical Center
Menghang Xia - NIH, Div Preclin Innovat, Chem Genom Ctr, Natl Ctr Adv Translat Sci, Rockville, MD USA
Nour Abdo - Univ N Carolina, Dept Environm Sci & Engn, Chapel Hill, NC USA
Oksana Kosyk - Univ N Carolina, Dept Environm Sci & Engn, Chapel Hill, NC USA
Stephen Friend - Sage Bionetworks
Allen Dearry - Triangle
Anton Simeonov - NIH, Div Preclin Innovat, Chem Genom Ctr, Natl Ctr Adv Translat Sci, Rockville, MD USA
Raymond R. Tice - Triangle
Ivan Rusyn - Univ N Carolina, Dept Environm Sci & Engn, Chapel Hill, NC USA
Fred A. Wright - N Carolina State Univ, Bioinformat Res Ctr, Dept Stat & Biol Sci, Raleigh, NC 27695 USA
Gustavo Stolovitzky - IBM Corp, IBM TJ Watson Res Ctr, Yorktown Hts, NY USA
Yang Xie - College Station Medical Center
Julio Saez-Rodriguez - European Bioinformat Inst, European Mol Biol Lab, Cambridge, England
Tero Aittokallio - University of Helsinki
Salvatore Alaimo - University of Catania
Alicia Amadoz - CIPF, Computat Genom Dept, Valencia, Spain
Muhammad Ammad-ud-din - Aalto University
Chloe-Agathe Azencott - Max
Jaume Bacardit - Newcastle Univ, Interdisciplinary Comp & Complex BioSystems ICOS, Newcastle Upon Tyne, Tyne & Wear, England
Pelham Barron - MIRCORE
Elsa Bernard - Mines Paris - PSL
Andreas Beyer - Biotec
Shao Bin - Peking University
Alena van Boemmel - Max
Karsten Borgwardt - Max
April M. Brys - Mécanique et Engrenage Moderne
Brian Caffrey - Max
Jeffrey Chang - Supreme Council Of Health
Jungsoo Chang - MIRCORE
Himanshu Chheda - University of Helsinki
Eleni G. Christodoulou - Biotec
Mathieu Clement-Ziza - Biotec
Trevor Cohen - Supreme Council Of Health
Marianne Cowherd - MIRCORE
Sofie Demeyer - University of Edinburgh
Joaquin Dopazo - CIPF, Computat Genom Dept, Valencia, Spain
Joel D. Elhard - Mécanique et Engrenage Moderne
Andre O. Falcao - University of Lisbon
Alfredo Ferro - University of Catania
David A. Friedenberg - Mécanique et Engrenage Moderne
Rosalba Giugno - University of Catania
Yunguo Gong - Supreme Council Of Health
Jenni W. Gorospe - Mécanique et Engrenage Moderne
Courtney A. Granville - Mécanique et Engrenage Moderne
Dominik Grimm - Max
Matthias Heinig - Max
Rosa D. Hernansaiz - CIPF, Computat Genom Dept, Valencia, Spain
Petteri Hintsanen - University of Helsinki
Sepp Hochreiter - Johannes Kepler University of Linz
Liang-Chin Huang - Supreme Council Of Health
Matthew Huska - Max
Alok Jaiswal - University of Helsinki
Yunlong Jiao - Mines Paris - PSL
Samuel Kaski - Aalto University
Ismeet Kaur - Adobe, San Jose, CA USA
Suleiman Ali Khan - Aalto University
Guenter Klambauer - Johannes Kepler University of Linz
Natalio Krasnogor - Newcastle Univ, Interdisciplinary Comp & Complex BioSystems ICOS, Newcastle Upon Tyne, Tyne & Wear, England
Michael Kuhn - Biotec
Miron Bartosz Kursa - University of Warsaw
Rintu Kutum - CSIR, Inst Genom Integrat Biol, New Delhi, India
Nicola Lazzarini - Newcastle Univ, Interdisciplinary Comp & Complex BioSystems ICOS, Newcastle Upon Tyne, Tyne & Wear, England
Inhan Lee - MIRCORE
Michael K. K. Leung - University of Toronto
Weng Khong Lim - Natl Canc Ctr Singapore, Singapore, Singapore
Charlie Liu - Stepping Stone Genom, Mclean, VA USA
Felipe Llinares Lopez - Max
Alessandro Mammana - Max
Andreas Mayr - Johannes Kepler University of Linz
Tom Michoel - University of Edinburgh
Misael Mongiovi - University of Catania
Jonathan D. Moore - University of Warwick
John-Patrick Mpindi - University of Helsinki
Ravi Narasimhan - Connect
Stephen O. Opiyo - The Ohio State University
Gaurav Pandey - Mt Sinai, New York, NY USA
Andrea L. Peabody - Mécanique et Engrenage Moderne
Juliane Perner - Max
Antti Poso - University of Eastern Finland
Alfredo Pulvirenti - University of Catania
Konrad Rawlik - University of Edinburgh
Susanne Reinhardt - Biotec
Carol G. Riffle - Mécanique et Engrenage Moderne
Douglas Ruderfer - Mt Sinai, New York, NY USA
Aaron J. Sander - Mécanique et Engrenage Moderne
Richard S. Savage - University of Warwick
Erwan Scornet - Mines Paris - PSL
Patricia Sebastian-Leon - CIPF, Computat Genom Dept, Valencia, Spain
Roded Sharan - Tel Aviv University
Carl Johann Simon-Gabriel - Max
Veronique Stoven - Mines Paris - PSL
Jingchun Sun - Supreme Council Of Health
Jing Tang - University of Helsinki
Ana L. Teixeira - University of Lisbon
Albert Tenesa - University of Edinburgh
Jean-Philippe Vert - Mines Paris - PSL
Martin Vingron - Max
Thomas Walter - Mines Paris - PSL
Krister Wennerberg - University of Helsinki
Sean Whalen - Mt Sinai, New York, NY USA
Zofia Wisniewska - University of Warsaw
Yonghui Wu - Supreme Council Of Health
Hua Xu - Supreme Council Of Health
Shihua Zhang - Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing, Peoples R China
Junfei Zhao - Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing, Peoples R China
W. Jim Zheng - Supreme Council Of Health
Dai Ziwei - Peking University
NIEHS-NCATS-UNC DREAM
Publication Details: Nature biotechnology, Vol.33(9), pp.933-940
Publisher: NATURE PORTFOLIO
Number of pages: 11
Grant note: Marie Curie Actions (COFUND) European Molecular Biology Laboratory Interdisciplinary Post-Docs (EMBL EIPOD) US National Institutes of Health (NIH); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA R01CA161608; R01HG006292; 5R01CA152301; 1R01CA172211 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA Y2-ES-7020-01 / National Institute of Environmental Health Sciences (NIEHS); United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Environmental Health Sciences (NIEHS) G0902104 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) STAR RD83516601; RD83382501 / US Environmental Protection Agency; United States Environmental Protection Agency G0902104 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC)
Identifiers: 9933855108331
Academic Unit: University of Tabuk
Language: English
Resource Type: Journal article