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Jun 11, 2013

NIEHS, NCATS, UNC, Others Launch Crowdsourced Toxicogenetics Challenge

  • The NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge launches today. The aim is to achieve a greater understanding about how a person’s individual genetics can influence cytotoxic response to exposure to widely used chemicals.

    The challenge is described as a crowdsourced computational challenge, which means it works by engaging communities of scientists to competitively solve a specific problem in a given time period by placing scientific data, tools, and the resulting predictive models into an open commons or workspace—hence, “crowdsourcing” data analysis. It is being led and organized by scientists from Sage Bionetworks, DREAM, the University of North Carolina (UNC), the National Institute of Environmental Health Sciences (NIEHS) and the National Center for Advancing Translational Sciences (NCATS).

    The NIEHS/NCATS/UNC team recently conducted what they claim to be the largest ever population-based in vitro cytotoxicity study by treating 1,086 human lymphoblastoid cell lines representing nine distinct geographic subpopulations (made available via the 1,000 Genomes Project), with 179 pharmaceutical and environmental chemicals. The resulting cytotoxicity data, when paired with the publicly available genetic and genomic data on each of the respective cell lines, reportedly provides a unique dataset that researchers can use to predict toxic responses to chemical compounds across a genetically diverse human population.

    By positioning this data for a DREAM challenge, a community of challenge participants will be asked to solve one or both of two related sub-challenges:

    1. Use the data to develop a model that accurately predicts individual responses to compound exposure based on genomic information and
    2. Use the data to develop a model that accurately predicts how a particular population will respond to certain types of chemicals.

    “The long-term strategic value of accurate predictive models will be invaluable for both protection of human health and the environment, and support of innovations in the chemical industry,” said Ivan Rusyn, M.D., Ph.D., professor of environmental sciences and engineering at UNC’s Gillings School of Global Public Health.

    The challenge will close on September 15, 2013, and the top-scoring team or teams will be announced at the November 2013 DREAM conference to be held in Toronto.

    Sage Bionetworks and DREAM, who announced their intention to run open science computational challenges to encourage broader collaboration within the research community back in February, also opened two other challenges to the public today: 

    • The Heritage Provider Network-DREAM Breast Cancer Network Inference Challenge: Infer the signaling networks in breast cancer cell lines, and
    • The Whole Cell Parameter Estimation Challenge: Infer the kinetic parameters underlying biological processes in whole cell models.

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