Researchers use crowdsourcing to explore how genetics affect our response to toxins
|June 10, 2013|
A new collaboration of industry, government agencies and academia aims to better understand – through crowdsourcing – how a person’s individual genetics can influence the body’s response when it is exposed to certain environmental and pharmaceutical chemicals.Organized and led by scientists from The University of North Carolina at Chapel Hill, Sage Bionetworks/DREAM, the National Institute of Environmental Health Sciences (NIEHS), and the National Center for Advancing Translational Sciences (NCATS), the effort will involve an innovative crowdsourced computational Challenge – the NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge – which will draw teams of scientists from around the world to compete next fall.
“We are delighted to partner with the Sage/DREAM to release this unique dataset obtained through a broad partnership with NIEHS and NCATS,” said Ivan Rusyn, MD, PhD, professor of environmental sciences and engineering at UNC’s Gillings School of Global Public Health. “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.”
More detailed information on the NIEH-NCATS-UNC DREAM Challenge can be found here.
Challenges such as this one engage diverse communities of scientists to competitively solve a specific designated problem in a given time period by placing scientific data, tools and the resulting predictive models into an open virtual workspace – in effect, “crowdsourcing” the analysis of data.
Those leading the Toxicogenetics Challenge believe it has potential to provide powerful scientific insights and meaningful public health impact. Toxicity testing that monitors health hazards from chemical exposure is a crucial component of protecting the public’s health. Yet at present, for every chemical that has been tested for toxicity, myriad others remain untested. Toxicologists want to leverage the dramatic technological advances in molecular biology and computer science, using novel technologies and innovative study designs to collect genomic data.
One such technology is high-throughput screening (HTS), a method that allows researchers to quickly conduct millions of chemical and genetic assays, or measurements.
Toward this goal, the NIEHS/NCATS/UNC team recently conducted the largest-ever population-based in vitro cytotoxicity study by treating 1,000 human lymphoblastoid cell lines with 156 environmental chemicals. The cell lines, made available through the 1,000 Genomes Project, represented worldwide geographic and racial diversity. The resulting cytotoxicity data, paired with genetic information on each of the respective cell lines already available, provides a unique and informative dataset that researchers can use to understand adverse effects of 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: to use the data to develop a model that accurately can predict individual responses to compound exposure, based on genomic information, and/or to use the data to develop a model that accurately predicts how a particular population will respond to certain types of chemicals.
“We anticipate that this Challenge will attract a lot of enthusiasm from the modeling community due to the size, scale and uniqueness of this fantastic dataset,” said Gustavo Stolovitzky, PhD, co-founder of the DREAM project and a key leader on the planning of the Challenge.
Stolovitzky said he expected submissions from more than 50 participating teams. “With the engaging features of this Challenge, including a real-time leaderboard and incentives to share and borrow model code, we expect that the challenge also will elicit submission of thousands of model predictions.”
Scientific thinkers interested in the project can register online to participate. After competition in the fall, the top-scoring teams will be announced at the November 2013 DREAM conference in Toronto.
NCI’s Columbia University-based magnet center and IBM Research will provide small travel grants to top performing teams to present their results at the annual DREAM conference.Additional information on the Challenge can be found online.