NIEHS - NCATS - UNC DREAM Toxicogenetics Challenge
On June 11, 2013, an innovative crowdsourced computational Challenge, called the NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge was launched. The objective of this Challenge was to obtain a greater understanding about how a person’s individual genetics can influence cytotoxic response to exposure to widely used chemicals. It was led and organized by scientists from Sage Bionetworks, DREAM, the University of North Carolina, the National Institute of Environmental Health Sciences (NIEHS) and the National Center for Advancing Translational Sciences (NCATS).
The Challenge closed on September 15, 2013, and the (top-scoring team(s)) were identified.
Challenge Winners Announced at 2013 Dream Conference
Winning team members from each subchallenge spoke at the 2013 DREAM Conference, on November 8th in Toronto, Canada, in conjunction with the RECOMB/ISCB Conference on Regulatory and Systems Genomics, one of the premier annual meetings for computational and experimental scientists in the areas of regulatory genomics and systems biology.
NIEHS Deputy Director Richard Woychik, Ph.D. attended the meeting. Woychik and his colleagues at NIEHS have been instrumental in working with Sage and others to develop and support the Challenges.
Teams from the Quantitative Biomedical Research Center (QBRC) at the University of Texas Southwestern Medical Center (UTSW) were named best performer in both of the subchallenges.
Team Yang Lab, represented in Toronto by Ph.D. student Tao Wang, took the honors for subchallenge 1. Team QBRC, also represented in Toronto by Tao Wang, on behalf of assistant professor Hao Tang, Ph.D., came in first in subchallenge 2. Associate professor Yang Xie, Ph.D., was also there to accept the award. The second best performer for subchallenge 1 was Team Cassis from the Centre for Computational Biology in Paris, which was represented at the conference by team member Elsa Bernard, a Ph.D. student at the Institut Curie one of the Centre’s joint laboratory member institutions.
Challenge Winners Present at NIEHS
In December, 2013, NIEHS brought the winning scientists to the NIEHS campus in North Carolina to present their models.
About 60 scientists gathered Dec. 2 for the informative seminar, "Crowdsourcing Tox21 Qualitative High Throughput Screening Data(956KB)", focusing on the NIEHS–NCATS–UNC DREAM Toxicogenetics Challenge.
Speakers described the Tox21 project that generated the data used in the Challenge, the innovative approaches employed by the teams that won the two subchallenges, and the value of crowdsourcing to advance and accelerate scientific knowledge.
Nature Biotechnology Publishes DREAM Challenge Paper
Nature Biotechnology published the results from the community-based DREAM challenge. The article “Prediction of human population responses to toxic compounds by a collaborative competition” appeared online August 10, 2015.
Additional Challenges by our TOX21 Partners
NCATS Data Challenge. In 2014, the National Center for Advancing Translational Sciences (NCATS), a partner in our Tox21(642KB) efforts, announced a follow-up crowd sourcing challenge. Challenge participants used data from nuclear receptor signaling and stress pathway assays (tests) run against Tox21’s 10,000-compound library to build models and look for structure-activity relationships. Winners were announced January 26, 2015.
EPA ToxCast Prediction Challenge. The US Environmental Protection Agency also issued a crowd sourcing challenge asking participants to design an algorithm that could qualitatively predict a chemical’s lowest effect level, or the lowest dose that shows adverse effects. This project launched in December, 2013 and was completed in June, 2014.
- Environmental Factor story: DREAM challenge results published in Nature Biotechnology (September 2015)
- Environmental Factor story: Predictive toxicology advances with new paper and data challenge (August 2014)
- NIH Catalyst story: Crowdsourcing: Accelerates the Pace of Toxicity Testing (January-February 2014)
- Environmental Factor story: Seminar showcases Toxicogenetics Challenge winners (January 2014)
- Environmental Factor story: Toxicogenetics Challenge winners announced (December 2013)
- Environmental Factor story: Partners launch DREAM Toxicogenetics Challenge (July 2013)