Bioinformatics scientific group wins second consecutive international DREAM challenge

By Deborah Wormser

UT Southwestern Medical Center bioinformatics scientists recently won first-place honors on two challenges in an international crowd-sourced competition.

The groups had to create quantitative models predicting individual responses to exposure to toxic compounds based on genetic data, as well as models for population-level responses based on toxic substances’ chemical properties.

Bioinformatics team members
Bioinformatics team members from UT Southwestern proudly show their two national first-place awards.

The UT Southwestern submissions for the 2013 NIEHS-NCATS-UNC DREAM Toxicogenetics Prediction Challenge employed a large data set co-organized by the National Institute of Environmental Health Science (NIEHS), the National Center for Advancing Translational Sciences (NCATS), the University of North Carolina at Chapel Hill, the DREAM (Dialogue for Reverse Engineering Assessments and Methods), and Sage Bionetworks.

In addition, some of the data came from the 1000 Genome Project, an international project to sequence diverse genomes from people around the world.

The computation models submitted by UT Southwestern’s Quantitative Biomedical Research Center (QBRC) teams were judged the best of 99 submissions from 34 teams on the first challenge (individual response based on genetic data) and also the top among 85 submitted by 24 teams on the second one (population-response modeling using chemical properties). The QBRC is in the Department of Clinical Sciences and also serves as the bioinformatics core for the Harold C. Simmons Comprehensive Cancer Center.

In all, UT Southwestern has claimed three first-place finishes in the two years that QBRC teams have entered the competition.

The victories come just three years after the creation of UT Southwestern’s first research-oriented statistical and informatics group, said Dr. Yang Xie, Associate Professor of Clinical Sciences.

“Three years ago, Dr. Milton Packer [Chairman of Clinical Sciences] told me his vision for the QBRC is to become an internationally recognized quantitative biomedical research group. I believe we have made great progress,” said Dr. Xie, who also noted the support of Dr. James Willson, Director of the Simmons Comprehensive Cancer Center.

Dr. Xie and graduate student Tao Wang accepted the awards at the DREAM8 conference in Toronto in November 2013. Dr. Hao Tang, Assistant Professor of Clinical Sciences who led the effort for population response, was invited to present a seminar titled “Estimating population-scale toxicities for environmental chemicals from genomic and chemical information” at NIEHS in Research Triangle Park, N.C., in December 2013.

Members of the winning individual response team were Dr. Xie, Dr. Tang, Mr. Wang, postdoctoral researcher Dr. Jichen Yang, graduate student Rui Zhong, Associate Professor Dr. Guanghua “Andy” Xiao, and Assistant Professor Dr. Xiaowei Zhan, all of the Department of Clinical Sciences. Members of the population-level response team were Drs. Tang, Yang, Xiao, Xie, and Mr. Wang.

The prize includes publication of the solutions in an upcoming issue of Nature Biotechnology and travel expenses for the two researchers to attend the Toronto meeting.

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Dr. Packer holds the Gayle and Paul Stoffel Distinguished Chair in Cardiology.

Dr. Willson holds the Lisa K. Simmons Distinguished Chair in Comprehensive Oncology.

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