On top. A team led by bioinformatics researcher Daniel Huson won a $1 million Pentagon prize.

Mike Steel

Controversial Pentagon DNA Analysis Contest Names Champion

A DNA analysis challenge posed by the U.S. Department of Defense proved more difficult than many contestants expected, but a winner has emerged. The agency announced this week that Team Huson—a latecomer to the competition that became an immediate front-runner—will take the $1 million prize for their speedy DNA analysis computer program. Earlier this year, the design and scoring of the contest drew heavy criticism from some top contenders after just three of 103 entrants made it into the final round.

One of those finalists, Daniel Huson, a bioinformaticist at the University of Tübingen in Germany, says that he and his teammates “had a pretty good feeling” they might take the top prize. They were thrilled to discover earlier this month that their intuition was sound.

The contest, officially known as the Defense Threat Reduction Agency's (DTRA's) Algorithm Challenge, sought a better way to identify organisms and genes in a DNA sample to identify possible bioterror threats. The challenge was open to anyone, and participants submitted their work using the online contest host InnoCentive. Huson says that he relished the frantic, round-the-clock work needed to win: “The only other time I ever had this much fun was when I was working on the human genome at Celera genomics.”

To qualify for the evaluation round, participants needed to earn a passing accuracy score on nine sets of genetic data. Several expressed frustration over DTRA’s opaque scoring algorithm and felt they had to reverse-engineer their programs to satisfy a set of unclear requirements.

The task proved so challenging that DTRA had to extend the deadline and relax the requirements. That’s when Huson and two colleagues—bioinformaticist Xie Chao of the Singapore Centre on Environmental Life Sciences Engineering and Benjamin Buchfink, a computer science graduate student at the University of Tübingen—teamed up and entered the game.

“The scoring scheme was delicate,” Huson admits. “There were things that did raise some eyebrows.” But he says his team was able to make steady progress by trying many alternate approaches.

Christian Whitchurch, the project manager, told ScienceInsider in July that a full report on the contest design and scoring would be released once the challenge was over.