Gains from Games
Gamers are better at identifying certain patterns than computer algorithms, so why not use them to pick out breast cancer-related gene profiles?
If you’ve ever dreamed of piloting your own spaceship through an asteroid belt while simultaneously performing cutting edge cancer research, then “Play to Cure: Genes in Space” is the app for you. While you’re busy plotting your course and harvesting “Element Alpha” in the intergalactic (genetic) landscape, what you are actually doing is inspecting gene copy number variation from state-of-the-art data gathered from the 2012 METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) study (1).
METABRIC looked at patterns in the tumors of nearly two thousand women and concluded that there were at least ten different subtypes of breast cancer, each with its own genetic fingerprint (Figure 1) But that left an ocean of genetic data to crunch.
Figure 1. Raw data from the METABRIC study (above) was converted into “Element Alpha” to create an interactive space-scape (left and below).
Oscar Rueda from Carlos Caldas’ group (Breast Cancer Functional Genomics, University of Cambridge) was involved in the project. He explains that, “The cancer types have different DNA copy number profiles. In some cases these form a narrow peak that describes the driver gene in that particular subtype; in other cases it is not so clear.” Current statistical methods can detect copy-number aberrations in the genome with an accuracy of 90-95 percent, Rueda says, “But for difficult cases, the human eye usually does a better job. It can spot the patterns in the copy number profile and distinguish whether a real copy number change is happening or if it is
just noise.”
The problem is, manual curation of 46,000 plots is not feasible. “Plus, we would still have problems with the inter-rater agreement, due to subjective scoring,” says Reuda. And so, the idea of a video game was born, tapping into the inexhaustible passion for tablets and smartphone games.
“Play to Cure” is available from Apple and Google Play stores and it’s fair to say that it’s addictive – consider it as a much more useful replacement for Flappy Bird. “We expect that with a large number of people analyzing each case, the average results will be more accurate than any statistical method,” says Reuda, “but of course we will have to formally prove it.”
If the project is a success, look out for more opportunities to put your game addiction to good use. “I think it will open the door to many other problems that can benefit from crowd sourcing initiatives,” Rueda says.
Can you beat the (meager) success of The Analytical Scientist’s first mission? Asteroids destroyed: 10, Element Alpha: 7120. Post your scores in Comments. And may the force be with you.
- Christina Curtis et al., “The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups”, Nature 486, 346–352 (2012). DOI:10.1038/nature10983
Rich Whitworth completed his studies in medical biochemistry at the University of Leicester, UK, in 1998. To cut a long story short, he escaped to Tokyo to spend five years working for the largest English language publisher in Japan. "Carving out a career in the megalopolis that is Tokyo changed my outlook forever. When seeing life through such a kaleidoscopic lens, it's hard not to get truly caught up in the moment." On returning to the UK, after a few false starts with grey, corporate publishers, Rich was snapped up by Texere Publishing, where he spearheaded the editorial development of The Analytical Scientist. "I feel honored to be part of the close-knit team that forged The Analytical Scientist – we've created a very fresh and forward-thinking publication." Rich is now also Content Director of Texere Publishing, the company behind The Analytical Scientist.
