Crowdsourcing approach to fighting cancer
Debron, Luke and Paula huddle around a laptop in a McGill University cafeteria in Montreal, Canada, deeply absorbed in an online game.
No rampaging monsters, brain-eating zombies or bloody explosions here. No violence or aggression of any sort. "Phylo" is much more serious than that. These three students are working to solve a DNA puzzle; to pinpoint mutations in the human genetic code that cause cancer and other human disorders.
DNA sequence alignment is what "Phylo" - developed by McGill researchers Jerome Waldispuhl and Mathieu Blanchette - is all about.
By aligning homologous DNA sequences from humans and a variety of other species, the gamer isolates mutations in the human version that could potentially trigger a genetic malfunction.
Mutations in the DNA sequence can lead to illnesses like cancer
Nothing beats the human eye
Accumulated mutations in "highly conserved" genes that have been around for millions of millennia, as far back as the birth of the fungi, are typically the bits of code that trigger diseases in humans or allow them to advance. Spotting candidate mutations in database sequences - establishing their precise "architecture" - is therefore an obvious thing to do.
But the process of finding the optimal solution is complex, says McGill bio-computer-scientist Guillaume Bourque, another contributor to "Phylo's" development. Supercomputers do a great job parsing raw DNA alignments for good fits, from which human differences - mutations - can be deduced. These could involve simple transpositions of one of the four DNA "letters" (A,G, C, T), and more complex shifts involving inserted or deleted chunks of code ("indels") that throw versions completely out of alignment with each other.
When it comes to fine tuning, though, there's nothing like the human eye. After all, humans can distinguish facial and vocal features that fly right over a computer's head. The human eye is nothing short of brilliant. This is where a game like "Phylo" comes in.
Discerning eyes focused, "Phylo" players scrutinize computer-derived alignments that have been turned into puzzles. Each puzzle consists of a set of DNA nucleotide sequences that have been turned into colored blocks, representing chunks of DNA code that humans and other animal species have in common.
Solving the puzzle
Each row in a "Phylo" game represents a different version of the code somewhere on the phylogenetic tree -- from a mouse, rat, snake, insect or other creature – each with its own unique gaps, insertions and deletions that throw it out of alignment with those above and below.
McGill students contribute to gathering information on genetic diseases by playing "Phylo"
Mouse in hand or finger on the touchpad, a "Phylo" player slides multicolored blocks this way and that, across each row, aligning them as best as they can, on behalf of the researcher who submitted the gene, and science-at-large.
In exchange for their time and visual intuition, "Phylo" players like Debron, Luke and Paula will be cited in future scientific papers simply as “Phylo users.” Anonymous gamers around the world have solved almost a quarter million Phylo puzzles, involving a variety of genetically linked disorders, demonstrating once again the power of crowd-sourcing in the advancement of science and technology.