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Database Toronto s Scherer Opens Chromosome 7 Database

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Perhaps it was a stroke of luck for Stephen Scherer that the Canadian government opted not to fund genome sequencing at the start of the industry. A senior scientist at The Hospital for Sick Children in Toronto, he has been working on chromosome 7 of the human genome since the 1980s, at first through his studies of the cystic fibrosis gene. By the ’90s, his lab was mapping the chromosome — but when the sequencing phase of the HGP kicked off, Scherer never got the money to participate.

And that started him down a road that led to a new, chromosome-7 specific database that Scherer hopes will become a model for scientists studying other regions of the genome.

Because his own lab couldn’t work on the sequence, Scherer made up for it by accessing all the public-effort data as well as subscribing to Celera’s database — with an agreement from the beginning that all Celera sequence data for that chromosome would be publicly released when he was ready to publish. (About 85 percent of the sequence Scherer published came from Celera’s assembly and 15 percent from sequences in the public database, which has resulted in some grumbling from scientists on the public side.)

In building the database, “we emphasized trying to incorporate as much clinical information as possible,” says Scherer, 39. Through his work in the hospital, he knows the value of making data accessible to non-genome scientists working in medical genetics.

His group went through all available literature to add as many links as possible and even updated them: old clones and RFLP markers didn’t have sequences associated with them, so Scherer’s group went back and sequenced them. They also included structural information, such as chromosome rearrangement data and chromosome break points.

Even this early, Scherer says the database seems like a hit. There have been thousands of visits to the database in the two weeks since it was released, he says. While he doesn’t want to compete with whole-genome giants like NCBI and UCSC’s databases, Scherer sees an important role for boutique banks like his. “Our database allows us to have a weighing station, essentially. We can put things in, and test it, see if it’s right,” he says. “I really hope that the large databases look at sites like this and grab the data that they want and try to make as many links as possible.”

— Meredith Salisbury

 

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