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Scientists have built a genetic version of Google Earth

PostPosted: Fri Jun 04, 2010 6:04 pm
by bimjim ... arth/2135/

Scientists have built a genetic version of Google Earth
By Boonsri Dickinson
Jun 2, 2010

When I got my DNA tested by three commercial testing companies - 23andMe, Navigenics, and deCODEme - my spit was checked for markers in my DNA called “snips.” And these markers were used to predict my risk of developing common diseases such as heart disease and diabetes.

But the results have hardly filled in the details I had hoped for.

Instead, I began to worry because the reports told me I have an increased risk of developing macular degeneration and Crohn’s disease. Even my doctor drew a blank when I handed him my genetic profile.

While the use of single nucleotide polymorphisms (SNPs) has become popular — it still provides an incomplete picture of what it is really going on.

That’s why the University of Wisconsin-Madison researchers are looking beyond SNPs. With their sights set on large structural variants, the researchers found variations “on the order of thousands to hundreds of thousands of DNA’s smallest pieces.”

UW-Madison’s David Schwartz knew that the structural differences in DNA were important, but the tools to actually study it in detail were unavailable.

So he decided to build the infrastructure to do so. Two decades later, Schwartz has finally created an intricate barcode computer system.

“We probably have the most comprehensive view of the human genome ever,” Schwartz said in a statement.

Like a copy machine, the current DNA sequencing machines cut up a few thousand DNA pieces, multiplied the copies of the base pairs, and then put them back together.

Schwartz thinks we lose a lot of information by treating the DNA like a jig-saw puzzle. So he created the “genetic version of Google Earth.” Enter his Optical Mapping System, which can identify millions of DNA molecules at once.

By paying attention to the structural differences, Schwartz can scan the unique strands along the genome, use high-powered microscopes to look at single molecules, label the strands with a barcode, and save them onto a database.

But it takes a grad student 30 days to sequence one humane genome. Good thing Schwartz is building a system that can sequence a genome in an hour for less than $1,000.

What’s new? Everyone else in the sequencing game wants a cheap and fast way to tap into our genome too.