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A local chemist, Reza Ghadiri at the Scripps Research Institute, has won a four-year, $5.1 million grant from the National Institutes of Health to find a different way of sequencing genomes quickly and cheaply.

His work is similar to that of two local companies, Life Technologies and Illumina, which are in a race to be the first to sequence a person’s entire genome for $1,000. A genome is the complete collection of genes that defines everything about you, from your eye color to your potential for developing Alzheimer’s, so the ability to read individual genomes could open the door to better diagnoses of genetic diseases and medicine tailor-made for your body.

Ghadiri’s approach borrows a pore from the staphylococcus bacteria (the bugs that cause staph infections) and uses it as a type of funnel to pass DNA through.

“If you imagine an old fashioned gramophone, it’s as if there’s a needle that’s going to read a strand of DNA one molecule at a time,” he said. “As you put the DNA through the pore, it’s like putting it against the reading head, so you can read one piece at a time.”

Ghadiri’s system will allow him to detect each of the four molecular components of DNA as they pass through the pore and will present him with a digital readout of the DNA’s structure, which he can then read like a book.

The idea is to use thousands of pores at the same time, which will cut the time required to sequence an entire genome to less than 15 minutes (currently, a full genome sequence can take days to complete). And the minimal chemicals and preparation required for the system to work means the process will “definitely cost less than $1,000 per genome,” Ghadiri said.

Ghadiri will work closely with Hagan Bayley at the University of Oxford and Amit Meller at Boston University on the project, which they hope to finish by 2014. Because the scientists do not work at for-profit companies, they are not competing with companies like Life Technologies and Illumina. Instead, Ghadiri said they hope to supply an alternative method for genome sequencing.

“This would be complementing, helping those kinds of approaches,” he said.

Although some criticize genome sequencing as frivolous because it does not directly treat diseases or provide other medical benefits, Ghadiri thinks the technology is worth the federal government’s investment.

To really take advantage of the knowledge gained by the Human Genome Project, the first full sequence of a genome that wrapped up a decade ago, scientists need the readouts of thousands of genomes, not just one or two. And sequencing genomes cheaply is the way to make that happen.

“In our lifetime I’m sure we will benefit from the fruits of this marvelous knowledge,” he said.

Please contact Claire Trageser directly at claire.trageser@gmail.com follow her on Twitter: twitter.com/clairetrageser.

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