Sequence in a snap
Rice lab acquires desktop gene sequencer

BY MIKE WILLIAMS
Rice News staff

A high-tech wonder in Rice’s Putnam Lab will give the university a new foothold in basic genome research. A desktop gene sequencer will allow Rice researchers to decode long sequences of DNA extracted from cells.

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While the device won’t be able to decode the billions of base pairs in the human genome – at least not all at once — it will easily handle bacteria-sized genomes as well as large, continuous pieces of others.

Nicholas Putnam, who joined Rice as an assistant professor of ecology and evolutionary biology in 2008, said the GS Junior System introduced by Roche’s 454 Life Sciences last month is one of the first of a new generation of sequencers.

“It’s a scaled-down version of an instrument that’s been around for a while, with the idea that it will be affordable and usable by individual labs,” Putnam said. “It will produce about 40 million bases of sequence in a single run. That means you could sequence a whole bacterial genome in one run, in about 10 hours.”

This 454 method of massively parallel sequencing was used to decode one of the relatively few complete sequences of a human, that of scientist James Watson, co-discoverer of the double-helix structure of DNA. Watson’s genome was presented to him on a DVD in 2007 in a ceremony at Baylor College of Medicine. Baylor’s Human Genome Sequencing Center was a collaborator on the project.

Putnam said his lab will use the $99,000, next-generation device to resequence specific regions of genomes already sequenced for other individuals. The team will also reverse-transcribe RNA into DNA to see which sequences code for which proteins.

“This sequencer doesn’t give us the most volume of data per dollar, but it gives very high-quality data in ways that matter to us,” Putnam said. “These reads are long enough that we can recognize what piece of the genome it is, even if there are many differences between that fragment and the reference genome.”

The Arnold and Mabel Beckman Foundation supported Rice’s acquisition of the sequencer.