Tuesday, August 18, 2009

A Human Genome in Record Time


August 10, 2009
A Human Genome in Record Time

A new type of technology has sequenced a human genome in a month and for less than $50,000 worth of reagents, according to a report today in Nature Biotechnology. But this step toward fast, cheap genomes doesn't spell the end for large sequencing centers.

Human genomes produced to date have all required many instruments running in parallel and have cost up to $500,000 per genome, says Stephen Quake, a biophysicist at Stanford University in Palo Alto, California, and founder of Helicos Biosciences of Cambridge, Massachusetts. The HeliScope Single Molecule Sequencer is the first commercial single-molecule sequencing instrument, so called because it does not require the production of millions of copies of the target DNA for the analysis. Instead, DNA is cut into small pieces and mounted at very high densities in a flow cell, where a very sensitive camera monitors the step by step addition of bases for each sequencing reaction.

In the new paper, Quake and colleagues report how the machine generated enough data to cover the 3-billion base human genome 28 times over. That sequence data consisted of short stretches of sequences 24 to 70 bases long, which were compared with the reference human genome sequence in public databases to piece together Quake’s own genome.

The demonstration brings “plug and play” sequencing one step closer to reality, wherein individual labs will be able to do what today is accomplished primarily in large sequencing centers. “This is the main coming out party for the Helicos machine,” says Jeffery Schloss of the National Human Genome Research Institute in Bethesda, Maryland.

However, the machines cost $1 million. That’s several times the price of other sequencing machines, notes Schloss. While such machines hint at a future where individual labs sequence large genomes, Schloss emphasizes that large centers will continue to play a role in improving technologies and their uses and developing analytical tools for genome projects.

— Elizabeth Pennisi

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