Saturday, February 09, 2008

The exponential curve for genome sequencing

Below is an update on progress towards less expensive gene sequencing. At the moment you can have your genome sequenced for $350k, but we might hit the $1k mark within just a few years. This progress is funded by a combination of taxpayer and venture capital dollars. The rate of technological advance would slow to a snail's pace without sophisticated capital markets, intellectual property rights and plain old human greed and ambition.

For a cost per base pair curve extending up to 2005, see here. As the cost nears $1k per genome we will see a tremendous explosion in detailed genetic data across all major population groups.

NYTimes: A person wanting to know his or her complete genetic blueprint can already have it done — for $350,000.

But whether a personal genome readout becomes affordable to the rest of us could depend on efforts like the one taking place secretly in a nondescript Silicon Valley industrial park. There, Pacific Biosciences has been developing a DNA sequencing machine that within a few years might be able to unravel an individual’s entire genome in minutes, for less than $1,000. The company plans to make its first public presentation about the technology on Saturday.

Pacific Biosciences, or PacBio, is just one entrant in a heated race for the “$1,000 genome” — a gold rush of activity whose various contestants threaten to shake up the current $1-billion-a-year market for machines that sequence, or read, genomes. But the company has attracted some influential investors. And some outside experts say that if the technology works — still a big if — it would represent a significant advance.

“They’re the technology that’s going to really rip things apart in being that much better than anyone else,” predicted Elaine R. Mardis, the co-director of the genome center at Washington University in St. Louis.

If the cost of sequencing a human genome can drop to $1,000 or below, experts say it would start to become feasible to document people’s DNA makeup to tell what diseases they might be at risk for, or what medicines would work best for them. A DNA genome sequence might become part of each newborn’s medical work-up, while sequencing of cancer patients’ tumors might help doctors look for ways to attack them.

To spur such advances, the federal government has awarded about 35 grants totaling $56 million to companies and universities for development of technology that could put the $1,000 genome sequence within reach. PacBio has received $6.6 million from that program.

The nonprofit X Prize Foundation, meanwhile, is offering $10 million to the first group that can sequence 100 human genomes in 10 days, for $10,000 or less per genome. Six companies or academic groups — although not PacBio — have signed up for the competition so far.

Computerized sequencing machines use various techniques to determine the order of the chemical units in DNA, which are usually represented by the letters A, C, G and T. Humans have three billion such units, or six billion if one counts the second copy of each chromosome pair.

The industry has long been dominated by Applied Biosystems, which sold hundreds of its $300,000 sequencers to the publicly financed Human Genome Project and to Celera Genomics for their sequencing of the first two human genomes, which were announced in 2000. But two newcomers — Solexa and 454 Life Sciences — have already started to cut into Applied Biosystems’ sales with machines that are faster and less costly per unit of DNA sequenced. Solexa is now owned by Illumina and 454 Life Sciences by Roche.

Applied Biosystems, which is a unit of Applera, recently started selling its own new type of sequencer, which it obtained by buying Agencourt Personal Genomics for $120 million in 2006. Helicos BioSciences, a newly public company, announced its first order on Friday. It has said its machine might be able to sequence a human genome for $72,000, with further improvements to come.

“We can look somebody in the eye and say, ‘This instrument is going to get you to the $1,000 genome,’ ” said Steve Lombardi, the president of Helicos, which is based in Cambridge, Mass.

Intelligent Bio-Systems, a privately held company in Waltham, Mass., says it will introduce a machine by the end of the year that might reduce the cost of a genome to $10,000. Other contenders include the privately held companies NABsys of Providence, R.I., VisiGen Biotechnologies of Houston and Complete Genomics of Mountain View, Calif.

Some contestants say that they might try for the X Prize as early as next year and that the $1,000 genome is as little as three years away. But other experts are more conservative. ...

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