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March 25, 2008

Whole genome sequencing costs continue to fall: $300 million in 2003, $1 million 2007, $60,000 now, $5000 by year end

Several companies are sequencing the human genome for about $60,000 to $100,000 and taking about 4 weeks. Whole genome sequencing could be $5000 or less and take 24 hours or less by the end of 2008. Inexpensive costs that will accelerate the transformation of medicine into personal genomics and personal medicine. Prices are going to keep falling with better nanopore and highly parallel approaches. Easy and widespread differential genetic analysis will provide more and better targets for gene therapy and modification. Inexpensive sequencing also helps speed up and reduce costs with DNA synthesis. They are closely related.
Genome sequencing is part of the overall mastery of the genome. Read it cheap and fast and change it, write it precisely, cheaply and safely and build stuff with DNA using DNA nanotechnology and synthetic biology.

In 2003 - just five years ago - the government-backed Human Genome Project, after 13 years of work, produced the first real data of a human genetic code for $300 million. Applied Biosystems said it had been able to analyse the human genome sequence for a cost of less than $60,000, which is the commercial price for all required reagents needed to complete the project. Using the company's SOLiD System, researchers used the system's capabilities to obtain deep sequence coverage of the genome of an anonymous African male of the Yoruba people of Ibadan, Nigeria, who participated in the International HapMap Project. The system generated 36 gigabases of sequence data in 7 runs of the system, achieving throughput up to 9 gigabases per run, which is the highest throughput reported by any of the providers of DNA sequencing technology.


In February of 2008 Illumina claimed it had sequenced a human genome in less than four weeks for approximately $100,000, which included the cost of paying off the purchase price of the company's $500,000 Genome Analyzer.

The company claimed its method produced a more reliable map of the genome. Both companies sequence the same genome multiple times, but Illumina made twice as many passes as Applied Biosystems, he said.

Illumina, Roche and Applied Biosystems are battling to become the technology of choice in a global gene sequencing market that is expected to reach approximately $850m in the next three years. Danaher Corp., based in Washington, said it shipped its first $150,000 Polonator sequencer this week.

Researchers are evaluating technologies for use in the government-led 1,000 Genome Project unveiled January, 2008. The project seeks to sequence genomes at a cost of about $30,000 each.

Intelligent Bio-Systems, a privately held company in Waltham, Mass., says it will introduce a machine by the end of 2008 that might reduce the cost of a genome to $5,000 and perform that work in 24 hours.

George Church Joined the IBS Scientific Advisory Board January 15, 2007.

IBS has a proprietary, patented DNA sequencing by synthesis (SBS) technology capable of reading out the sequence of DNA with very a high precision, rapid pace and low cost. They sequence millions of sequences in parallel on a chip.

In this process the DNA is first broken into fragments, amplified, attached to a DNA sequence primer, then affixed as a high-density array of spots onto a glass chip. To read out the sequence of each of the spots, the array of fragments is first subjected to reagents containing uniquely engineered DNA bases that include a removable fluorescent dye and an end cap. These bases attach themselves (Extend) to the end of the growing strand of DNA in accordance with the base on the complementary strand. The array is scanned by a high-resolution electronic camera (Measure) and the fluorescent output of each of four dye colors at each array position is measured and recorded. The color indicates which base (A, C, G or T) was just incorporated in the DNA fragment in the previous step. Finally, the array is exposed to cleavage chemistry (Cleave) to break off the fluorescent dye and end cap that will now allow additional bases to be added. The Extend, Measure and Cleave cycle is then repeated


UPDATE:
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.

Pacific Biosciences 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. Some contestants say that they might try for the X Prize as early as next year (2009) and that the $1,000 genome is as little as three years away.

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.

4 comments:

Anonymous said...

Why do you trust the 5,000 figure? Was this company's press release accurate in the past? Or just the big name scientist on the board of directors convincing enough?

5,000 is almost worth it.

bw said...

I believe that many companies and institutions are all trying to radically reduce the costs. The NIH has funded many projects targeting $10,000 and $1000 genome and $100 genome. So it is a race with many participants.

I see the pace of the progress and see that the $5000 price would be in line with progress from 2003 to 2004, 2004 to 2005, 2005 to 2006 and 2006 to 2007 and 2007 to this month.

They have many ways to bring the costs down and speed up many parallel nanopores, more parallelized sequencing, more computational assistance, more automation, etc..

This like Moore's law is like looking at Nascar and saying the last few laps had an average fastest speed of 2 minutes. I think the next lap will also be about 2 minutes and I think it will car X that might have the best lap.

Maybe at the end of 2008 it will be Applied Bio with $15,000 for whole genome or Illumina with $12,000 or someone else at $8000 or $3500. The trend is rapidly falling costs. I think 2009 ought to be the year of the $1000 whole genome sequence but if it is 2010 the world will still be changing soon and fast. Before 2013, less than $100. The progress is clearly very fast, exactly who wins and in which quarter they are ahead will matter for stock price and options but the overall societal effects will be from the application and usage of very inexpensive sequencing. Inexpensive sequencing also helps speed up and reduce costs with DNA synthesis. They are closely related.
Genome sequencing is part of the overall mastery of the genome. Read it cheap and fast and change it in precisely, cheaply and safely and build stuff with DNA using DNA nanotechnology and synthetic biology.

Anonymous said...

The trend is clear, but specific cost and winners are very hard to know beforehand.

My sister has a master's in chem and she didn't believe the generalization of a moore's law like trend applied to DNA sequencing. Of course I got that info. from Kurzweil many years ago.

It's hard to generalize, but my opinion is that if you are in a scientific field, and some silly futurist predicts rapid progress, it will be ignored because it's a very hard problem and *you* are not that smart. If you are the genius working on the solution, you are publically over optimistic for psychological as well as monetary reasons.



What I truly love about this revolution is to end a long standing quarel with my sis: how much influence do genes have on behavior? Oh, I also have a bet that by 2054 we will know 99.9% of every human protein structure. I said she could just take me out to a nice dinner.

One of these days i'll fix my google identity...pass doesnt work.

Anonymous said...

Check out the Polonator, a $150K fully automatic sequencer at www.polonator.org