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Mapping Genes

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Group Offers Genetic Code Mapping Prize

Here's a chance to win some money.

The people who spurred private spaceflight with a $10 million prize are doing the same for personalized medicine. The X Prize Foundation is offering $10 million to the first company that can process the genetic codes of 100 people in just 10 days - an advancement that experts say is still at least five years away.

"We need new and better technology to get down the road to individualized medicine," said genome mapping pioneer J. Craig Venter, co-chair of the Archon X Prize scientific advisory board. The prize is funded by a $12.8 million gift from Stewart Blusson of Archon Minerals Ltd., a Canadian diamond exploration firm.

The idea is that one day doctors will be able to treat patients based on their individual genetic makeup. The big prize is an effort to jump-start the technology to quickly sequence individual gene maps.

To win the prize, a company has to map in 10 days a specific 100 diverse human genomes provided by the X Prize Foundation. Then it will be paid extra to map the genomes of 100 celebrities, scientists and multimillionaires, said X Prize Chairman Peter Diamandis.

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Francis Collins, director of the National Human Genome Research Institute, said in 1990 it cost about $10 to sequence one base pair in the 6 billion base pair human genome. Now the cost is down to one-tenth of a cent per base pair and that cost is cut in half every 22 months, he said. But to reach the goal and the X Prize, it'll take a cost reduction factor of 1,000 more than the current price, he said.

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We are one step closer to achieving this goal due to novel sequencing biochemistry called Solexa (now since January of this year a part of Illumina).

This machine is not available on the market yet but my company was lucky to get it through the back door and for the past few months we have been working on improving the method (I am one of the people involved).

Conventional DNA sequencing equipment typically delivers no more than approximately 1,200 bases per sample preparation, using Solexa we have been able to obtain 1.4 billion bases from a single sample (which took me two and a half days to make - in contrast Sage libraries take close to 14 days).

Equipment cost of one machine is about half a million (we will soon own 3 of those - there is so much demand) - cost per run is 3,000. It takes two days for sample preparation, then 3 days to run it. Data analysis roughly a day (bioinformaticians are highly in demand nowdays!).

There is more info for anybody who is interested in details:

Solexa sequencing

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We are one step closer to achieving this goal due to novel sequencing biochemistry called Solexa (now since January of this year a part of Illumina).

This machine is not available on the market yet but my company was lucky to get it through the back door and for the past few months we have been working on improving the method (I am one of the people involved).

Conventional DNA sequencing equipment typically delivers no more than approximately 1,200 bases per sample preparation, using Solexa we have been able to obtain 1.4 billion bases from a single sample (which took me two and a half days to make - in contrast Sage libraries take close to 14 days).

Equipment cost of one machine is about half a million (we will soon own 3 of those - there is so much demand) - cost per run is 3,000. It takes two days for sample preparation, then 3 days to run it. Data analysis roughly a day (bioinformaticians are highly in demand nowdays!).

There is more info for anybody who is interested in details:

Solexa sequencing

Fascinating. Whose DNA do you sequence? Can you do your own? What do you do with your results?

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Conventional DNA sequencing equipment typically delivers no more than approximately 1,200 bases per sample preparation, using Solexa we have been able to obtain 1.4 billion bases from a single sample (which took me two and a half days to make - in contrast Sage libraries take close to 14 days).

Equipment cost of one machine is about half a million (we will soon own 3 of those - there is so much demand) - cost per run is 3,000. It takes two days for sample preparation, then 3 days to run it. Data analysis roughly a day (bioinformaticians are highly in demand nowdays!).

That's cool. I assume that the large number of bases indicates a high degree of overlap from many DNA copies? Does it include software to reassemble them into gene sequences?

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Fascinating. Whose DNA do you sequence? Can you do your own? What do you do with your results?

So far we have been only working on samples prepared for research purposes (rather than diagnostics for individuals). I think in the near future another company will provide such service. We have done some lot of cancer patients (I work for cancer research center) and some samples given to us for processing by our scientific collaborators. Applications of this technology are endless. One of the things we are doing is going after novel transcription factors on a very large scale. I can't talk about this too much because most of this data is unpublished.

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That's cool. I assume that the large number of bases indicates a high degree of overlap from many DNA copies? Does it include software to reassemble them into gene sequences?

Yes and yes.

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Good interview of Craig Venter in Der Spiegel:

http://www.spiegel.de/international/world/...,709174,00.html

SPIEGEL: The genome project hasn't just raised hopes -- but also worries. Do you understand those concerns?

Venter: Yes. There are two groups of people. People either want to know the information or they prefer to live like an ostrich with their head in the sand, not knowing anything.

(...)

SPIEGEL: Some scientist don't rule out a belief in God. Francis Collins, for example …

Venter: … That's his issue to reconcile, not mine. For me, it's either faith or science - you can't have both.

SPIEGEL: So you don't consider Collins to be a true scientist?

Venter: Let's just say he's a government administrator.

(...)

Venter: There is currently no reason for us to synthesize human cells. I am, for example, a fan of the work that was done a short time ago that led to the decoding of the Neanderthal genome. But we don't need any more Neanderthals on the planet, right? We already have enough of them.

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Good interview of Craig Venter in Der Spiegel:

http://www.spiegel.de/international/world/...,709174,00.html

SPIEGEL: The genome project hasn't just raised hopes -- but also worries. Do you understand those concerns?

Venter: Yes. There are two groups of people. People either want to know the information or they prefer to live like an ostrich with their head in the sand, not knowing anything.

(...)

SPIEGEL: Some scientist don't rule out a belief in God. Francis Collins, for example …

Venter: … That's his issue to reconcile, not mine. For me, it's either faith or science - you can't have both.

SPIEGEL: So you don't consider Collins to be a true scientist?

Venter: Let's just say he's a government administrator.

(...)

Venter: There is currently no reason for us to synthesize human cells. I am, for example, a fan of the work that was done a short time ago that led to the decoding of the Neanderthal genome. But we don't need any more Neanderthals on the planet, right? We already have enough of them.

Thanks!

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