June 02, 2007
James Watson DNA Sequence Marks Drop In Costs
DNA double helix co-discoverer James D. Watson has had his DNA sequenced at a much lower cost than previous genome sequencing attempts.
On Thursday, James Watson was handed a DVD containing his entire genome, sequenced in the past few months by 454, a company based in Branford, CT, that's developing next-generation technologies for efficiently reading the genome. At a cost of $2 million, 454 sequenced Watson's genome for roughly an order of magnitude less than it would have cost using traditional machines.
The $2 million and two months that it took to sequence Watson's genome is a far cry from the more than ten years and $3 billion required for the Human Genome Project's reference genome, released in 2003.
454 Life Sciences claims their DNA sequencing cost for Watson's genome was only $1 million.
454 Life Sciences Corporation, in collaboration with scientists at the Human Genome Sequencing Center, Baylor College of Medicine, announced today in Houston, Texas, the completion of a project to sequence the genome of James D. Watson, Ph.D., co-discoverer of the double-helix structure of DNA. The mapping of Dr. Watson's genome was completed using the Genome Sequencer FLX(TM) system and marks the first individual genome to be sequenced for less than $1 million.
But 454 and other sequencing technology companies say that costs have already dropped another order of magnitude.
And technology companies like Illumina, Applied Biosystems and 454 Life Sciences, which solicited Dr. Watson’s DNA to prove its abilities, say the price of a complete human genome has already dropped to $100,000. They are competing for a $10 million “X prize” to sequence 100 human genomes within 10 days. (Dr. Watson’s took about two months.)
The rapid advance of DNA testing technologies is possible because DNA is small and DNA testing relies on computer chip technologies. While I've made this claim for years this latest news provides a much dramatic demonstration that this trend is really happening. This rate of advance that bodes well for future advances across a wide range of biotechnologies.
What will come from very cheap DNA sequencing? Lots of things:
- Discovery of genetic variations that contribute to disease risk.
- Discovery of genetic variations that contribute to intelligence, personality characteristics, and behavioral tendencies including criminal tendencies.
- Discovery of "best of breed" genetic variations that contribute to superior athletic performance, vocal ability, dancing ability, and other areas where humans can excel.
- Discovery of genetic variations that contribute to appearances such as genes for eye and hair color, complexion, hair texture, facial shape, and other attributes that contribute to visual desirability.
- Acceleration of cancer research as researchers gain the ability to identify many more genetic mutations that occur in cancers as the cancers develop.
- Acceleration of research into accumulation of mutations that cause aging as researchers gain the ability to cheaply compare youthful and old cells to identify mutations that most contribute to aging.
- Changes in mating choices as people start testing prospective mates for suitable genetic traits for offspring and even for genetic attributes that contribute to personality attributes.
- Changes in choices for sperm and egg donors based on genetic testing results.
- Cheap DNA testing will make use of sperm donors more attractive to women who can't find genetically suitable men to marry.
- More people will use in vitro fertilization (IVF) to start pregnancies since they'll be able to genetically test a set of embryos to choose one that has more of what they want to pass along to their offspring.
Most of us will live to see full genome testing become commonplace.
In a few years time we will know the important genes for IQ, a pleasant personality, athletic ability, as well as susceptibility to Alzheimer, criminality, cancer and so on, as stated in the article. Some people would like to choose their offspring. There is a certain chance that a "minimal" sperm will be chosen on which people can simply add the traits they like. This will of course be illegal but medical tourism will make it happen anyhow. Initially we will first choose existing sperm, but very rapidly after designer sperm will be fabricated. The technology to add genes and knock-out genes is known since a long time so the technology is here. In a primitive form but as soon as things are commercialised it will become trivial.
We are in for a very interesting future indeed and this future is very close. The most important factor why it is so close is medical tourism which probably will be more important for advances in medicine than any reorganisation of FDA or any increase in the budget of NIH. Medical tourism is a billion dollar + industry now and is growing at a breathtaking speed, being almost non-existing a decade ago. Anybody thinking medical tourism can be outlawed have to think again, when realising that tax-havens exist despite all the hate and bitterness of US and European governments.
but still in 2007 1 million for a genome prety lame
The speed of the price drop is astounding.
Though I wonder whether the sequencing method used detects large copy variations.
Well, we can do a loose analysis: 1993-2003 @ $3 billion, take midpoint of 1998 for $1 billion. $1 million in 2007 implies 3 orders magnitude every 9 years or 1 order of magnitude every 3 years. So we can say with some certainty that the $1000 point is no later than 2016.
If today's true cost is already at $100K as some manufacturers claim, that's a 4 orders of magnitude drop in 9 years. So an order of magnitude every 2.25 years implies the $1K point is 4.5 years away in 2012.
Purists might want to use a sigmoidal Fisher-Pry curve to do the same, it will be a little more precise.
For genome scanning of embryos, I estimate the rich would reasonably do that at any price below a total outlay of about $100K for about 10 embryo's or $10K a piece. So the time is ripe for embryo scanning to come about in the next 5 years.
Imagine now, what the exponential price drop would be if medicine were unregulated and markets free to function effectively in that area, so that the true synergy between the fields could take place without the cost and regulatory overhead.
pyrosequencing has two main downsides:
1) The reads that it produces are unpaired, and short. This means that it is impossible to assemble a genome in a meaningful sense without a reference genome sequenced by sanger sequencing. It also means that copy number variations are hard to detect. They're hard to detect using sanger sequencing too. SNP chips are, for the forseeable future, the way to do this. They're cheaper than resequencing too. Similarly, no meaningful information about repeats can be gained by this method.
2) Although there are methods to get around it, 454 pyrosequencing is poor at sequencing long (> about 6nt, I think) stretches of homonucleotides. Genetic differences caused by expansions of such repeats aren't detectable.
Most genes have an allele that's in 50% of the population, and another in 25%, and another in 12%, and so forth ... sequencing everybody will come up with a complete set of alleles that are out there, all the way down to ones that appear in only one or two people. A large fraction of the promising alleles in humanity happened in the last 300 years, and are only in a handful of people today. A lot of the most-favored genes are going to be ones almost nobody's ever seen. And their interactions will be entirely untested.
if you guys are so smart, and know so much about genomes and sequences
give me a link to watson's genome
or to J. Craig Venter's genome.
That will be interesting to see. I've seen hundreds of articles claiming the genomes are publicly available on GenBank, but I cant find them. So, I would like to know if any of you intelligent individuals could show me where the sequences are?
"Alpha children wear grey They work much harder than we do, because they're so frightfully clever. I'm really awfuly glad I'm a Beta, because I don't work so hard. And then we are much better than the Gammas and Deltas. Gammas are stupid. They all wear green, and Delta children wear khaki. Oh no, I don't want to play with Delta children. And Epsilons are still worse. They're too stupid to be able …"