August 05, 2005
Harvard Group Lowers DNA Sequencing Cost Order Of Magnitude

Biotechnology increasingly resembles electronics technology as costs fall by multiples.

BOSTON-August 4, 2005-The theoretical price of having one's personal genome sequenced just fell from the prohibitive $20 million dollars to about $2.2 million, and the goal is to reduce the amount further--to about $1,000--to make individualized prevention and treatment realistic.

The sharp drop is due to a new DNA sequencing technology developed by Harvard Medical School (HMS) researchers Jay Shendure, Gregory Porreca, George Church, and their colleagues, reported on August 4 in the online edition of Science. The team sequenced the E. coli bacterial genome at a fraction of the cost of conventional sequencing using off-the-shelf instruments and chemical reagents. Their technology appears to be even more accurate and less costly than a commercial DNA decoding technology reported earlier this week.

The commercial DNA decoding technology they are referring to is from 454 Life Sciences Corporation and you can read about it in my post "New Tool Speeds Up DNA Sequencing By 100 Times". Whether the Harvard or 454 Life Sciences approach can go further in lowering DNA sequencing costs in the long run remains to be seen. But these are not the only two efforts aimed at lowering DNA sequencing costs and another company or academic group might yet bypass both of them.

The Church group built their sequencer using an assembly of existing technologies. How creative.

The Church group's technology is based on converting a widely available and relatively inexpensive microscope with a digital camera for use in a rapid automated sequencing process that does not involve the much slower electrophoresis, a mainstay of the conventional Sanger sequencing method.

"Meeting the challenge of the $1,000 human genome requires a significant paradigm shift in our underlying approach to the DNA polymer," write the Harvard scientists.

The new technique calls for replicating thousands of DNA fragments attached to one-micron beads, allowing for high signal density in a small area that is still large enough to be resolved through inexpensive optics. One of four fluorescent dyes corresponding to the four DNA bases binds at a specific location on the genetic sequence, depending on which DNA base is present. The fragment then shines with one of the four colors, revealing the identity of the base. Recording the color data from multiple passes over the same sequences, a camera documents the results and routes them to computers that reinterpret the data as a linear sequence of base pairs.

In their study, the researchers matched the sequence information against a reference genome, finding genetic variation in the bacterial DNA that had evolved in the lab.

"These developments give the feeling that improvements are coming very quickly," said HMS professor of genetics Church, who also heads the Lipper Center for Computational Genetics, MIT-Harvard DOE Genomes to Life Center, and the National Institutes of Health (NIH) Center for Excellence in Genomic Science.

"The cost of $1,000 for a human genome should allow prioritization of detailed diagnostics and therapeutics, as is already happening with cancer," Church said.

The Church lab is a member of the genome sequencing technology development project of the NIH-National Human Genome Research Institute.

I predict that within 10 years most of us who survive the coming killer flu pandemic will know our primary DNA sequences. Many debates about the degree of heritability of various human characteristics - especially cognitive characteristics - will then be resolved very quicky. The knowledge spawn many uses and not just medical uses (valuable though they will be). Social science as a field will become orders of magnitude more productive as genetics becomes a much better controlled variable in social science studies.

I'm also looking forward to improvements in stem cell therapy development when many genetic sequences that affect longevity are identified. We'll be able to use stem cells not only to build replacement parts but also to build longer lasting replacement parts.

Thanks to Brock Cusick for the heads-up.

Share |      Randall Parker, 2005 August 05 09:43 AM  Biotech Advance Rates

James Bowery said at August 6, 2005 7:02 AM:

So how many people have the scientific anti-racists killed with their vicious pseudoscientific suppression of the use of race-data during the time the only economically viable techniques for imputing genetic characters involved inference from more obvious characters? Try as they might, the scientific anti-racists will eventually have to admit that cost-of-acquisition of precise genetic information must be traded-off against other costs of treatment and diagnosis. Doctors do that kind of trade-off all the time when ordering various lab tests and making various observations in estimating the likelihood of various diagnoses.

We don't wait for all the data to be in on the effect of gene-based medicine for every individual on the planet to make an estimate how many people the scientific anti-racists have killed with their pseudoscience.

James Bowery said at August 6, 2005 10:27 AM:

Here's a place to start making such a casualty estimate:

An Algorithm to Construct Genetically Similar Subsets of Families with the Use of Self-Reported Ethnicity Information

Andrew D. Skol,1 Rui Xiao,1 Michael Boehnke,1 and Veterans Affairs Cooperative Study 366 Investigators*

1Department of Biostatistics, University of Michigan, Ann Arbor

Received March 31, 2005; accepted for publication June 15, 2005; electronically published July 14, 2005.

We present a simple algorithm that uses self-reported ethnicity information, pedigree structure, and affection status to group families into genetically more homogeneous subsets. This algorithm should prove useful to researchers who wish to perform genetic analyses on more-homogeneous subsets when they suspect that ignoring heterogeneity could lead to false-positive results or loss of power. We applied our algorithm to the self-reported ethnicity information of 159 families from the Veterans Affairs Cooperative Study of schizophrenia. We compared these estimates of population membership with those obtained using the program structure in an analysis of 378 microsatellite markers. We found excellent concordance between family classifications determined using self-reported ethnicity information and our algorithm and those determined using genetic marker data and structure; 158 of the 159 families had concordant classifications. In addition, the degree of admixture estimated using our algorithm and self-reported ethnicity information correlated well with that predicted using the genotype information.

Marvin said at August 7, 2005 7:24 PM:

It looks like the coming avian flu human species extinction event is acquiring all the magnitude of disaster of the late Y2K cataclysm and the horrific global warming end of the world event. Humans need something to fear and one must choose wisely in selecting one's boogey-men. Personally, I prefer the yellow terror and fanatical scimitar wielding mussulmen, but to each his own. Regardless, "get out yur guns, Annie, them human sardines are gunna be pourin' outa the city any minute now, lookin to steal our food horde."

Mr. Parker, you are to be commended for presenting actual scientific advances along with the bad prognoses. A lot of Cassandras only present the doom-side of things.

Randall Parker said at August 7, 2005 9:07 PM:

Geez Marvin, I do try to stick to the facts. The 19th century saw 4 worldwide flu pandemics. The 20th century saw 3 flu pandemics and one of those pandemics killed somewhere between 20 and 100 million people (estimates vary because in much of the world no one counted).

So we have precedents and those precedents were produced by the still working powerful force of natural selection.

Natural selection is an extremely powerful force. It made humans all sorts of nasty to each other and different from each other in all sorts of ways that a lot of people (intellectuals especially) recoil from accepting. It has thrown up all sorts of killer pathogens. One of these pathogens has greatly lowered average life expectancy in Africa over the last 25 years. This pathogen looks set to continue to do so for some years to come while also selecting against and for assorted alleles that influence sexual behavior. In other words, it is changing human nature in Africa. Wow. Impressive stuff for a pathogen that at one time couldn't even replicate in humans.

By contrast, I worried not at all about Y2K software problems. Also, I've repeatedly argued that global warming is a problem that will be solved by technological advances that will obsolesce oil and that there may not be enough oil in the ground to sustain high CO2 emissions anyway. So trying to brand me as a Cassandra when I'm pretty selective about my fears seems a real stretch.

So Marvin, I reject your criticsm.

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