Gene Therapy, Sequencing at The Scientist

The Scientist has been putting out a quality product since their relaunch, and it's all open and free at the moment. All done to attract attention, of course, but one can hope they'll figure out a way to move forward without closing the blast shutters of paid registration once more. That does seem to be the prevailing business model for more traditional content producers these days, however - so enjoy it while it lasts.

With that in mind, let me point you to a few recent articles. I had commented already on the profile of aging researcher Judith Campisi:

Dealing with the accumulation of senescent cells is one of the seven Strategies for Engineered Negligible Senesence (SENS). This profile of researcher Judy Campisi at The Scientist gives some insight into where the mainstream of aging research is on this topic: "senescent cells not only exist in vivo but also accumulate in aging tissue. ... in culture, these nonreplicating cells are far from inert. They produce a plethora of unpleasant proteins that can, among other things, destroy the structural integrity of the tissue that surrounds them. ... The critical test would be to create an organism in which you prevent senescent cells from accumulating ... She and her colleagues are working on devising a system to do that test. They are developing a mouse in which an inducible promoter allows them to activate a gene that will selectively eliminate senescent cells."

Less immediately relevant to aging research, but still of interest to those who look ahead in medical technology, are these two pieces on genetic science.

Whither Gene Therapy?

A few successes notwithstanding, gene therapy remains highly experimental. Only a limited number of rare genetic diseases are candidates for gene therapy, and a few recipients have experienced severe adverse reactions from the treatment. Critics have argued that the technique has fallen short of its expectations.

Nevertheless, proof-of-principle studies showing that severe combined immunodeficiencies (SCID) can be corrected in a sustained way for a patient's benefit have been published.1,2 Some 20 patients now live as a direct result of genetic interventions. For the field to progress, and for that number to rise, we must learn from these successes what we did right, and from failure what went wrong. Only then can we make gene therapy safe enough and effective enough to become a routine component of the medical response to genetic diseases.

My Own Private Genome

But that's just one sequence pass, and according to vice president for molecular biology Michael Egholm, "It's simply ludicrous to say you can sequence a human genome with 1x coverage." He suggests 8x or 15x coverage, which would boost my costs to between $7.2 million and $13.5 million, and increase my sequencing time to about a year.

Another firm, Solexa, announced in December its plans to sequence a human genome in 2006. According to chief scientist David Bentley, "We're aiming for one billion bases per [two-day] run" on the company's new single-molecule sequencer, the 1G Genetic Analyzer. At that rate 15-fold genome coverage is just six months of work. Solexa has announced its sequencing of a 162,000-bp human BAC, but has yet to publish its findings in a peer-reviewed journal.

Bentley says Solexa will begin shipping instruments in the second quarter of 2006. Pricing has not been fixed, but, "We anticipate a similar unit price to a single high-end capillary electrophoresis machine, plus around $3,000 per run for reagents [initial costs]." He adds, "We're aiming to go to 30-fold coverage for $100,000."

There is a school of thought that says the cost of sequencing is a good measure for the state of play in bioinformatics as a whole - now that this has become a real race, I'm not so sure that continues to be true. It's certainly the case that you could pick a worse enabling technology to reduce to near zero-cost first of all - low-cost genome sequencing will enable all sorts of very impressive, targeted, effective medicine.

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