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Biotech Makes the News
hoppy wrote to us in regards to the recent EE Times article about a tuberculosis detecting biochip. The United States and Russia are teaming up to make the chip, as variant drug-resistant strains are infecting thousands in Russian jails, and making a big comeback in poorer areas in the US. The chip will be used to identify the strain of TB, so that appropriate treatment can be used, rather then the shotgun approach In other news, James Clark, co-founder of SGI and Netscape has given 150 million US to his former school, Stanford. The donation is to be used just for biotech.
There were actually two chips announced this last week. The drug diagnosis chip from Argonneand a research-based expression chip from Peter Small's lab at Stanford.
The Argonne chip is a competitor to Affymetrix/BioMerioux's TB chip which is also still in development. What these gizmos are designed to do is DNA sequencing by hybridization. The TB genome is sequenced and we roughly understand how many of the antituberculosis drugs work and what genes mutate to confer drug resistance (mostly). The traditional (and only FDA approved) way is to grow the patient's TB specimen in the presence in each of these drugs and see if growth is inhibited. For strains that are multi-drug resistant (MDR), that can take many weeks or even months to correctly diagnose. In the early days of the MDR outbreak in NY city in the early 90's, many of the patients were dead before the results were available (aggrevated by HIV/AIDS in the pre-protease inhibitor days).
Peter Small's chips are designed to understand which genes are turned on/off under different conditions. Their paper in the Oct 26th issue of PNAS is their results using these chips on TB treated with isoniazid (the first anti-TB drug).
So molecular diagnostics is a goal of everyone's. Here in our lab we use both the traditional methods and then direct DNA sequencing as an experimental program. Direct DNA sequencing is a bit tedious and can get expensive for each hunk of the TB chromosome you need to sequence to cover all the potential sites for drug-resistance conferring mutations. Arrays let you "do it in one shot".
And Argonne's reported ability to reuse these things 50x would be a huge thing. George Soros is probably footing some of this bill since he's been donating a ton of cash to try to check the expansions of TB in post-cold war Russia. Their prison system is a real nightmare and their "tough on crime attitude (much like the US!) doesn't mind if these prisoners give each other TB and they end up dying. But at least a few of these prisoners do get released and then the problem goes into the general population. The TB we're seeing from Russian immigrants now is really strange. It's not always resistant to the first line of drugs used (safer and more effective) but resistant to many of the second line drugs (full of nasty side effects, less effective, and much more expensive). Wealth individuals in Russia seem to be assuming they have drug resistant TB and just starting in the on the second line drugs.
Our prison system was caught a bit off guard when TB resurfaced in the 80's. They've *vastly* improved now and while TB is still diagnosed in prisons, the transmissions seem to be checked. Here in NY about 20% of our prison population is HIV+ so keeping TB checked is really important.
Problems with these chips arise when you have mixed populations of TB in a patient. Some cells have the mutation that causes resitance, and some don't. Since all these arrays start off with a PCR amplification reation, if the susceptable cell's DNA gets amplified over the mutant ones, you might get the wrong diagnosis. Or if a patient has two different strains of TB in them (can happen but mostly in immunocompromised individuals). But this is much less a concern than in the situation of HIV where these molecular diagnostics sometimes run into trouble.
With 1 billion people in the world infected with TB (and here in NY, it's nearly 1 out of 15...though most will never come down with "active" disease even untreated), don't assume it's a Russia/third world/poor thing!
Cheers!
Two comments, actually.
1) PacketBioStorm. Every time I see an announcement about Biotech, I feel like I'm seeing a convergence between the both utterly dissimilar and disturbingly reminiscent fields of Network Security and Human Biology. Beyond the obvious "virus" appelation, much of the technology being applied to deal with both script kiddies and randomly evolved pathogens (you decide who you'll respect more) has to do with quick identification of massive streams of information through ingeneous code. Biotech adds another layer, since organic materials must be parsed, but it's still the same old schtick.
Sorry to the speakers at Linuxworld, incidentally, but the Human Genome Project is easily the world's largest reverse engineering effort. And will you take a look...a battle between open and closed source. Who's surprised?
2) So Jim Clark has specified the task his money is to be used for. There's actually alot of controversy about that--should donors be able to demand budget parameters? To what degree? Should donations be revokable if, say, a professor at the university violates some specific usage clause? Keeping in mind that most of our college educations either are, were, or will be endowed quite heavily by Alumni and Corporate Sponsorship.
Also remember that Gates intends to donate his fortune in entirety, and that Microsoft is a tremendous benefactor of educational institutions across the country. Think about what Clark's specification means in that context.
There are no easy answers, are there?
Yours Truly,
Dan Kaminsky
DoxPara Research
http://www.doxpara.com
Wouldn't it be just as bad if we let people suffer from tuberculosis without administering antibiotics
You're missing the point. Or I wasn't clear. The problem isn't the administration of antibiotics, it's the improper administration thereof. Doctors have been known to prescribe antibiotics just to shut up whining patients, and this is a bad thing. Almost as bad is the hapless patient who feels better half way through the course, and decides not to bother finishing them. This allows any remaining nasties in the body to survive and multiply.
I wasn't suggesting antibiotics never be used; just that they be used more judiciously.