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DNA Helix

FDA sends letters to 5 genetic testing companies

It appears that the FDA sent letters to several different direct to consumer genetic testing companies. They are 23andme, Navigenics, DeCode, Illumina, and Knome, which provides whole genome sequencing. The FDA is claiming the tests must undergo approval as a medical device, but did not say anything about removing them from the market. The article also mentions that Pathway Genomics, the company producing the genetics tests that Walgreens considered selling in its stores, also received a letter.

Having recently received my 23andme results, I’m a little concerned by this statement:

Concern about the tests was also raised this week when 23andMe said that because of a laboratory mix-up, up to 96 customers might have received genetic information belonging to someone else.

I certainly hoped that they notified these customers of the potential error…

OpenPCR: DNA amplification for anyone

OpenPCR is a cool new project dedicated to building plans for an open source PCR machine. There’s not much inherently complicated about a PCR machine and it’s about time — a PCR machine built with $300 in parts using a modern software controller will likely be as powerful as any non-realtime PCR out there. Of course, the reagent pricing is what gets you.

Josh and Tito are raising money for this project using Kickstarter. $1024 gets them to build you a PCR machine, which is a reasonably good deal in the scheme of scientific equipment. I gave them $8, because I like stickers and already have a PCR machine that doesn’t exactly get a lot of use.

Singularity Summit 2010 in San Francisco to Explore Intelligence Augmentation

Kevin: I’ve been volunteering for the Singularity Institute these last few months. Each year, the Singularity Institute hosts the Singularity Summit, a two-day conference in San Francisco this August that may be of interest to many of the readers of this blog.

Will it ever become possible to boost human intelligence using brain implants, or create an artificial intelligence smarter than Einstein? In a 1993 paper presented to NASA, science fiction author and mathematician Vernor Vinge called such a hypothetical event a “Singularity“, saying “From the human point of view this change will be a throwing away of all the previous rules, perhaps in the blink of an eye”. Vinge pointed out that intelligence enhancement could lead to “closing the loop” between intelligence and technology, creating a positive feedback effect.

This August 14-15, hundreds of AI researchers, robotics experts, philosophers, entrepreneurs, scientists, and interested laypeople will converge in San Francisco to address the Singularity and related issues at the only conference on the topic, the Singularity Summit. Experts in fields including animal intelligence, artificial intelligence, brain-computer interfacing, tissue regeneration, medical ethics, computational neurobiology, augmented reality, and more will share their latest research and explore its implications for the future of humanity.

“This year, the conference shifts to a focus on neuroscience, bioscience, cognitive enhancement, and other explorations of what Vernor Vinge called ‘intelligence amplification’ (IA) — the other route to the Singularity,” said Michael Vassar, president of the Singularity Institute, which is hosting the event.

Irene Pepperberg, author of “Alex & Me,” who has pushed the frontier of animal intelligence with her research on African Gray Parrots, will explore the ethical and practical implications of non-human intelligence enhancement and of the creation of new intelligent life less powerful than ourselves. Futurist-inventor Ray Kurzweil will discuss reverse-engineering the brain and his forthcoming book, How the Mind Works and How to Build One. Allan Synder, Director, Centre for the Mind at the University of Sydney, will explore the use of transcranial magnetic stimulation for the enhancement of narrow cognitive abilities. Joe Tsien will talk about the smarter rats and mice that he created by tuning the molecular substrate of the brain’s learning mechanism. Steve Mann, “the world’s first cyborg,” will demonstrate his latest geek-chic inventions: wearable computers now used by almost 100,000 people.

Other speakers will include magician-skeptic and MacArthur Genius Award winner James Randi; Gregory Stock (Redesigning Humans), former Director of the Program on Medicine, Technology, and Society at UCLA’s School of Public Health; Terry Sejnowski, Professor and Laboratory Head, Salk Institute Computational Neurobiology Laboratory, who believes we are just ten years away from being able to upload ourselves; Ellen Heber-Katz, Professor, Molecular and Cellular Oncogenesis Program at The Wistar Institute, who is investigating the molecular basis of wound regeneration in mutant mice, which can regenerate limbs, hearts, and spinal cords; Anita Goel, MD, physicist, and CEO of nanotechnology company Nanobiosym; and David Hanson, Founder & CEO, Hanson Robotics, who is creating the world’s most realistic humanoid robots.

You can watch videos from past summits and register at www.singularitysummit.com.

Seeking a lab

I’m working on a startup to develop a new pharmaceutical drug, and I need a lab to help with some of the development and testing. I figure the Thinkgene community might be able to help me out. I’m going to be a little sparse on details in the post, but I can give more information to those who ask.

I’m essentially looking for a lab that can perform an assay to screen a range of compounds for their effectiveness at activating a g-protein coupled receptor, preferably a cell based assay that uses cultured cells.

I have a lab that will generate the compounds that I’m interested in testing, but I need a lab to measure their ability to activate various receptors in neurons. Simple assays that just measure the Kd for the compounds and these particular receptors tend to underestimate the actual effectiveness in the studies I’ve read, so I would prefer an assay that measures something downstream of the receptor; hence why I think a cell based assay would be best. I have a few ideas of different approaches to do this, but it would be complicated by the fact that not much seems to be known about the downstream pathway of these receptors.

If a cell based assay is infeasible or unpractical, simply measuring the Kd would probably be sufficient (I have a protocol for this).

Eventually I would need a lab that can do animal studies with mice to test the compounds after the initial screening. So it would be great if the lab has experience with animal testing.

If anyone has lab or knows someone with a lab that would be capable and willing to help with these tests, please either post a comment with your contact information or email me at [email protected]

A Step Closer to Immortality?

I just read a short, interesting piece at the Telegraph about an increasing population of jellyfish that can apparently reverse their aging. I’m not entirely sure how this is possible and will be reading through published papers to see if I can figure it out.

From what I gather from the mainstream article, the cells dedifferentiate. Perhaps some of the pathways used are still present in humans? This species most likely has modified pathways that wouldn’t be the same in humans, and if they are unused in us chances are they are no longer in tact due to no selection pressure to maintain them. It could give some interesting clues about which areas to focus on for human aging research. Perhaps once day we will also be able to grow “younger” instead of just older. I’m sure Malthus would not be pleased…

Why the DTC companies will fail…or not?

There have been plenty of other posts here on Think Gene foretelling the failure of the DTC market, such as free microarray tests. The consensus is that for these companies to survive, they must enter the medical market.  Critics will say that while companies such as 23andme, Navigenics, and deCODE are just waiting for the right time to enter the medical market, I think there is a different reason why they haven’t entered this market: malpractice.

Let’s first examine the issues in pharmacogenomics with genetic testing. There’s a very well written academic paper by Gary Marchant titled Legal Pressures and Incentives for Personalized Medicine. Additionally, at Redorbit, Olga Pierce writes:

Thus far, lawsuits based on a failure to offer genetic testing before prescribing a drug have mainly targeted drug manufacturers’ deep pockets. But drug companies have circumvented legal problems by including information on genetics and the potential danger of the drugs in package inserts given to consumers with their medication.

That means doctors have become the new targets, Marchant said. It’s a short matter of time before we see a new wave of these cases. Juries are going to say ‘you should’ve done something different.’

But doctors are faced with a catch-22, he said. Most health insurance plans do not cover such genetic tests. If patients cannot afford them, the doctor must decide whether to risk malpractice allegations or simply not prescribe a potentially helpful medication.

Doctors are in a very difficult position, Marchant said.

Doctors’ general lack of training in genetics makes matters worse, he added. Anybody practicing medicine in the country in the next ten years has to understand genetics — or go out of practice.

Institutions and professional organizations can help by establishing clear guidelines for when genetic testing is required, he said, and medical schools should offer new doctors more genetics training.

Nonetheless, there will be a dangerous period for doctors, he said. It’s doctors that are going to bear a lot of the risk during the transition period.

So doctors are liable if they do not give a genetic test when one is available and it may help with prescribing medication. An example is Wafarin/Coumadin, which Dr. Steve Murphy talks about often at his blog, where people can have extremely adverse side effects if they have a particular genotype.

If a doctor did have the genetic data and still prescribed the medication, then it would be pretty clear grounds for malpractice.

Now imagine if a doctor or institution had access to a full microarray of genomic data (including high penetrance mutations). On the one hand, it would be great because if a doctor is prescribing Warfarin, he can easily check the genetic data on file to see if Warfarin is an appropriate medication for the patient. On the other hand, what about mutations that aren’t widely known yet but can be used to determine adverse reactions to drugs such as Warfarin?  If the data is on file, regardless of whether the doctor knows about the mutation, then he may be held liable for malpractice. Negligence could be argued.

This poses quite a problem for the current SNP microarray testing companies. Why would doctors get a whole genome scan which could potentially put them at higher risk for malpractice when they could simply order individual tests? It costs more, but it keeps them safer.

I now propose a simple solution: involve a third party. Say a doctor at a hospital orders a test for Warfarin. The cost of doing a microarray is essentially the same as doing a single genetic test, but the hospital doesn’t want all that data on file. Instead, a third party can do the test and instead only give the hospital access to the specific region that request. In addition to malpractice issues, the other reason for doing it this way is to reduce the cost of licensing fees; why pay the license fee for a BRCA1/2 test if it’s not actually needed? If another doctor later requests a BRCA1/2 test, it can be made available immediately without having to perform another test, and the patient or the patient’s insurance is billed accordingly.

This leaves the microarray DTC providers in quite a bind though. They spent significant resources to develop their genome browser, which is really what gives them their competitive advantage in the DTC market. However, this genome browser doesn’t help them in the medical arena, and in fact may even hurt them for the reasons stated above — information overload and malpractice liability from it.