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Personal genomics and making your sequence public

As a geneticist from the Human Genetics program at University of Pittsburgh School of  Medicine I have always been a  proponent of Personalized Medicine.

There are many ways genetics is spun in the day to day news. Personalized medicine really involves, at it’s simplest, 3 parts. The first is getting a map or sequence of your genes. This is done by using large machines that look for A,T,C,G’s (Left image is a sequencing farm and right is a sequencing gels..

The second is to gain an understanding of what the pieces of the map mean. These changes come in the form of mutations or polymorphisms, and are usually called single nucleotide polymorphisms. What do these differences mean on a person by person basis and how does that affect how drugs work on that individual. The final step is one of being able to “print” or somehow produce a drug that takes those interactions into consideration and would work best in that individual. This is an extremely simplified view of course, since there are many regulatory steps, safety steps, etc, for a whole ecosystem like this to work.

The take home message is that there is a big push by industry, healthcare, government and others to create these maps of peoples’ genes and mutations to better understand ethnic and population diversity in how drug interactions work. There is also a mad rush like the gold mining days to patent any and every gene and their mutations. Companies want to own this data because they could potentially own the cures and the therapies attached alongside. The validity of Gene patents is still being disputed by the courts in particular on if Myriad owns the rights to BRCA1 and BRCA2, genes potentially involved in breast cancer and ovarian cancer. Hopefully this is put to rest soon as companies owning genes is a frightening thought that could lead to all sorts of patent disputes

In addition, the technology to sequence full genomes has increased in speed and accuracy while rapidly reducing the associated costs almost comparable to the speed at which computers become cheaper and yet more powerful every year. We are left with two booming fields, one is to isolate and determine what these above “SNP” are. The second is how to use bioinformatics to sort out all of the available information and discover and compare this complex information.The two graphs below demonstrate how the cost of sequencing has gone down in the last few years.

Lets look at 23andme first, for ~$200 a year they will look at a large preselected SNP library and compare them to yours (they don’t sequence everything just the SNP section). They then provide you with percentages or averages that you are susceptible to a disease. They also use information you provide them through surveys and questionares that help them grow their library and make it more accurate. Of course a Dr would not really use these  low percentages to decide on surgery just yet but maybe some day.

It is thought that about 30,000 human genomes will have been sequenced by the end of 2011 at a price below $5,000/person. That is a lot of information to sort through and understand. There are also very few federal guidelines available that protect your genetic information from say ‘insurance companies’ that could deny certain coverages based on this sequencing information and percentages. Below are a few links to companies that will sequence your DNA for a price as comparison.

http://www.personalgenomes.org/

http://www.everygenome.com/

http://www.bizjournals.com/sanjose/stories/2008/11/10/daily100.html

http://knome.com/

This leads me to some very important questions for our community. How many of you have already sequenced yourself through 23andme or another service? Do you find this service useful, intuitive and meaningful. If we could anonymize your personal information from your 23andme reports (among others) would you host them on our site such that the larger scientific community may have access. We have access to supercomputing power through the Pittsburgh Super Computing Center so if an enterprising student would be interested in taking on the task of gathering “donated” sequences, making them anonymous and available to the public I could see this as much needed information for the community at large.

Thanks,

David Vitrant PhD

First FundScience Meetup Follow-up

What is science to me? By Eli Horrowitz

“Science”?
After taking twelve-plus years of science classes and spending a good chunk of time investigating the philosophy of science, the one thing I can confidently say about the subject as a whole is that I’m bad at it.  As much as the word is used to indicate a body of knowledge or a governing organization of sorts, science is at its heart a performance – and one that makes use of a wide variety of skills.  Pertaining as it does to the physical world, scientific investigation requires a certain level of dexterity and patience.  But since science is knowledge-oriented, it also calls for a measure of ingenuity and more than a little detachment.  An excellent scientist will, therefore, be a hard thing to find.

But science progresses despite this – could science not be so difficult after all? I doubt it – as in every other field, the history of science is littered with mistakes, overconfidence, and even outright dishonesty.  Scientists, after all, are only as human as the rest of us.  In fact, there are many cases in which scientists – that is, paid practitioners of science – are more human (in the pejorative sense) than the general population.  Experiments require money and money, even money provided with the best of intentions, comes with strings.  Take this into account and the above list of characteristics grows to include “brave”: it’s never an easy thing to work at a job that could well inspire your benefactor to stop sending you checks.

Luckily, scientists don’t have to go it alone.  For starters, there’s a scientific community, a group of roughly like-minded individuals aiming at the same goals.  Where one of these individuals lacks practical imagination, for example, another can step forward to provide it.  I imagine, then, that the best scientists aren’t necessarily the best scientists – a brilliant researcher or two can’t progress anywhere near as far as five or ten less talented but more cooperative ones.  I hope that most scientists operate in this spirit of cooperation, but the odds of that aren’t good – again, scientists are only human.

However the details work themselves out, it’s certain that science is a messier endeavor than one would guess by the stereotyped image of dispassionate scholars in white lab coats peering at beakers.  Although the process clearly works in at least the broadest of senses – you’re reading this on a computer, aren’t you? – the day-to-day workings of this thing called “science” remain utterly mysterious to me.  As for the scientists themselves, it would be very surprising indeed if they had the time or energy to worry about PR.  These facts combine to pose an interesting problem for the various scientific fields: to what extent does the public need to understand “science” – and who should be in charge of teaching us?

Antibiotics that Don’t Kill Bacteria.

Antibiotics and drug resistant bacteria are a little talked about yet growing problem. I recently saw a well written and lay person oriented article about creating antibiotics that don’t kill bacteria. The article is here. 

Ok. Now to the question everyone is probably asking by now: Why is that a good thing? Isn’t more bacteria around a bad thing ? 

In order to answer that question I have to say a few general things about bacteria in general:

1. Bacteria grow and reproduce very very quickly.
2. It usually only takes one or a few bacteria to re-grow a complete colony.
3. Most if not all therapies deal with inhibiting the bacteria and killing it off (usually while killing other types of bacteria as well)… 

How some research is never published.

One issue that you will hear us gripe about here (and try to find a solution for) is the lack of mediums to discuss or publish “non-data”. What i mean by non-data is anything that can’t be published but might be useful. In that list I include hypotheses that were not correct, or data that is unpublishable or unreproducible.

You ask why non-data would ever be published eh ? Well while positive results are great and lead to new avenues, all the negative results help others not waste time doing useless time consuming experiments. Another reason why non-data is important is that your non-data may actually support somebody else’s research (some examples I will get to in another post). The problem is how to organize it, and how to constitute exactly what a piece of non-data entails.

Anyway. on to the meat of this “depressing” story. Let’s talk about Antidepressants

This NYT article describes how some makers of antidepressants didn’t disclose about 1/3 of their drug related studies. This is nothing new for most of us in the scientific field. Many times when we receive funds from biotech firms or pharmaceutical firms to do research there are strings attached. That’s not to say the strings are all bad. The funding is necessary to bring some research into industry but one of the most prevalent string is that the corporation funding a research project usually has the final say on what data can be published, and when. They pay the research, they own the rights, and are accountable to shareholders.

Most of the time that is alright, but for drug trials that is another story. When patients are involved it is important to weigh the good aspects of a drug to the bad aspects. Well what if the FDA never sees the really bad data? Can they still make an informed decision on the safety of a drug? I’ll let the public think about that one. To be fair it’s not the FDA’s problem if information doesn’t come their way. There needs to be less ambiguous congressional guidelines set to monitor drug studies either earlier on in the process, or to require full disclosure.

David Vitrant

Our Innaugural Post

Hello,

I’m David Vitrant the Executive Director of FundScience Inc. Here at FundScience we are looking to get the public to fund individual pilot research projects. This will drive innovation in many scientific fields, and open up complex scientific discussions to the public. In the end research is meant to help understand nature and for the benefit of society in general. With our blogs, wiki’s, forums, and soon project proposals we hope to bring a community of scientists and laypeople together to discuss the future of science and help fund our future generation of scientists.

The aspect of introducing the public to the life of a scientist, how scientists think, how we tackle problems, what our problems are, is critical to this step and I hope that by providing these blogs you will be able to peer into the life of a scientist, and go past political pandering, and marketing, to arrive at the issues and possibly the solutions.

In order for us to be Successful we need your help though in the following aspects:

1) We need content and bloggers to talk about the issues. If you know somebody please spread the word help us find scientists willing to blog (or laypeople willing to blog about science)

2) Are you interested in a specific topic, want to understand some research as a layperson? Email us or make a post on our forum. We will see what we can do.

3) Digg our posts please. This will help get our word out and get attention to our site.

4) Are you willing to fund a research project or have thoughts on how to do so? Email us again.

Lastly, we are all here to learn about science, talk about science, and collaborate. So please be courteous and don’t be shy to ask questions.

Thanks for joining us,

David Vitrant

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