Be still my beating heart cell!

In this Technology Review aritcle, I describe a company called Cellular Dynamics International (CDI) that has offered to run a first-ever test on me that could marry cutting edge stem cell technologies with DNA testing.

Using technology developed by stem cell pioneer James Thomson of the University of Wisconsin in Madison, CDI last month started selling heart cells that are derived from Induced Pluripotent Stem (IPS) cells.

IPS cells are made by extracting any cells from a person (say T-cells from the blood) and reverse-engineering them back to stem cell that can then be programmed to turn into any other cell in the body--in this case, heart cells that researchers will use to test for toxicity to old and new drugs and for basic research in heart cell biology.

CDI has offered to run an experiment on me in the coming weeks involving their process. They propose to draw cells from my blood, reverse them back to IPS cells, and then create heart cells that are a perfect genetic match to me. They will then test these heart cells by applying various drugs that show some cardio-toxic effects, to see how sensitive to them I am.

These drugs might include statin drugs used to lower cholesterol--to see if they show evidence of a rare side effect for these medications. I carry a genetic marker that makes me high risk to myopathy--a weakening of muscle tissue--a side effect that impacts about two percent of patients who take statins.

CDI scientists told me that they don't know how these experiments will come out, and the company does not plan to offer this service publicly anytime soon. But one day this sort of test could become a powerful tool--combining genetic profiling and cell-toxicity screening using IPS cells--to determine adverse reactions to drugs in genetically high-risk individuals before they ever take a given drug.

This could be particularly useful to me since a range of high-tech tests I took for my recent book, Experimental Man, suggest that I have a high risk for heart attack linked in part to even a modestly high level of cholesterol. Normally, a physician might prescribe statins to me, which is safe for 98 percent of the population. But my genes suggest that I have a five-times risk factor of myopathy--a probability that indicates I am high risk, but does not mean I will definitely experience this side effect.

Possibly, the CDI test will provide an answer. I will report my results on this blog.

Scientists have revealed 7,495 specific genetic markers for diseases and other traits tucked into my DNA. But what does it mean to have so much self-knowledge?

I've been asking this question since I was first sequenced in 2001, and since I wrote the book Experimental Man almost a year ago.

The variations in my nucleotides suggest that I'm either at high risk, or not, for traits ranging from heart disease and creativity to heroin addiction and narcolepsy. I'm also a poor metabolizer of the blood thinner warfarin, have a slightly higher IQ, and have both a higher and lower risk of going bald.

Most of these markers -- which detect differences in my DNA from other's DNA that suggest higher or lower risk of disease -- remain preliminary and need to be further researched to validate whether or not they are real for an individual like me or you.

Finding meaning in all of this data will be a major theme of this blog in 2010: to cover the growing field of DNA analysis and interpretation as genetic sequencing companies continue to act on a Moore's Law curve on steroids to bring costs down and to speed up the time it takes to spew out a person's genetic data.

The need to speed up and lower the costs of interpreting all of the As, Ts, Cs, and Ts being churned out should be as much a priority as producing the raw data--even if it is less sexy than the cool machines being made by the likes of Complete Genomics and Pacific Biosciences. In 2010, we'll see hundreds, possibly thousands of complete human genomes sequenced.

Check out all of my 7,495 markers at the website SNPedia--not because they're mine, but because you will one day have all of this data at your fingertips, too. SNPedia has a program called Promethease (this is spelled correctly) that automatically keeps up with the latest studies that link genetic variations with diseases and other traits. Just six months ago, I had a mere 5094 traits annotated by the program--that's 2400 new traits since late June, 2009.

Geneticists tell me that about 50 to 100 of the genetic traits on my list of 7,495 have been tested and found to have some predictive power. The rest remain unverified and are often contradictory (I have a high and low risk for heart attack, baldness, Parkinson's disease, and so forth).

For more about the pluses and minuses of these early days of genetic testing, check out my You 2.0 series.

Another major focus will be reporting on the nascent but growing movement to link genetics--which is only part of what makes you you and me me--with the environment, behavioral sciences, neuroscience, proteomics, epigenetics, and much more.

Producing huge piles of DNA for less money is exciting, but it's time to move to the next step: to discover what all of this means.

For more information, go to The Experimental Man Project website.

A decade ago, genomics-based companies were all the rage. Then one by one nearly all of the high-fliers of that era went bust, were acquired, or restructured (Celera, Orchid, etc). One of the last to hang on has been deCode Genetics of Iceland, a company that has produced a raft of important genetic association studies for a range of diseases and traits, from diabetes to heart disease. In 2007 they launched a direct-to-consumer website, deCodeme, and have been trying to build a genomic diagnostic business.

Now deCode has fallen, too, after several rough years punctuated by the recent financial meltdown and the collapse of the Iceland economy. The company recently filed for chapter 11 bankruptcy protection in the U.S.

But deCode will continue in some form thanks to a group of investors that have funded an enterprise called Saga Investments, apparently named for the collection of "sagas" written centuries ago that tell the tales of the Vikings who settled Iceland in the ninth century. (These epic tales are favorites of deCode CEO and co-founder Kari Stefansson). The investors include original funders of the deCode "saga"--Polaris Venture Partners and Arch Venture.

Details of the deal and what exactly the company will look like after the dust settles is unclear, though I got an email from deCodeme saying that their direct to consumer service will continue uninterrupted.

The lesson here this is that genomics and genome-wide association studies continue to be merely one part of the equation of what goes on inside a human's body. As both science and a business proposition, other crucial factors that make us who we are--and perhaps who we will be in the future in terms of disease--need to be integrated and understood. These include environmental factors, proteomics, epigenetics, microbiomics, and much more.

And yet genomics continues to much of the attention from the media and in one conference after another--and in the continued attention being paid to direct-to-consumer genomics companies that are offering DNA data that is at best just one factor in a person's proclivity for acquiring a common disease.

This near obsession with genomics comes in part because DNA is much simpler and tidier with its neat rows of code than the rest of biology, which is dynamic and variable--and therefore sloppier to get a handle on and to understand. For more on this, check out my recent article on bio-computational wiz Eric Schadt and complex biology in the New York Times.

As deCode's demise (or restructuring?) suggests, genomics alone can't provide the answers we are seeking in personalized and predictive healthcare--though we can be appreciative of the contributions made by deCode researchers in the past and, hopefully--as the saga continues--in the future.