Tag Archive: biotech


As a story in the New York Times reports, some people respond well to aerobic exercise, while others seem to benefit less or not at all. There are studies that show there is a genetic component to this: various exercise traits (and the drive to exercise at all) do certainly run in families. A new study has scanned to genomes of 473 individuals subjected to the same 5-month exercise regime and found that particular SNPs (pronounced “snips;” we’ve talked about these before, see this post) are associated with a robust response to exercise. From the New York Times story:

The researchers looked at 324,611 individual snippets over all. Each of the volunteers had already completed a carefully supervised five-month exercise program, during which participants pedaled stationary bicycles three times a week, at controlled and identical intensities. Some wound up much fitter, as determined by the increase in the amount of oxygen their bodies consumed during intense exercise, a measure called maximal oxygen capacity, or VO2 max. In others, VO2 max had barely budged. No obvious, consistent differences in age, gender, body mass or commitment marked those who responded well and those who continued to huff and struggle during their workouts, even after five months.

But there was a divergence in their genomes. The researchers identified 21 specific SNPs, out of the more than 300,000 examined, that differed consistently between the two groups. SNPs come in pairs, since each of us receives one paternal copy and one maternal copy. So there were 42 different individual versions of the 21 SNPs. Those exercisers who had 19 or more of these SNPs improved their cardiorespiratory fitness three times as much as those who had nine or fewer.

One interesting question that is raised by this research is: if one finds that they do not have the advantageous SNPs, will they simply not try to exercise at all?

Our keynote speaker John Hawks describes this study and harps on the New York Times reporting on his blog.

References

Bouchard, C., et al. Genomic predictors of maximal oxygen uptake response to standardized exercise training programs. Journal of Applied Physiology in press.

Researchers at the Royal Institute of Technology in Stockholm have now set the world record for number of simultaneous DNA sequence analyses: 5,000. Now, we’re not talking about whole-genome sequencing here; they’re just sequencing parts of an individual’s DNA sequence, but it’s impressive nonetheless. From the summary in ScienceDaily:

“Today the great majority of samples are run ten at a time. This yields a cost of SEK 10,000 (USD $1,600) per sample. We have run 5,000 samples at the same time at the same cost, that is, SEK 100,000. This computes to SEK 20 (USD $3) per sample,” says Peter Savolainen.

He points out several areas where his and his colleagues’ new method can have a great impact. One of them is cancer research, where there is a great need to scan numerous cell samples from many individuals. This is to see which cells and genes are involved in the cancer.

“Another field where our method can be of huge importance is in organ transplants. Many DNA analyses are needed to create a database for matching organ donors with transplant recipients. This will be of major importance to DNA research,” says Peter Savolainen.

Pretty cool stuff…

Ok, let’s start off with the basics:

Parkinson’s disease is a neurological disorder where nerve cells that make dopamine are destroyed. Dopamine is an important neurotransmitter and without it, nerve cells are unable to properly send messages to other parts of the body. Eventually, the destruction of dopamine-producing cells leads to a loss of muscle function that gets worse over time. The typical symptoms of Parkinson’s are shaking and difficulty with walking, movement, and muscle coordination.  Unfortunately, not a lot is known about why these nerve cells waste away in the first place.

In gene therapy, a gene variant is used to alter the function of a cell or an organ. The way that genes are transferred into cells is pretty interesting: the gene is put into an inert virus, which is then injected into the target cell to deliver the gene.

Now, a new large-scale study suggests that a type of gene therapy (called NLX-P101) may be able to improve Parkinson’s symptoms. The gene that was targeted is called GAD (stands for glutamic acid decarboxylase). This gene produces a chemical called GABA (stands for Gamma-aminobutyric acid), which is a neurotransmitter than inhibits the excessive firing of neurons seen among Parkinson’s patients. From an interview in ScienceDaily with one of the researchers, Dr. Matthew During:

“In Parkinson’s disease, not only do patients lose many dopamine-producing brain cells, but they also develop substantial reductions in the activity and amount of GABA in their brains. This causes a dysfunction in brain circuitry responsible for coordinating movement,” explains Dr. During.

So, what they’ve done is inject a fully-functioning GAD gene into the brains of Parkinson’s patients. Those that were injected showed substantial improvement compared to individuals that did not receive the treatment.  

References

LeWitt, P.A. et al. (2011). AAV2-GAD gene therapy for advanced Parkinson’s disease: a double-blind, sham-surgery controlled, randomised trial. Lancet Neurology in press.

The FDA held a meeting on March 8th and 9th about direct-to-consumer (DTC) genetic testing. According to the FDA’s executive summary, DTC is:

…clinical genetic tests that are marketed directly to consumers (DTC clinical genetic tests), where a consumer can order tests and receive test results without the involvement of a clinician.

As Dan Vorhaus of the Genomics Law Report describes it, the main issue of the meeting was to decide how (and if) the FDA will regulate DTC genetic tests. There were really two perspectives:

1. Those who oppose DTC genetic testing worry that incorrect or misinterpreted tests could produce harmful outcomes, and they even questioned whether anything of value is actually gained from the tests in the first place.

2. Those who support DTC genetic testing argue that the information empowered patients to explore their “genetic selves” without any ill effects.

The meeting will sum up with recommendations for the FDA from the Molecular and Clinical Genetics Panel (MCGP), which is an FDA committee that “reviews and evaluates data concerning the safety and effectiveness of marketed and investigational in vitro devices for use in clinical laboratory medicine including clinical and molecular genetics and makes appropriate recommendations to the Commissioner of Food and Drugs.” Vorhaus suspects that the MCGP will recommend:

that clinical (as defined by the FDA, which is itself a separate issue) direct-to-consumer genetic testing, when offered without a requirement that a clinician participate in the ordering, receipt and interpretation of the test, be removed from the marketplace. At least for the time being.

Our keynote speaker, John Hawks, blogs about this issue and considers himself a “genetic libertarian.” He describes his position:

I believe that I have a fundamental right to my own biological information. What I mean is that, if anybody has biological information about me, I should be able to access and use it. Additionally, I think it is immoral for anyone to charge me excessive rates to access my own information. So that’s where I’m coming from. I’m a genetic libertarian. 

For more info see the FDA’s website for the event.

What do you think about DTC genetic testing? Do you think it’s a good idea? How much regulation (if any) should be provided by government agencies?

Continuing with our exploration of the vignettes in Science’s 10th anniversary celebration of the human genome project, we run across an interview with Eric Green, who just recently became the director of the National Human Genome Research Institute. As with all of these pieces, there’s lots of interesting stuff here. A couple of highlights from the interview:

Q: Why did you set 2020 for when genomics will begin affecting health care? Why is it going to take so long?

Eric Green: When we talk to people who have a historic view of medical advances, they have pointed out that truly changing medical care takes a substantial amount of time. Often decades. And I’ve grown sensitive to the criticisms of genomics by some who believe that since 2003, when the genome project ended, we haven’t sufficiently improved human health 7 years later. So part of the reason is just to be a little bit more realistic and a little more cautious.  

Q: Where are you hoping we will be by 2020?

Eric Green: I’m hoping that by 2020 we will have this incredible mountain of information about how genetic variants play a role in disease, that it will just provide an entirely new venue for really thinking about how to both predict disease, maybe prevent disease, and certainly treat disease.

Notice that Dr. Green seems pretty confident in our ability to use genomics to predict and treat disease, but puts a “maybe” in front of prevention.

References

Kaiser, J., Green, E. (2011). The genome project: what will it do as a teenager? Science 331: 660.

We’ve talked about SNPs (single nucleotide polymorphisms) before on the blog. These are mutations in single bases along the DNA molecule. Because it has been found that some SNPs are associated with particular diseases, geneticists scan genomes to identify SNPs that may either explain a disease or at least identify individuals that may be at risk for a disease. As described in a recent report in Reuters, one unintended consequence of these genome scans has been the identification of incest. As many of you know, the development of abnormalities in offspring is more common in incestuous (i.e., mating with a close relative–how “close” is “close” varies by culture)  matings. Because closely related individuals share a greater proportion of their genes, the chances are greater that deleterious recessive genes (genes that are only expressed when an individual has two copies, one from either parent) will pair up in their offspring and cause problems.

Although this new information of course has important legal implications, in most cases the physicians were already aware of the incestuous relationship.

References

Schaaf, C.P., Scott, D.A., Wiszniewska, J., Beaudet, A.L. (2011). Identification of incestuous parental relationships by SNP-based DNA microarrays. Lancet 377: 555-556.

Can (and should) genes be private?

Matthew Herper of Forbes.com has posted an interview with Misha Angrist, who is the author of “Here is a Human Being: At the Dawn of Personal Genomics.” The jumping off point here is that Angrist participated in an experiment where not only was his genome sequenced, but it was made public. From there, the interview touches on three things:

1. It’s really cool to be able to see your own sequence data right in front of you.

2.  In the not-too-distant future, everyone is going to go through full-genome sequencing.

3. Can, and should, genome data be kept private and anonymous?

Angrist also provides a guest post on the blog Genetic Future in response to a paper in Trends in Genetics. The paper outlines the arguments for, and against, returning genetic data to research participants. The authors take the view that if (and only if) something “life threatening and actionable” is found within an individual’s genome, researchers have the moral obligation to say something but full disclosure is not recommended because it puts full sequence data in the hands of research participants. You can read Angrist’s guest post, but his stance is revealed by a great quote from the Forbes.com interview: “Genetics is too important to be left to geneticists.”

Do you think that complete sequencing data should be fully disclosed to research participants? Would you make your genome public? For more discussion and to participate in a poll, check out The personal genome project, genetic privacy, personal medicine on the blog.

References

Angrist, M. (2010). Here is a Human Being: At the Dawn of Personal Genomics. Harper: New York.

Brendenoord, A.L., Kroes, H.Y., Cuppen, C., Parker, M., van Delden, J.J.M. (2011). Disclosure of individual genetic data to research participants: the debate reconsidered. Trends in Genetics 27: 41-47.

Genetic screening for diseases

What would you do if a genetic screening indicated that you had a 70% chance of developing Alzheimer’s? Well, a recent study published in the New England Journal of Medicine suggests that people really don’t seem to care. From a summary in the New York Times:

…the Scripps Translational Science Institute followed more than 2,000 people who had a genomewide scan by the Navigenics company. After providing saliva, they were given estimates of their genetic risk for more than 20 different conditions, including obesity, diabetes, rheumatoid arthritis, several forms of cancer, multiple sclerosis and Alzheimer’s. About six months after getting the test results, delivered in a 90-page report, the typical person’s level of psychological anxiety was no higher than it had been before taking the test.

Although they were offered sessions, at no cost, with genetic counselors who could interpret the results and allay their anxieties, only 10 percent of the people bothered to take advantage of the opportunity. They apparently didn’t feel overwhelmed by the information, and it didn’t seem to cause much rash behavior, either.

Would you want to be screened for diseases? What would you do with the information once you had it?

References

Bloss, C.S., Schorck, N.J., Topol, E.J. (2011). Effect of direct-to-consumer genomewide profiling to assess disease risk. New England Journal of Medicine

Gene doping

Doping among elite athletes may have reached a new level…

As laid out by Discovery News, some athletes are trying to “turn on molecular switches inside the body’s own DNA to produce more oxygen-carrying blood or creating bigger muscle cells.” In essence, people are trying to make the genes that code for oxygen carrying capacity or muscle cell development work harder and faster. Scientists are in the process of developing a test for this sort of thing that may be in use before the 2012 Olympic Games in London.

One of the more interesting aspects of this story is the potential side effects. For example, mice that were genetically modified to produce more red blood cells (whose major job is to carry oxygen throughout the body) actually died of stroke because too many cells were being created. In another example, experts suspect that modifying the genes that code for muscle cell creation may only work on part of the body–you could have a super buff right arm and a normal left arm, for instance.

A team of researchers have scanned genes that are known to impact hair color and found that analyzing an individual’s DNA can predict their hair color with a high degree of accuracy. There are upwards of a dozen or so genes that may contribute to hair color in some way, and mutations that change a single nucleotide (Single Nucleotide Polymorphisms, or SNPs) in a gene are largely responsible for color and shade differences. From a summary in Wired Science:

To see if hair color could be predicted using 45 SNPs from 13 genes, Kayser and his team sampled DNA from 385 Polish volunteers and had dermatologists record their hair color. Their testing singled out 13 SNPs on 11 genes that could predict red and black hair colors with about 90 percent accuracy, as well as blond and brown colors with better than 80 percent accuracy.

As if you needed another excuse not to leave your DNA at a crime scene…

One of the genes examined in this study was MC1R, mutations in which have been linked specifically to red hair. Interestingly, the red hair genotype has been identified in some Neandertal individuals (although the specific mutation is different from that seen among modern humans). 

References

Branicki, W., Liu, F., van Duijn, K., Draus-Barini, J., Pośpiech, E., Walsh, S., Kupiec, T., Wojas-Pelc, A., Kayser, M. (2011). Model-based prediction of human hair color using DNA variants. Human Genetics.

Lalueza-Fox, C., Römpler, H., Caramelli, D., Stäubert, C., Catalano, G., Hughes, D., Rohland, N., Pilli, E., Longo, L., Condemi, S., de la Rasilla, M., Fortea, J., Rosas, A., Stoneking, M., Schöneberg, T., Bertranpetit, J., Hofreiter, M. (2007). A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318: 1453-1455.