Archive for December, 2010


Discover Magazine recently posted an interesting interview with Leroy Hood, who invented the automated DNA sequencer (among other things) and was a key player in the Human Genome Project. He has since founded the Institute for Systems Biology, which is a non-profit research center focused on understanding how genes and proteins function in complete biological systems.  

There is a lot of provocative stuff here, but we’ll just quote one of Dr. Hood’s more interesting predictions. When asked about his claim that medicine is on the edge of an ‘information revolution’:

In less than a decade, each of us will be surrounded by a virtual cloud of billions of points of medical data. Genome sequencing will cost only a few hundred dollars, so that will become a part of the medical record of each individual. A fraction of a drop of blood will be used to measure 2,500 blood proteins that assess the possibility of disease in each of your 50 major organs. Medicine will be personalized and preventive: Your genome might predict that you have an 80 percent chance of breast cancer by the time you are 50, but if you take a preventive drug starting when you are 40, the chance will drop to 2 percent. We will have the computational tools to connect all this information so we can gain enormous insights into health and disease and fashion an unbelievably predictive medicine of the future.

What do you think? Where will we be in 10 years? 20 years?

The genetics of HIV resistance

The International HIV Controllers Study is an international team of scientists dedicated to understanding HIV “controllers,” which are individuals that are infected with HIV but are somehow able to resist the virus without any medication. A new study by the group in Science finds that “controllers” share particular gene variants that appear to play an important role in regulating HIV resistance. From a summary in Discover Magazine:

After looking at over 1.3 million points around their genomes, the team found that just 313 separate the controllers from the other recruits. Amazingly, every single one of these variants sits within a specific part of our sixth chromosome, among a set of genes called class I HLA genes. The proteins they produce form part of the internal security checks that defend us from infections. They grab small pieces of other proteins from inside our cells and display them on the outside, waving them under the noses of passing T-cells. If the T-cells recognise these pieces as parts of bacteria, viruses or other foreign invaders, they tell the infected cell to self-destruct and set the immune system on red alert.

All of this depends on a single groove in the HLA proteins. This is the bit that embraces the pieces of other proteins and displays them so prominently to the immune system. If this groove isn’t structured correctly, our defenders don’t get an advanced warning about threats.

True enough, the team found that the groove of a single protein called HLA-B is especially important. At five positions in the groove, the HIV controllers have different amino acids than those whose disease progresses normally. These five amino acids aren’t the only things separating the controllers from the others, but they have a major impact.

Obviously, there’s still a lot of work to be done here, but these results are promising.

References

The International HIV Controllers Study (2010). The major genetic determinants of HIV-1 control affect HLA Class 1 peptide presentation. Science 330: 1551-1557.

Just as we are trying to digest the implications of the draft Neandertal genome (which, by the way, suggests that Neandertals contributed up to 4% of their genomes to non-African modern human populations), a new study published in Nature by David Reich (Harvard Med School) and colleagues reports the genome of an unclassified (all we have is a pinky bone and an isolated tooth) ca. 40,000-year-old hominin from Denisova Cave in southern Siberia. The genome appears distinct both from that of European Neandertals and contemporary modern humans. However, there is evidence that early modern human populations interbred with these “Denisovans” and, in fact, modern Melanesian populations (represented in the paper by genomes from Papua New Guinea and Bougainville) appear to have received approximately 4% of their genomes from this extinct group of humans.

So, taken together, these genetic data seem to indicate that modern Melanesians derive up to 8% of their genomes (4% Neandertal and 4% “Denisovan”) from now-extinct human groups. Pretty cool stuff.   

Check out the summaries from Science News and Nature for more information, and our keynote speaker John Hawks’s weblog provides very detailed commentary on these exciting findings.

UPDATE 12.23.11. Dr. Hawks is also interviewed in an NPR story from Dec. 23 that summarizes the implications of these data.  

References

Green, R.E., et al. (2010). A draft sequence of the Neandertal genome. Science 328: 710-722.

Krause, J., et al. (2010). The complete mitochrondrial DNA genome of an unknown hominin from southern Siberia. Nature 464: 894-897.

Reich, D., et al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060.

Here is an interesting video conversation with Alondra Nelson, one of our panelists for this year’s event, about how people construct their racial identity in the age of genomics.

Not exactly, but a new study by Cary Frydman and colleagues published in the Proceedings of the Royal Society examine variation in MAOA, DRD4, and 5-HTT, which are genes that affect either the breakdown or transport of the neurotransmitters serotonin and dopamine (both of which can affect things like aggression, risk-taking and risk aversion, and anxiety). As laid out in the summary of the study in the journal Nature, Frydman and colleagues found that individuals with a particular variant of the MAOA gene were more likely to make better finanical decisions in risky circumstances.

It would be interesting to screen World Series of Poker winners for MAOA gene variants…

References

Frydman, C., Camerer, C., Bossaerts, P., Rangel, A. (in press). MAOA-L carriers are better at making optimal financial decisions under risk. Proceedings of the the Royal Society (Biological Sciences).

Last month, Diane Rehm of NPR had an interesting dicussion on DNA sequencing and personal genomics (you can listen to the 51-minute show in its entirety here). The completion of the human genome project in 2003 held the promise of using an individual’s genetic information to optimize their treatment. One example that the show uses is that of Google co-founder Sergey Brin, who has discovered that he possesses a mutation in his LRRK2 gene that may increase the likelihood of him developing Parkinson’s disease later in life. Nevertheless, the program’s guests demonstrate that there are still significant hurdles to truly effective genetic-based “personalized medicine.” A couple of interesting points from the show:

1. The cost of genome sequencing has declined greatly over the past decade or so. Some companies, like 23andMe (which was founded by Brin’s wife Anne Wojcicki) will sequence parts of your genome for about $500. For those of you interested in getting your entire genome (all 3 billion base pairs) sequenced, you can, with the consent of your doctor, send samples to companies like Illumina for the bargain price of about $20,000 (if you think that’s a bit pricey, consider that a decade ago it would have cost you about $1,000,000).

2. One of the guests, Dr. Arthur Caplan, provides examples of how people can react to genetic information. The most striking is the case where a father wanted to have his 13-year-old daughter tested for mutations associated with breast cancer risk (the family had a history of the disease). The father stated that if his daughter tested positive for one or more of the mutations, he would have her breast buds surgically removed to make sure that she did not suffer the same fate as other family members (Dr. Caplan does not tell us what ultimately happened with this case). One of the points that Dr. Caplan makes with this and other examples is that, although genetic screening can provide useful information, external environmental factors interact with genes in very complex ways, which currently makes it very difficult to assess an individual’s chances of developing conditions like cancer based simply on the presence or absence of particular genetic mutations (but see Personalized medicine in 10 years?).

3. All three of the guests discuss the issues surrounding genetic privacy. Once you submit samples for genetic sequencing, how can you be sure that your information will be kept private? If it is not kept private, what can it be used for? The importance of this issue is revealed by the signing of the Genetic Information Non-discrimination Act (GINA) by president Bush in 2008, which prevents discrimination based on genetic information when it comes to insurance and/or employment.  

Check out the show and hit us up with your comments: Would you want your genome to be publicly available? Would you even want to know what your genome looked like? If you had the information, what would you do with it?

Participate in our poll:

The Department of Anthropology at UNCG welcomes you to our Harriet-Elliott lecture series blog! We are pleased to announce the 2011 theme, “Our genetic past and genomic future.”

Our purpose in creating this blog is threefold: first, we want to provide students and the public with an archive of current issues pertaining to human genetic evolution and, importantly, its applications to everyday life–from biomedical practice to issues of social identity. Second, we hope you will use this blog as an opportunity to join in on the conversation about these topics. Finally, we will be asking our users—all of you—to supply questions for us to present to our panelists and keynote speaker on the day of the event.  

So, first thing’s first, a little sneak peak on the event…

1. It will be held on Wednesday, March 23, 2011 and is composed of a panel discussion followed by a keynote lecture.

2. Our panel discussion will run from 3-5pm in the main auditorium at the Elliot University Center on UNCG’s campus (see the lecture series main page for information on our panelists). This roundtable-style discussion will focus on the scientific study of human origins, evolution, and variability and the application of this knowledge to everyday life.

3. Our keynote address will run from 7-9pm in the Mead Auditorium in the Sullivan Science Building (Room 101), also on UNCG’s campus. Our keynote speaker is John Hawks, an Associate Professor of biological anthropology at the University of Wisconsin-Madison. The lecture topic is pending, but will focus on human genetic evolution within the past 30,000 years. Dr. Hawks hosts a well-known paleoanthropology blog himself, and we encourage you to check it out here.

Ok, so now that you know what the event is all about, check back with us as we begin our conversation on, “Our genetic past and genomic future”…