Tag Archive: DNA


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…

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?

Amelia Earhart and her navigator, Fred Noonan, disappeared in 1937 during her attempt to become the first female to fly around the world. Flying near Howland Island in the Pacific, communication with her plane was lost. Finally, after an intense search by the U.S. government, she and Noonan were officially pronounced dead  on January 5, 1939. Since then, there has been speculation about whether they actually died in a crash at sea, or survived for some time on a deserted island.

Amelia Earhart disappeared in 1937. Image from Discover Magazine.

Two years ago, the International Group for Historic Aircraft Recovery found bone fragments on Nikumaroro Island that may be part of Earhart’s finger. However, a dead sea turtle was found nearby, raising the reasonable possibility that the bone fragments also belong to the turtle. Apparently the bone fragments are too small to identify just by looking at them, so researchers want to extract DNA from the bone to compare to Earhart’s. How do we get DNA from her, you may ask? From National Geographic:

The new Earhart DNA project will be headed by Dongya Yang, a genetic archaeologist at Simon Fraser University in Burnaby, Canada. Yang will examine Earhart’s letters and attempt to extract DNA from mouth-lining cells that would have been in the saliva she used to seal the envelopes. Mining a trove of more than 400 correspondences between Earhart and various people, the researchers have chosen four letters to family—deemed the most likely to have been written and sealed by Earhart herself—for analysis.

Yang is aiming to gather two kinds of DNA from the letters: mitochondrial DNA, which children inherit from their mothers only, and nuclear DNA, which contains the bulk of a person’s genetic information and is housed in each human cell’s nucleus. If both DNA types can be obtained, the team says it can create a genetic profile of Earhart that is complete enough to positively identify any potential remains.

If the project proceeds smoothly, Yang said, the team could have a genetic profile for Earhart in “a couple months.”

Let’s see what happens…

No, we’re not talking about brooms here…

When a mutation arises that confers some sort of advantage, those individuals with the mutation have more kids than those without it. Over time, of course, the mutated gene will become more prevalent in a population (this is simply natural selection).  In some cases, other pieces of DNA will hitch-hike along with the advantageous mutant gene because they are linked (i.e., close-by) on the same chromosome and will thus also increase in frequency. A SELECTIVE SWEEP occurs when the positively selected gene and all its neighbors (called a haplotype) become the only variant in a population. So, the result of a selective sweep is a reduction in overall genetic diversity in that region of the genome. 

Selective sweeps have certainly occurred in recent human evolution: for example, the genes (and associated DNA neighbors) for skin pigmentation and lactose tolerance appear to have arisen among modern human populations in a manner consistent with a selective sweep.     

According to a newly published study in Science, selective sweeps were considered to be a relatively common occurrence among humans. However, the new research suggests that this is not so. From a summary in ScienceNews:

Scientists have favored a model of evolution in which beneficial gene mutations quickly and dramatically sweep through a population due to the evolutionary advantages they confer. Such mutations would become nearly universal in a population. But this selective sweep model may not be accurate for humans, a new study indicates. Human evolution likely followed a more subtle and complicated path, say population geneticists Molly Przeworski of the University of Chicago and Guy Sella of Hebrew University of Jerusalem and colleagues.

It may have been difficult for selective sweeps to take hold in humans because of demographics…[p]eople are scattered throughout the globe, so a beneficial mutation would have a long way to spread. Such a mutation would have to have dramatic effects on evolutionary fitness to go global.

References

Hernandez, R.D., et al. (2011). Classic selective sweeps were rare in recent human evolution. Science 331: 920-924.

Laron syndrome (also referred to as Growth Hormone Insensitivity Syndrome, Pituitary Dwarfism II, and Growth Hormone Receptor Deficiency) is an autosomal recessive disorder (i.e., you have to have two copies of the mutated gene–one from mom and one from dad) caused by a mutation on chromosome 5 that results in an individual being non-responsive to growth hormone. Those that are non-responsive fail to produce insulin-like growth factor I, which ultimately leads to short stature.

Jaime Guevara-Aguirre stands with some of the people who took part in his study of Laron syndrome in Ecuador. Photo credit: Valter Longo.

NPR reports on a study in Ecuador that shows that this mutation, while causing Laron syndrome,  seems to prevent diseases such as diabetes and cancer (diseases typically, though not exclusively, associated with ageing). What is super interesting is that a mutation similar to Laron syndrome is known to extend lifespans in other organisms like yeast and worms. From the interview with researcher Valter Longo:

The mutation seems to prevent diabetes by allowing people to get by on very low levels of insulin, Longo says. It wards off cancer by reducing DNA damage in cells, and helping to eliminate abnormal cells. You might expect all this protection would allow the small people in Ecuador to live longer than their taller relatives, Longo says. But that’s not what he found. “The majority of them die of strange causes,” he says, including alcohol abuse and accidents. These are things that are preventable and not caused by a disease, Longo says. Subtract these deaths, he says, and it looks like people with Laron syndrome really would live longer than their relatives. Longo says his study suggests that a whole group of people might be able to lower their risk of cancer and diabetes if they could lower their levels of growth hormone, or change the body’s response to it. The benefit would probably be greatest in people who have unusually high levels of the hormone, he says.

Connecting to a previous post on the blog, scientists also suggest that people with pituitary tumors (a similar situation to these growth hormone abnormalities) may also be at greater risk for cancer (see Irish giants and DNA)

Based on archaeology, linguistics, and, most recently, genetics, it is traditionally thought that Polynesia was inhabited by mariners originating in Taiwan or south China beginning about 3,500 years ago (in fact, our departmental reading, Relethford’s “Reflections of Our Past,” has an interesting chapter on this issue).

Polynesia is made up of hundreds of islands. Figure from acmecompany.com

A recently published study modifies this story somewhat. This study looked at the largest mtDNA (which is only passed through the maternal line) sample to date in order to determine which populations were most similar to modern Polynesians. From an interview with Martin Richards, one of the members of the research team, in the ScienceDaily summary:

“Most previous studies looked at a small piece of mtDNA, but for this research we studied 157 complete mitochondrial genomes in addition to smaller samples from over 4,750 people from across Southeast Asia and Polynesia. We also reworked our dating techniques to significantly reduce the margin of error. This means we can be confident that the Polynesian population — at least on the female side — came from people who arrived in the Bismarck Archipelago of Papua New Guinea thousands of years before the supposed migration from Taiwan took place.”

 What is especially interesting here is that the linguistic and archaeological evidence still strongly suggest some sort of connection with Taiwan. For one, modern Polynesian languages are thought to belong to the Austronesian language family, which is a group of languages spoken from Madagascar to Easter Island, but differ from the native languages of Australia and New Guinea. Archaeologists maintain that the earliest Polynesian pottery (called the “Lapita Culture”) shares many similarities to earlier pottery found on Taiwan and in south China. So, how do we reconcile these findings with the genetics? Again, Dr. Richards:

“Although our results throw out the likelihood of any maternal ancestry in Taiwan for the Polynesians, they don’t preclude the possibility of a Taiwanese linguistic or cultural influence on the Bismarck Archipelago at that time,” explains Professor Richards. “In fact, some minor mitochondrial lineages back up this idea. It seems likely there was a ‘voyaging corridor’ between the islands of Southeast Asia and the Bismarck Archipelago carrying maritime traders who brought their language and artefacts and perhaps helped to create the impetus for the migration into the Pacific.

“Our study of the mtDNA evidence shows the interactions between the islands of Southeast Asia and the Pacific was far more complex than previous accounts tended to suggest and it paves the way for new theories of the spread of Austronesian languages.”

This implies that later populations were moving through the area with their language and culture, but they were not necessarily bringing their genes (i.e., interbreeding), at least on the female side.

References

Soares, P., et al. Ancient Voyaging and Polynesian Origins. American Journal of Human Genetics 88: 239-247.

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.

See our keynote speaker Dr. John Hawks talking about rapid genetic evolution among modern humans (“Rapid evolution: Can mutations explore historic events?”) at the Council for the Advancement of Science Writing.

For those of you who don’t know, all students in UNCG’s 300+ level anthropology courses are reading a book and several articles in preparation for the Harriet-Elliott events. One of these readings, John Relethford’s “Reflections of Our Past,” has a chapter on the peopling of the Americas. Traditionally, most scholars contend that the first humans entered the Americas about 15,000 years ago (or maybe a bit earlier) and came from Asia via the Bering Land Bridge that then existed between modern-day Alaska and eastern Siberia.

Possible migration routes for the first colonization of the Americas

According to Relethford, who was writing in 2003, the genetics strongly supports an origin of Native Americans somewhere in Asia:

1. Contemporary Native Americans and northern Asians tend to have high frequencies of the Diego blood group allele DI*A (this allele is relatively rare among other populations).

2. Based on genetic distance analysis (which takes into account the relative frequency of many different genes simultaneously to look at overall genetic difference/similarity), contemporary northeast Asian populations are most genetically similar to Native Americans.

3. Native Americans share a number of mitochondrial DNA haplotypes (sections of DNA that are inherited together as a single unit) with Asian populations (some from Siberia, some from Japan and Korea).

Relethford also discusses another interesting question: how many migrations occurred? Was it a single migration event? Two? Three? More? The genetic data seem to suggest at least two separate migration events, if not more.

Finally, when did the first colonization of the Americas take place? Here, Relethford shows that the genetic data are pretty cloudy because any estimate based on a genetic clock will be affected by population size and the overprinting of multiple migrations. Indeed, Relethford suspects that “the final determination of the age of the first Americans will be settled by archaeology and not by genetics.”

Dr. Alondra Nelson, one of the panelists for our event, was recently interviewed by Radio Boston in connection with the opening of the exhibit RACE: Are We So Different? at the Museum of Science in Boston. The exhibit has been touring the US since 2007 and will be at the Durham Museum of Life and Science from October 8, 2011 through January 22, 2012.  This exhibit is an outgrowth of the American Anthropological Association’s RACE Project, which provides an integrated look at the history, biology, and culture of the race concept. A couple of interesting points are made both by Dr. Nelson and Dr. Alan Goodman (Hampshire College and past president of the AAA):

1. Darwinian evolution, with its focus on change over time, is antithetical to the popular, modern conception of “race,” which is all about sorting people into 2, 3, 4, 5 (or whatever) unchanging types.

2.  Modern genetics has shown us that modern humans are, on average, about 99.9% genetically identical. There is a lot of interesting and important information that can be revealed in that 0.1% difference, such as ancestry, geography, or adaptation. But, what is fascinating is that many people choose to focus only on that 0.1% difference to the near exclusion of that 99.9% similarity.   

3. As a species, we are pretty good at categorizing things (can you imagine how difficult it would be to negotiate the world without that ability?). What we tend to do with human categorization, however, is to mesh those categories with the creation and upkeep of power relations between different groups (be it by “race,” ethnicity, socio-economic status, or some combination of these). People in power, of course, do not want to relinquish that power and so, in order to legitimize their relationships with other groups, they often resort to biology (something that is presumably unchangeable) rather than human institutions (which are presumably changeable).

4. The rise of DNA ancestry tests have, in many ways, complicated how people think about who they are and where they come from. Dr. Nelson notes that when a DNA ancestry test does not match up with how an individual construes their own social identity, the scientific tests often do not transform the way an individual thinks about themself. 

5. Science does not exist in a vacuum. Just like anyone else, scientists can bring their own social, historical, and political biases to the lab.

For more on this issue, see Dr. Nelson’s video interview on the Race in the age of genomics post on the blog.