It has been known for decades that having the gum disease periodontitis increases a person’s risk for heart attack (free registration required), stroke and other forms of cardiovascular disease. Research suggests that the link is due to inflammation in the gums causing an immune reaction throughout the entire body. That can increase blood pressure and encourage the accumulation of atherosclerotic plaques in the arteries.

Now researchers have drawn a genetic link between periodontitis and heart disease as well. It turns out that variations in a region of chromosome 9 that have already been associated with heart disease also influence a person’s chances of developing periodontitis.

The specific genetic marker identified by the study is not part of the 23andMe Personal Genome Service. But another marker that has also been linked to heart disease and lies in the same chromosomal neighborhood is described in the Heart Attack research report.

Arne Schäfer of the Institute for Clinical Molecular Biology in Kiel, Germany presented the research in Vienna, Austria, last week at the annual meeting of the European Society of Human Genetics. He and his colleagues found that people with a marker for increased cardiovascular risk in a stretch of DNA known as 9p21 were more likely to have gum disease as well.

The high-risk version of the marker increased a person’s chances of having generalized aggressive periodontitis by 1.99 times, and localized aggressive periodontitis 1.72 times. Aggressive periodontitis generally strikes early in life and progresses rapidly, leading to tooth loss as early as age 20.

The 9p21 region of chromosome 9 contains several genes involved in suppressing the proliferation of cells. In a recent PLoS Genetics paper the researchers suggest that the variation they studied somehow affects the function of one of these genes.

Rather than superceding previous findings linking the effects of periodontal inflammation itself on heart disease, the researchers said, their study provides valuable additional information that could help unravel the connection between the two conditions.

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Every family has its legends. Maybe it’s a story about how they’re descended from a passenger on the Mayflower, a Confederate soldier or Charlemagne.

Of all the classic American family legends, stories of a Native American ancestor are among of the most common. Many times there’s a well-documented link to a Native forbear: Two First Ladies (Edith Wilson and Nancy Reagan) and one Duchess of Windsor (Wallis Simpson) are proven descendants of Pocahontas.

Other times, the evidence amounts to little more than vague tales about a rugged pioneer and a Cherokee princess. (Learn what’s wrong with that scenario here.)

Now 23andMe customers who are curious about whether they may have Native American ancestors can look for evidence of it in their genes. The Native American Ancestry Finder uses some existing 23andMe features — Ancestry Painting, Maternal Line and Paternal Line — to look for genetic signatures that are likely to have come from a Native American ancestor.

The Maternal Line and Paternal Line elements of the Finder are pretty straightforward; certain mitochondrial DNA (maternal) and Y chromosome (paternal) haplogroups are often found among Native Americans. These include mitochondrial haplogroups A2, B2, C1, D1 and X2a — which are found exclusively among Native Americans. People in some other branches of the A, B, C and D haplogroups may also have Native American ancestry, but their maternal lines could also trace to Asia. On the paternal side, only Q3 is exclusive to Native Americans, though anyone with a Y chromosome in the C, C3 or Q haplogroup could conceivably have Native American forbears.

A Native American’s Ancestry Painting.

The part of the Finder that uses Ancestry Painting to find evidence for Native American forbears is a little more complicated. It relies on the fact that people of full Native American descent have Ancestry Paintings that are consistently about 75% orange (Asian) and 25% blue (European). This is due to the fact that Native Americans are ultimately descended from populations that lived in northern and central Asia about 15,000 to 20,000 years ago, and the fact that those regions are intermediate between the reference populations that Ancestry Painting classifies as fully Asian (Japanese and Chinese) and fully European (European-Americans living in Utah).

Then the Finder compares your Ancestry Painting proportions to a table that contains the results of an extensive series of simulations that we performed to determine what would happen to that three-to-one Asian/European proportion over the generations if a Native American and a partner of all-European descent had a child who then reproduced with another all-European partner, and so on. We did the same analysis for a Native American marrying into an all-Asian pedigree. Unfortunately, partly due to inadequate sampling of Africa’s genetic diversity, this method cannot yet establish Native American ancestry for African Americans.

We found that it takes at least five generations after the appearance of a single Native American in an otherwise all- European pedigree for the percentage of Asian (orange) DNA to reach zero. In an otherwise all-Asian pedigree that process is much faster — in two generations, the grandchild of that single Native American can have no trace of European in his or her Ancestry Painting.

There are, of course, plenty of Eurasian populations that also have blue-and-orange Ancestry Paintings. So the Native American Ancestry Finder performs a second analysis that can distinguish people of South Asian, Central Asian, Middle Eastern and Ashkenazi descent from those with Native American ancestry. Unfortunately, there is still some uncertainty when it comes to distinguishing people with Native American ancestry.

It’s still a work in progress — that’s what Labs are all about. But we hope customers will help us by trying out the Native American Ancestry Finder and letting us know if anything doesn’t mesh with what they know about their genealogy. You can also contribute by taking the “Where Are You From?” survey in 23andWe.

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We’ve set out to build the world’s largest online PD genetics community, and we’re thrilled to report that more than 2,000 people have enrolled since the initiative was launched last month. Owing to tremendous support from The Parkinson’s Institute and Clinical Center and The Michael J. Fox Foundation, their networks of patients have responded overwhelmingly. Assembling this many participants for traditional research studies usually takes months, if not years, to accomplish — by harnessing the power of the web and the enthusiasm of individuals, 23andMe can dramatically change the pace of research.

This puts us well on the way to our goal of enabling 10,000 individuals to help advance research into the genetics and other aspects of the condition. With this number of participants, we hope to be able to make discoveries about aspects of the causes, progression and treatment of Parkinson’s that smaller studies simply haven’t had the power to detect.

As members of the community, PD patients receive the the 23andMe Personal Genome Service™  for $25 instead of the usual $399. Along with all the benefits of the service, the Parkinson’s community gives members:

• research surveys aimed at gathering each patient’s experience with the disease, including age of onset, rate of progression and response to therapies.
• the opportunity to ask questions and share stories with other members.
• PD-specific reports relating to currently known genetic correlations.

Individuals who have been diagnosed with PD can sign up to participate via the website of the Michael J. Fox Foundation.

Even if you don’t have Parkinson’s, anyone can help with this research by setting up a free 23andMe demo account and taking the Parkinson’s background survey.  And, of course, 23andMe customers are encouraged to join the effort by filling out the survey, too.  Together, we’re changing the pace of research!

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The 23andMe Personal Genome Service™ offers information about customers’ maternal and paternal ancestry by examining their mitochondrial DNA (which we all inherit from our mothers) and the Y chromosome (which is passed by fathers to their sons).

Over our species’ history new genetic variations have arisen spontaneously in those pieces of DNA, and been passed down through the generations. So researchers know that every person alive today who has a particular variation — say a T instead of a G at a certain spot on the mtDNA — is descended from a single common ancestor. By sampling people from around the world, scientists have been able to assemble “family trees” that trace all the way back to the dawn of the human species in eastern Africa more than 100,000 years ago. Those trees are the basis of the haplogroup assignments we give our customers. Each haplogroup represents a particular branch — and therefore a unique sequence of SNPs.

Now you can see exactly which SNPs we use to generate the 23andMe mitochondrial and Y chromosome haplogroup trees, using a feature we’ve developed called the Haplogroup Tree Mutation Mapper. This isn’t the kind of information everyone would necessarily want, but a number of customers who are especially interested in genetic genealogy have requested it. It can be used to compare our haplogroup assignments to those obtained elsewhere, for example.

The Haplogroup Tree Mutation Mapper is the first arrival in 23andMe Labs, our new technology sandbox where we will showcase experimental features not currently available in our Personal Genome Service™.  These features may still be in development, require specialized knowledge or be of interest only to a subset of our customers. Each lab will have its own community so customers can compare notes, ask questions and share ideas.

Some labs will be requested by customers. In fact, we welcome your suggestions. Others will be dreamed up by our scientists.

Finally, you can expect labs to be a little less refined than what’s available within the Personal Genome Service, and somewhat fluid as well. A feature could be discontinued at any time, or it might be elevated to full integration with our Personal Genome Service.

We’re really excited about having this new outlet for our ingenuity, and we hope it will engage some of yours as well!

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The genetics of height is incredibly complex. Though height is strongly determined by genetics, no single gene appears to have much influence over how tall a person will be. Instead, there appear to be dozens of genetic variants involved, none of which account for more than a few millimeters’ height difference.

It will be no small feat for geneticists to identify all of the genetic contributors to height and out how they work together. But by analyzing growth data for a group of 3,538 people who were born in northern Finland in 1966, an international group of researchers has taken a step in that direction by figuring out when a few height-related genes exert their effects. They describe their research in the March issue of PLoS Genetics.

Humans tend to do most of their growing in two spurts, once during infancy and then again around the onset of puberty. Growth during infancy tends to be associated with how much nutrition a child absorbs, whereas the second growth spurt is governed more by hormonal signals. So it would not be surprising to find that different sets of genes are associated with growth during the two periods.

The researchers tested that theory by selecting 48 SNPs that have been associated with adult height in previous studies. Then they looked at growth data for each subject from birth to age 20 to determine whether any of those SNPs was associated with growth during infancy, around puberty or both.

Five SNPs were significantly associated with growth during infancy, and seven with the puberty-associated growth spurt. Only one was associated with growth during both periods.

The researchers were especially interested in two SNPs. One was in the gene SOCS2, which influences growth hormone signaling, and was associated with growth during puberty. The other was in the gene HHIP, which is involved in embryogenesis and development, and was associated with growth during infancy.

(23andMe customers can check their genotype for both of these SNPs using the Genome Browser. Each T version of the SOCS2 SNP rs11107116 was associated with faster growth during infancy, and 4.7 mm of adult height. Each A version of the HHIP SNP rs6854783 was associated with faster growth around the time of puberty, but was not significantly related to adult height.)

This research illustrates the value of collecting data over time in genetic association studies. Knowing not just whether, but when, a particular genetic variation exerts its effects can provide vital clues to how it works.

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Diagnostic imaging of King Tut’s mummy suggests the pharaoh may have had a slightly cleft palate.

Last year researchers reported in Nature Genetics their discovery that a SNP in the gene IRF6, on chromosome 1, is associated with clefting of the lip and/or palate. About one child in 700 is born with clefting, which results from improper fusing during fetal development of the different elements that will make up the lower part of the face. Though some rare conditions are associated with clefting, most cases do not have any identifiable cause.

Now an international team led by German researchers has discovered a second genetic marker that increases the odds of cleft lip and/or palate six-fold among people who inherit the high-risk version of the marker from both parents.

Birnbaum et al. genotyped 224 people who had been born with cleft lips and/or palates and compared them to 383 controls. In the most recent issue of Nature Genetics they report finding an association between clefting and a cluster of SNPs on chromosome 8.

The most statistically significant association was with rs987525. Subjects with one A at the SNP had 2.57 times the odds of clefting compared to those with a C at both copies. And subjects with an A at both copies had about six times the odds of clefting.

(23andMe customers can check their data using SNP rs987525 in the Browse Raw Data feature.)

The stretch of chromosome 8 where rs987525 is located is a particularly featureless region of the human genome, so it is difficult to pin down the mechanism behind the association. But whatever that mechanism is, the authors estimate that it accounts for 41% of the clefting cases in the population they studied.

Clefting is most common among Asian populations, with intermediate incidence among Europeans and the lowest rates observed among Africans. Yet the high-risk version of rs987525 shows the opposite distribution; it is almost three times more common among Africans than Europeans, and nearly absent among Asians.

In their Nature Genetics paper, the authors offer several possible explanations for this anomaly. It could be that there are other genetic or environmental factors associated with clefting that remain undiscovered, or that the linkage between rs987525 and the as-yet-unknown genetic mechanism it is pinpointing differs in the various continental populations.

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Almost since the 1871 publication of “The Descent of Man,” in which Charles Darwin applied his theory of natural selection to the human species, biologists have argued over whether the dramatic series of evolutionary events that led to the emergence of Homo sapiens continues to this day.

Some have argued that culture and technology have eclipsed the powerful biological forces that shaped our species in its formative years. In their view the species, no longer faced with a daily struggle for survival, is adrift in an evolutionary Sargasso Sea.

“There’s been no biological change in humans in 40,000 or 50,000 years. Everything we call culture and civilization we’ve built with the same body and brain,” the famed evolutionary biologist Stephen J. Gould once said in an interview.

In their new book “The 10,000 Year Explosion,” anthropologists Henry Harpending and Gregory Cochran argue the contrary position. They claim that in fact, far from grinding to a halt, human evolution has accelerated dramatically since the origins of agriculture about 10,000 years ago.

“We intend to make the case that human evolution has accelerated in the past 10,000 years, rather than slowing or stopping, and is now happening about 100 times faster than its long-term average over the 6 million years of our existence,” they write.

In evolutionary terms, 10,000 years is no time at all — about 400 human generations. Rabbits can go through 400 generations in not much more than a century — can you imagine rabbits being substantially different than they were 100 years ago?

Far from ending the chain of dramatic evolutionary changes that led to upright walking, advanced cognitive abilities and spoken language, Cochran and Harpending argue, the adoption of agriculture so dramatically changed the human environment that a new wave of genetic innovations flourished. These new genetic variants thrived because they helped people cope with the challenges an agricultural way of life presented, such as the shift to a low protein, high carbohydrate diet; the creation of an organized, stratified society and the rise of infectious diseases in response to increased population density.

In fact, many of the genetic variations that 23andMe provides information about are relics of those evolutionary changes. The SNP that confers lactose tolerance, for example, appears to have arisen in Europe about 8,000 years ago among the first people to herd cows and other milk-producing animals. The lactose-digesting variant quickly spread throughout the parts of Eurasia that were ecologically suited to pastoralism.

There are also a number of genetic variations covered by 23andMe that cause physiological problems when two mutated copies are present, but provide protection against infectious disease when a person has one of each version of the gene. For example, the genetic variations that cause sickle cell anemia and G6PD deficiency confer resistance to malaria. Geneticists call this situation balancing selection; over the entire population, the reproductive cost to those who end up with the genetic disease is outweighed by the benefit to others who are resistant to the infectious one.

At the end of the book, Cochran and Harpending make the controversial argument that balancing selection is responsible for the increased incidence of a number of genetic diseases among people of Ashkenazi Jewish descent — and for their higher intelligence relative to other groups.

The authors do raise some interesting points about the anomalously high frequency among Ashkenazi of genetic disorders that stimulate the growth of neurons in the brain. And they cite studies that have shown increased intelligence among people with some of these diseases.

But genetic explanations for between-group differences in intelligence are best taken with a whopping dose of skepticism. Even the definition of intelligence is a matter of intense debate, not to mention the degree to which it can be inherited through genetics. in the end, their case is little more than a just-so story.

In telling it Cochran and Harpending blunt the rest of their book’s powerful message: human evolution is not over by a long sight.

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Generally when you think about what separates humans from other species, features like upright walking, large brains and language come to mind.

But diet has actually played an enormous role in human evolution. Today at the annual meeting of the American Association for the Advancement of Science, a panel of anthropologists, geneticists and paleontologists got together to discuss how who we are has been shaped by what we eat.

Perhaps the most surprising conclusion was that — despite what some diet gurus may say — there is no “natural” human diet. Not only can humans thrive on a wide variety of diets, from the highly carnivorous fare of nomadic Siberians to the virtually all-potato menu consumed by native Peruvians, but thanks to evolution our species can change its diet surprisingly readily.

“You can find humans living well and healthily from a tremendous diversity of diets,” said William Leonard, an anthropologist at Northwestern University in Evanston, Ill.

But all cultures have one dietary feature in common, said Harvard University primatologist Richard Wrangham — they cook their food. Wrangham believes the advent of cooking during human prehistory was a major evolutionary milestone, because it essentially pre-digested starches and proteins and softened food, helping increase the amount of energy that could be extracted on it. In fact, he pointed out that people in modern technological societies who take up so-called “raw food” diets usually lose substantial amounts of weight.

Many diet books advise following a high-protein, low-carbohydrate diet in order to emulate the eating habits of pre-agricultural humans. Whatever the benefits of such a diet, however, it is clear that in the 10,000 years since the development of farming our genes have responded to the increasing availability of foods such as rice, grains and milk.

“I would say most people who descend from agricultural populations are actually pretty well adapted to a starch diet, because most of the world eats a lot of rice, a lot of corn and a lot of potatoes, said Anne Stone, a geneticist at Arizona State University.

Stone and her colleagues have studied the gene AMY1, which encodes a salivary protein called amylase that breaks down starch. All people have multiple copies of the AMY1 genes. But those from traditionally agricultural populations, such as the Japanese and Europeans, have many more than those from cultures that have never practiced agriculture.

Customers of 23andMe may be able to see the evolutionary effects of an agricultural heritage in their own genetic data. Before people started herding cattle, goats and sheep, the human biological machinery for digesting milk was turned off not long after infancy — perhaps to prevent older children from getting in destructive fights over breast milk. But with herd animals on the scene, when a genetic modification that kept milk digestion functioning into adulthood arose in Europe around 8,000 years ago, it was so beneficial that it eventually spread throughout the continent.

23andMe customers have one modified version of the lactase gene for each A at the SNP rs4988235.

Similar scenarios happened in several other parts of the world as well, so that now many people of European and some of African ancestry can easily digest large amounts of milk.

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We’re pleased to announce that 23andMe Science Advisory Board member Russ Altman has won the Nature Network 2008 Science Blogging Challenge for his blog, “Building confidence.”

Russ was commended for his insights about pharmacogenomics, science funding, the implications of rapidly decreasing genotyping costs and other topics. His account of how cool it is to have access to your genetic data (“One of my first post-genomic moments”) was also selected by the judges to be part of an anthology of last year’s best science blogging.

The people who created the prize run an online social network for scientists that is part of the Nature Publishing Group, which also sponsors the annual Science Foo Camp (SciFoo) at Google headquarters in Mountain View, Calif. Russ won a free trip to this year’s SciFoo camp (But since he lives just a few miles away the money that would have gone to his travel expenses will be used to help deserving attendees who have farther to travel!).

Congratulations, Russ. Keep blogging.

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For an insightful and thought-provoking essay on the present and future of personal genomics, as well as the role that 23andMe is playing in its advancement, check out Steven Pinker’s essay “My Genome, My Self” in this week’s New York Times magazine.

Pinker, who is a 23andMe customer himself and also a participant in George Church’s Personal Genome Project, recommends taking genetic data with a grain of salt. Because as we often point out on The Spittoon, genetics is not fate and the science is still evolving.

Pinker, for example, has discovered that he has a genetic variation that increases his chances of going bald. Considering the man’s trademark thick and curly tresses, that one genetic toggle is not the whole story.

Pinker recommends personal genomics if you’re curious about how the countless genetic discoveries that are being made almost daily may apply to you personally, and might be relevant to your health down the road. And, we might add, becoming part of the 23andMe community also gives you the opportunity to help advance genetic research into diseases, conditions or traits that interest you. Combined with our community features, which let you find people with whom you share elements of nature AND nurture, personal genomics has great potential to become a tool not just for utilizing scientific advancements but making new ones as well.

As Pinker makes it clear however, personal genomics is not about to supplant, or even supplement, preventive medicine any time soon. “If you want to know whether you are at risk for high cholesterol, have your cholesterol measured,” he rightly recommends. (For some other takes on the Pinker piece and the state of personal genomics, check in with our colleagues at Gene Expression and Genetic Future.)

One of the most fascinating, albeit technical, parts of the essay is Pinker’s prediction that personal genomics will have more success elucidating the genetic underpinnings of personality than intelligence. Assuming from an evolutionary standpoint that it’s better to be smarter (it also kind of depends on how you define intelligence, but we won’t dwell on that), then over the millennia natural selection has done the work of deleting any genetic variations that substantially decrease intelligence but left intact hundreds or thousands that have negligible influence. Thanks to their tiny effect, those variations will prove very difficult to identify.

Evolution appears to foster large personality differences, on the other hand, because different types of people tend to thrive as the environment changes. Consider the recent history of the world’s financial markets — it’s easy to see how both pessimists and optimists could do well, though not necessarily at the same time. And it’s also easy to see how the number of bulls and bears could oscillate as first one side, then the other, got the upper hand. If you’re smart (and lucky) enough, you can make money in the market using either approach.

Evolutionary biologists call it balancing selection when two opposing traits are maintained in this way. And geneticists have had considerable success identifying genetic variations that have been subject to balancing selection, just as they have ones that make some people more adventurous, or prone to depression.

“It’s still a messy science, with plenty of false alarms, contradictory results and tiny effects. But consumers will probably learn of genes linked to personality before they see any that are reliably connected to intelligence,” Pinker contends.

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